@article {pmid39837038,
year = {2025},
author = {Zhao, M and Huang, K and Wen, F and Xia, H and Song, B},
title = {Biochar reduces plasmid-mediated antibiotic resistance gene transfer in earthworm ecological filters for rural sewage treatment.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137230},
doi = {10.1016/j.jhazmat.2025.137230},
pmid = {39837038},
issn = {1873-3336},
abstract = {The spread of antibiotic resistance genes (ARGs) in rural wastewater threatens both ecological environment and human health. Earthworm ecological filters (EEFs) represent a green technology for rural sewage treatment. However, their effectiveness in removing ARGs remains a significant challenge. This study aims to investigate the role and underlying mechanisms of biochar addition in enhancing ARGs removal in rural sewage using EEFs. To achieve this, the fate of chromosome- and plasmid-carried ARGs was quantified in constructed EEFs, both with and without biochar addition. The results showed that the biochar could effectively remove ARGs from rural sewage, with a better removal efficiency for plasmid-carried ARGs. The absolute abundance of plasmid-carried ARGs in the effluent was reduced by 0.4-11 times compared to chromosomal ones, showing removal stability improved by 13.11-74.51 %. Additionally, the functional microbial community attached on the high porosity of biochar surface promoted ARGs retention, increasing diffusion limitation in microbial assembly mechanisms by 4.61-29.44 %, which played a key role in plasmid-mediated horizontal gene transfer (HGT). Partial least squares structural equation modeling (PLS-SEM) revealed that biochar-mediated environmental changes and the HGT of mobile genetic elements (MGEs) were critical factors in reducing plasmid-carried ARGs in EEFs.},
}

@article {pmid39836086,
year = {2025},
author = {Xia, R and Yin, X and Balcazar, JL and Huang, D and Liao, J and Wang, D and Alvarez, PJJ and Yu, P},
title = {Bacterium-Phage Symbiosis Facilitates the Enrichment of Bacterial Pathogens and Antibiotic-Resistant Bacteria in the Plastisphere.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c08265},
pmid = {39836086},
issn = {1520-5851},
abstract = {The plastisphere, defined as the ecological niche for microbial colonization of plastic debris, has been recognized as a hotspot of pathogenic and antibiotic-resistant bacteria. However, the interactions between bacteria and phages facilitated by the plastisphere, as well as their impact on microbial risks to public health, remain unclear. Here, we analyzed public metagenomic data from 180 plastisphere and environmental samples, stemming from four different habitats and two plastic types (biodegradable and nonbiodegradable plastics) and obtained 611 nonredundant metagenome-assembled genomes (MAGs) and 4061 nonredundant phage contigs. The plastisphere phage community exhibited decreased diversity and virulent proportion compared to those found in environments. Indexes of phage-host interaction networks indicated significant associations of phages with pathogenic and antibiotic-resistant bacteria (ARB), particularly for biodegradable plastics. Known phage-encoded auxiliary metabolic genes (AMGs) were involved in nutrient metabolism, antibiotic production, quorum sensing, and biofilm formation in the plastisphere, which contributed to enhanced competition and survival of pathogens and ARB hosts. Phages also carried transcriptionally active virulence factor genes (VFGs) and antibiotic resistance genes (ARGs), and could mediate their horizontal transfer in microbial communities. Overall, these discoveries suggest that plastisphere phages form symbiotic relationships with their hosts, and that phages encoding AMGs and mediating horizontal gene transfer (HGT) could increase the source of pathogens and antibiotic resistance from the plastisphere.},
}

@article {pmid39833926,
year = {2025},
author = {Li, Z and Zhao, C and Mao, Z and Zhang, F and Dong, L and Song, C and Chen, Y and Fu, X and Ao, Z and Xiong, Y and Hui, Q and Song, W and Penttinen, P and Zhang, S},
title = {Structure and metabolic function of spatiotemporal pit mud microbiome.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {10},
pmid = {39833926},
issn = {2524-6372},
support = {2022HX04//Youth Fund of Postdoctor/ ; 2021JDJQ0038//Youth Fund of Sichuan Province/ ; },
abstract = {BACKGROUND: Pit mud (PM) hosts diverse microbial communities, which serve as a medium to impart flavor and quality to Baijiu and exhibit long-term tolerance to ethanol and acids, resulting in a unique ecosystem. However, the ecology and metabolic functions of PM remain poorly understood, as many taxa in PM represent largely novel lineages. In this study, we used a combination of metagenomic analysis and chemical derivatization LC-MS analysis to provide a comprehensive overview of microbial community structure, metabolic function, phylogeny, horizontal gene transfer, and the relationship with carboxyl compounds in spatiotemporal PM samples.

RESULTS: Our findings revealed three distinct stages in the spatiotemporal changes of prokaryotic communities in PM: an initial phase dominated by Lactobacillus, a transitional phase, and a final state of equilibrium. Significant variations in α- and β-diversity were observed across different spatial and temporal PM samples. We identified 178 medium- and high-quality non-redundant metagenome-assembled genomes (MAGs), and constructed their phylogenetic tree, depicting their roles in the carbon, nitrogen, and sulfur cycles. The Wood-Ljungdahl pathway and reverse TCA cycle were identified as the main carbon fixation mechanisms, with both hydrogenotrophic and aceticlastic methanogens playing a major role in methane production, and methylotrophic pathway observed in older PM. Furthermore, we identified relationships between prokaryotes and 29 carboxyl metabolites, including medium- and long-chain fatty acids. Horizontal gene transfer (HGT) was widespread in PM, particularly among clostridia, Bacteroidota, Bacilli, and Euryarchaeota, and was shown to play critical roles in fermentation dynamics, carbon fixation, methane production, and nitrogen and sulfur metabolism.

CONCLUSION: Our study provides new insights into the evolution and function of spatiotemporal PM, as well as its interactions with carboxyl metabolites. Lactobacillus dominated in new PM, while methanogens and clostridia were predominant in older or deeper PM layers. The three distinct stages of prokaryotic community development in PM and HGT played critical roles in metabolic function of spatiotemporal PM. Furthermore, this study highlights the importance of α-diversity, β-diversity, methanogens, and Clostridium as useful indicators for assessing PM quality in the production of high-quality Baijiu.},
}

@article {pmid39829789,
year = {2025},
author = {Robinson, LR and McDevitt, CJ and Regan, MR and Quail, SL and Swartz, M and Wadsworth, CB},
title = {Re-visiting the potential impact of doxycycline post-exposure prophylaxis (doxy-PEP) on the selection of doxycycline resistance in Neisseria commensals.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.09.632169},
pmid = {39829789},
issn = {2692-8205},
abstract = {Doxycycline post-exposure prophylaxis (doxy-PEP) is a preventative strategy demonstrated to reduce bacterial sexually transmitted infections in high-risk populations. However, the impact of doxy-PEP on antibiotic resistance acquisition in key members of our microbiomes, is as of yet unclear. For example, commensal Neisseria are known reservoirs of resistance for gonococci through horizontal gene transfer (HGT), and are more likely to experience bystander selection due to doxy-PEP as they are universally carried. Thus, the consequences of doxycycline selection on commensal Neisseria will be critical to investigate to understand possible resistance mechanisms that may be transferred to an important human pathogen. Here, we use in vitro antibiotic gradients to evolve four Neisseria commensals (N. cinerea, N. canis, N. elongata, and N. subflava, n=4 per species) across a 20-day time course; and use whole genome sequencing to nominate derived mutations. After selection, 12 of 16 replicates evolved doxycycline resistance (> 1 μg/mL). Across resistant lineages: An A46T substitution in the repressor of the Mtr efflux pump (MtrR) and a V57M substitution in the 30 ribosomal protein S10 were clearly associated with elevated MICs. Additional mutations in ribosomal components also emerged in strains with high MICs (i.e., 16S rRNA G1057C , RplX A14T). We find the MtrR 46T, RpsJ 57M, and RplX 14T circulating in natural commensal populations. Furthermore, in vitro co-evolution of N. gonorrhoeae with Neisseria commensals demonstrated rapid transfer of the pConj plasmid to N. subflava and N. cinerea , and p bla to N. cinerea . Finally, collection of novel commensals from human hosts reveals 46% of isolates carrying doxycycline resistance; and doxycycline resistance was significantly greater in participants self-reporting doxycycline use in the past 6 months. High-level doxycycline resistance (> 8 μg/mL) was always associated with carriage of the ribosomal protection protein (tetM) and pConj. Ultimately, characterizing the contemporary prevalence of doxycycline resistance, and underlying resistance mechanisms, in commensal communities may help us to predict the long-term impact of doxy-PEP on Neisseria , and the likelihood of transferring particular genotypes across species' boundaries.},
}

@article {pmid39827804,
year = {2025},
author = {Ye, T and Li, Y and Zhou, X and Ye, Y and Liu, X and Xiong, W},
title = {Hormesis-like effects of black phosphorus nanosheets on the spread of multiple antibiotic resistance genes.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137207},
doi = {10.1016/j.jhazmat.2025.137207},
pmid = {39827804},
issn = {1873-3336},
abstract = {The production scalability and increasing demand for black phosphorus nanosheets (BPNSs) inevitably lead to environmental leakage. Although BPNSs' ecotoxicological effects have been demonstrated, their indirect health risks, such as inducing increased resistance in pathogenic bacteria, are often overlooked. This study explores the influence of BPNSs on the horizontal gene transfer of antibiotic resistance genes (ARGs) facilitated by the RP4 plasmid, which carries multiple resistance genes. The results indicated that BPNSs exhibited concentration-dependent hormesis-like effects on bacterial conjugation gene transfer. Specifically, at sub-inhibitory concentrations (0.0001-1 mg/L), BPNSs promoted both intra- and intergeneric conjugative transfer, demonstrating an initial increase followed by a decline, with transfer rates rising by 1.5-3.1-fold and 1.5-3.3-fold, respectively. BPNSs were found to induce reactive oxygen species (ROS) production, increase malondialdehyde levels, and trigger the SOS response, enhancing plasmid uptake. Additionally, BPNSs increased membrane permeability by forming pores and upregulating outer membrane porins (OMPs) genes. At higher BPNSs concentrations (0.1-1 mg/L), conjugative frequency was inhibited due to the disruption of the cellular antioxidant system and changes in the adsorption process. These findings underscore the influence of BPNSs on the conjugative transfer of ARGs, complementing current knowledge of the biotoxicity and potential ecological risks associated with BPNSs.},
}

@article {pmid39529437,
year = {2025},
author = {Curtsinger, HD and Martínez-Absalón, S and Liu, Y and Lopatkin, AJ},
title = {The metabolic burden associated with plasmid acquisition: An assessment of the unrecognized benefits to host cells.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {47},
number = {2},
pages = {e2400164},
doi = {10.1002/bies.202400164},
pmid = {39529437},
issn = {1521-1878},
support = {1R35GM150871-01 (AJL)/GM/NIGMS NIH HHS/United States ; },
mesh = {*Plasmids/genetics/metabolism ; Humans ; *Conjugation, Genetic ; *Bacteria/metabolism/genetics ; Gene Transfer, Horizontal ; },
abstract = {Bacterial conjugation, wherein DNA is transferred between cells through direct contact, is highly prevalent in complex microbial communities and is responsible for spreading myriad genes related to human and environmental health. Despite their importance, much remains unknown regarding the mechanisms driving the spread and persistence of these plasmids in situ. Studies have demonstrated that transferring, acquiring, and maintaining a plasmid imposes a significant metabolic burden on the host. Simultaneously, emerging evidence suggests that the presence of a conjugative plasmid can also provide both obvious and unexpected benefits to their host and local community. Combined, this highlights a continuous cost-benefit tradeoff at the population level, likely contributing to overall plasmid abundance and long-term persistence. Yet, while the metabolic burdens of plasmid conjugation, and their causes, are widely studied, their attendant potential advantages are less clear. Here, we summarize current perspectives on conjugative plasmids' metabolic burden and then highlight the lesser-appreciated yet critical benefits that plasmid-mediated metabolic burdens may provide. We argue that this largely unexplored tradeoff is critical to both a fundamental theory of microbial populations and engineering applications and therefore warrants further detailed study.},
}

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

@article {pmid39826759,
year = {2025},
author = {Wang, C and Yin, X and Xu, X and Wang, D and Wang, Y and Zhang, T},
title = {Antibiotic resistance genes in anaerobic digestion: Unresolved challenges and potential solutions.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132075},
doi = {10.1016/j.biortech.2025.132075},
pmid = {39826759},
issn = {1873-2976},
abstract = {Antimicrobial resistance (AMR) threatens public health, necessitating urgent efforts to mitigate the global impact of antibiotic resistance genes (ARGs). Anaerobic digestion (AD), known for volatile solid reduction and energy generation, also presents a feasible approach for the removal of ARGs. This review encapsulates the existing understanding of ARGs and antibiotic-resistant bacteria (ARB) during the AD process, highlighting unresolved challenges pertaining to their detection and quantification. The questions raised and discussed include: Do current ARGs detection methods meet qualitative and quantitative control requirements? How can we conduct risk assessments of ARGs? What happens to ARGs when they come into co-exposure with other emerging pollutants? How can the application of internal standards bolster the reliability of the AD resistome study? What are the potential future research directions that could enhance ARG elimination? Investigating these subjects will assist in shaping more efficient management strategies that employ AD for effective ARG control.},
}

@article {pmid39826720,
year = {2025},
author = {Akhoon, BA and Qiao, Q and Stewart, A and Chen, J and Rodriguez Lopez, CM and Corbin, KR},
title = {Pangenomic analysis of the bacterial cellulose-producing genera Komagataeibacter and Novacetimonas.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {139980},
doi = {10.1016/j.ijbiomac.2025.139980},
pmid = {39826720},
issn = {1879-0003},
abstract = {Bacterial cellulose (BC) holds significant commercial potential due to its unique structural and chemical properties, making it suitable for applications in electronics, medicine, and pharmaceuticals. However, large-scale BC production remains limited by challenges in bacterial performance. In this study, we compared 79 microbial genomes from three genera-Komagataeibacter, Novacetimonas, and Gluconacetobacter-to investigate their pangenomes, genetic diversity, and evolutionary relationships. Through comparative genomic and phylogenetic analyses, we identified distinct genome compositions and evolutionary patterns that differ from previous reports. The role of horizontal gene transfer (HGT) in shaping the genetic diversity and adaptability of these bacteria was also explored. Key determinants in BC production, such as variations in the bacterial cellulose biosynthesis (bcs) operon, carbohydrate uptake genes, and carbohydrate-active enzymes, were examined. Additionally, several biosynthetic gene clusters (BGCs), including Linocin M18 and sactipeptides, which encode for antimicrobial peptides known as bacteriocins, were identified. These findings reveal new aspects of the genetic diversity in cellulose-producing bacteria and present a comprehensive genomic toolkit that will support future efforts to optimize BC production and improve microbial performance for commercial applications.},
}

@article {pmid39826554,
year = {2025},
author = {Kirsch, R and Okamura, Y and García-Lozano, M and Weiss, B and Keller, J and Vogel, H and Fukumori, K and Fukatsu, T and Konstantinov, AS and Montagna, M and Moseyko, AG and Riley, EG and Slipinski, A and Vencl, FV and Windsor, DM and Salem, H and Kaltenpoth, M and Pauchet, Y},
title = {Symbiosis and horizontal gene transfer promote herbivory in the megadiverse leaf beetles.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.12.028},
pmid = {39826554},
issn = {1879-0445},
abstract = {Beetles that feed on the nutritionally depauperate and recalcitrant tissues provided by the leaves, stems, and roots of living plants comprise one-quarter of herbivorous insect species. Among the key adaptations for herbivory are plant cell wall-degrading enzymes (PCWDEs) that break down the fastidious polymers in the cell wall and grant access to the nutritious cell content. While largely absent from the non-herbivorous ancestors of beetles, such PCWDEs were occasionally acquired via horizontal gene transfer (HGT) or by the uptake of digestive symbionts. However, the macroevolutionary dynamics of PCWDEs and their impact on evolutionary transitions in herbivorous insects remained poorly understood. Through genomic and transcriptomic analyses of 74 leaf beetle species and 50 symbionts, we show that multiple independent events of microbe-to-beetle HGT and specialized symbioses drove convergent evolutionary innovations in approximately 21,000 and 13,500 leaf beetle species, respectively. Enzymatic assays indicate that these events significantly expanded the beetles' digestive repertoires and thereby contributed to their adaptation and diversification. Our results exemplify how recurring HGT and symbiont acquisition catalyzed digestive and nutritional adaptations to herbivory and thereby contributed to the evolutionary success of a megadiverse insect taxon.},
}

@article {pmid39824780,
year = {2025},
author = {Wu, X and Peng, J and Malik, AA and Peng, Z and Luo, Y and Fan, F and Lu, Y and Wei, G and Delgado-Baquerizo, M and Liesack, W and Jiao, S},
title = {A Global Relationship Between Genome Size and Encoded Carbon Metabolic Strategies of Soil Bacteria.},
journal = {Ecology letters},
volume = {28},
number = {1},
pages = {e70064},
doi = {10.1111/ele.70064},
pmid = {39824780},
issn = {1461-0248},
support = {42122050//National Science Foundation for Excellent Young Scholars of China/ ; 42277307 & 41977038//National Natural Science Foundation of China/ ; 2021YFD1900500//National Key Research and Development Program of China/ ; },
mesh = {*Soil Microbiology ; *Carbon/metabolism ; *Bacteria/metabolism/genetics ; *Genome, Bacterial ; *Genome Size ; Gene Transfer, Horizontal ; Microbiota ; Biomass ; },
abstract = {Microbial traits are critical for carbon sequestration and degradation in terrestrial ecosystems. Yet, our understanding of the relationship between carbon metabolic strategies and genomic traits like genome size remains limited. To address this knowledge gap, we conducted a global-scale meta-analysis of 2650 genomes, integrated whole-genome sequencing data, and performed a continental-scale metagenomic field study. We found that genome size was tightly associated with an increase in the ratio between genes encoding for polysaccharide decomposition and biomass synthesis that we defined as the carbon acquisition-to-biomass yield ratio (A/Y). We also show that horizontal gene transfer played a major evolutionary role in the expanded bacterial capacities in carbon acquisition. Our continental-scale field study further revealed a significantly negative relationship between the A/Y ratio and soil organic carbon stocks. Our work demonstrates a global relationship between genome size and the encoded carbon metabolic strategies of soil bacteria across terrestrial microbiomes.},
}

*Soil Microbiology
*Carbon/metabolism
*Bacteria/metabolism/genetics
*Genome, Bacterial
*Genome Size
Gene Transfer, Horizontal
Microbiota
Biomass

@article {pmid39824112,
year = {2025},
author = {Farooq, A and Rafique, A and Han, E and Park, SM},
title = {Global dissemination of the beta-lactam resistance gene blaTEM-1 among pathogenic bacteria.},
journal = {The Science of the total environment},
volume = {963},
number = {},
pages = {178521},
doi = {10.1016/j.scitotenv.2025.178521},
pmid = {39824112},
issn = {1879-1026},
abstract = {Antibiotic resistance presents a burgeoning global health crisis, with over 70 % of pathogenic bacteria now exhibiting resistance to at least one antibiotic. This study leverages a vast dataset of 618,853 pathogenic bacterial genomes from the NCBI pathogen detection database, offering comprehensive insights into antibiotic resistance patterns, species-specific profiles, and transmission dynamics of resistant pathogens. We centered our investigation on the beta-lactam resistance gene blaTEM-1, found in 43,339 genomes, revealing its extensive distribution across diverse species and isolation sources. The study unveiled the prevalence of 15 prominent antibiotic resistance genes (ARGs), including those conferring resistance to beta-lactam, aminoglycoside, and tetracycline antibiotics. Distinct resistance patterns were observed between Gram-positive and Gram-negative bacteria, indicating the influence of phylogeny on resistance dissemination. Notably, the blaTEM-1 gene demonstrated substantial prevalence across a wide array of bacterial species (8) and a high number of isolation sources (11). Genetic context analysis revealed associations between blaTEM-1 and mobile genetic elements (MGEs) like transposons and insertion sequences. Additionally, we observed recent horizontal transfer events involving clusters of blaTEM-1 genes and MGEs underscore the potential of MGEs in facilitating the mobilization of ARGs. Our findings underscore the importance of adopting a One Health approach to global genomic pathogen surveillance, aiming to uncover the transmission routes of ARGs and formulate strategies to address the escalating antibiotic resistance crisis.},
}

@article {pmid39824023,
year = {2025},
author = {Guo, X and Yu, P and Guo, J and Zhao, HP and Lai, CY},
title = {Viral auxiliary roles in hydrolytic and biosynthetic metabolism regulate prokaryotic microbial interactions in anaerobic digestion.},
journal = {Water research},
volume = {274},
number = {},
pages = {123140},
doi = {10.1016/j.watres.2025.123140},
pmid = {39824023},
issn = {1879-2448},
abstract = {Anaerobic digestion (AD) viruses have gained recognition as significant regulators of microbial interactions within AD communities, yet their ecological roles remain largely unexplored. In this study, we investigated the ecological roles of AD viruses in regulating microbial interactions among syntrophic hosts. We recovered 3921 diverse viral sequences from four full-scale anaerobic digesters and confirmed their widespread presence across 127 global metagenomic sampling sites (with >95 % sequence similarity), underscoring the ubiquity of prokaryotic viruses in AD-related systems. Through the construction of virus-prokaryote interactions (66.8 % validated at the transcriptional level) and analysis of viral-host transcriptional abundances, we identified significant associations between AD viruses and key processes, including hydrolysis, acidogenesis, and methanogenesis. Notably, polyvalent viruses were found to interact with both hydrolytic and fermentative communities. We further characterized viral auxiliary metabolism, hydrolytic substrate spectra, and microbial auxotrophy, showing that viruses not only could enhance the breakdown of complex substrates (e.g., cellulose, chitin, peptidoglycan) but also potentially supported the biosynthesis of essential nutrients (e.g., cysteine, methionine, heme, and cobalamin). These activities were proposed to regulate resource fluxes through alternating lysogenic and lytic cycles. Phylogenetic analysis of viral gene and horizontal gene transfer (HGT) identification suggest that AD viruses employ promiscuous infection on syntrophic hosts, potentially as an adaptive evolutionary strategy in the AD ecosystem. This study provides new insights into the ecological roles of AD viruses, highlighting their potential impact on the stability and functionality of AD systems.},
}

@article {pmid39823837,
year = {2025},
author = {Zhang, S and Ye, Q and Wang, M and Zhu, D and Jia, R and Chen, S and Liu, M and Yang, Q and Zhao, X and Wu, Y and Huang, J and Ou, X and Sun, D and Tian, B and He, Y and Wu, Z and Cheng, A},
title = {Isolation and characterization of a broad-spectrum bacteriophage against multi-drug resistant Escherichia coli from waterfowl field.},
journal = {Poultry science},
volume = {104},
number = {2},
pages = {104787},
doi = {10.1016/j.psj.2025.104787},
pmid = {39823837},
issn = {1525-3171},
abstract = {Escherichia coli (E. coli) is a significant pathogen responsible for intestinal infections and foodborne diseases. The rise of antibiotic resistance poses a significant challenge to global public health. Traditional antibiotic therapy is becoming increasingly ineffective, highlighting the urgent need for innovative control strategies. This study explores the potential of bacteriophages as a sustainable alternative to traditional antibiotics. From 2021 to 2022, a total of 183 non-repetitive duck source fecal samples were collected from Mianyang City, Sichuan Province, and 126 strains of E. coli were isolated. The minimum inhibitory concentration (MIC) test showed that these strains exhibited high resistance to piperacillin (96.8%), tetracycline (88.9%), and chloramphenicol (86.5%). It is concerning that 93.7% of the isolates are classified as multidrug-resistant (MDR), posing a significant threat to existing treatment options. 20 bacteriophages were isolated from fecal and soil samples, among which 5 bacteriophages were selected for further analysis. Bacteriophage YP6 showed excellent lytic effects on MDR strains, especially strain MY104, as well as representative serotypes O1 (E. coli MY51) and O18 (E. coli MY106). The identification of YP6 as a member of the Myoviridae family was conducted using transmission electron microscopy, and it was found to have an optimal infection factor of 0.1. Bacteriophages exhibit significant thermal and pH stability, maintaining survival at temperatures up to 60 °C and pH ranges of 4 to 10. Whole genome sequencing confirmed that YP6 has a double stranded DNA genome of 139,323 base pairs (bp), and no antibiotic resistance or virulence genes were found, indicating a low possibility of horizontal gene transfer. In addition, YP6 effectively inhibits the formation of E. coli biofilm, which is a key factor in chronic infections. The in vivo experiments using Galleria mellonella (G. mellonella) larvae have shown that it has a significant protective effect against MDR E. coli infection. In summary, bacteriophage YP6 is expected to become a therapeutic agent against MDR E. coli infection due to its broad host range, environmental stability, and biofilm inhibition properties. Future research should optimize bacteriophage preparations, evaluate the safety and efficacy of animal models, and establish clinical application plans in the field of food safety.},
}

@article {pmid39818750,
year = {2025},
author = {Shao, D and Ju, X and Wu, Y and Zhang, Y and Yan, Z and Li, Y and Wang, L and Parkhill, J and Walsh, TR and Wu, C and Shen, J and Wang, Y and Zhang, R and Shen, Y},
title = {Quaternary Ammonium Compounds: A New Driver and Hidden Threat for mcr-1 Prevalence in Hospital Wastewater and Human Feces.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c11368},
pmid = {39818750},
issn = {1520-5851},
abstract = {The emergence of mobile colistin resistance gene mcr-1 has attracted global attention. The prevalence of mcr-1-positive Escherichia coli (MCRPEC) in humans largely decreased following the ban of colistin as an animal growth promoter in China. However, the prevalence of MCRPEC in the hospital environment and the relationship between disinfectants and mcr-1 remain unclear. We found that MCRPEC prevalence was low in the feces of healthy humans attending physical examinations in six hospitals (4.6%, 71/1532) but high in hospital wastewater (50.0%, 27/54). mcr-1 was mainly located on IncI2 (63.0% in wastewater and 62.0% in feces) and IncHI2 plasmids (18.5% in wastewater and 21.1% in feces). High similarity of the mcr-1 context and its carrying plasmids was observed in human and wastewater MCRPEC, with several isolates clustering together. The coexistence of the ESBL gene blaCTX-M with mcr-1 occurred in 19.7% of IncI2 plasmids. Notably, 60.0% of IncHI2 plasmids exhibited co-occurrence of mcr-1 with the disinfectant resistance gene (DRG) qacEΔ1, conferring resistance to quaternary ammonium compounds (QACs). We revealed that QACs, rather than the other two types of disinfectants─ortho-phthalaldehyde (OPA) and povidone-iodine (PVP-I)─select for plasmids carrying both qacEΔ1 and mcr-1 and elevate their conjugative transfer frequency. Monitoring of DRGs in MCRPEC and managing disinfectant use are urgently needed in healthcare settings to mitigate the spread of colistin resistance from hospital environments to inpatients.},
}

@article {pmid39817515,
year = {2025},
author = {Djordjevic, M and Zivkovic, L and Ou, HY and Djordjevic, M},
title = {Nonlinear regulatory dynamics of bacterial restriction-modification systems modulates horizontal gene transfer susceptibility.},
journal = {Nucleic acids research},
volume = {53},
number = {2},
pages = {},
pmid = {39817515},
issn = {1362-4962},
support = {7750294//Science Fund of the Republic of Serbia/ ; //Ministry of Science and Technological Development of the Republic of Serbia/ ; 32370186//National Natural Science Foundation of China/ ; },
mesh = {*Gene Transfer, Horizontal ; *DNA Restriction-Modification Enzymes/genetics ; Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Nonlinear Dynamics ; Models, Genetic ; Bacteria/genetics ; Plasmids/genetics ; },
abstract = {Type II restriction-modification (R-M) systems play a pivotal role in bacterial defense against invading DNA, influencing the spread of pathogenic traits. These systems often involve coordinated expression of a regulatory protein (C) with restriction (R) enzymes, employing complex feedback loops for regulation. Recent studies highlight the crucial balance between R and M enzymes in controlling horizontal gene transfer (HGT). This manuscript introduces a mathematical model reflecting R-M system dynamics, informed by biophysical evidence, to minimize reliance on arbitrary parameters. Our analysis clarifies the observed variations in M-to-R ratios, emphasizing the regulatory role of the C protein. We analytically derived a stability diagram for C-regulated R-M systems, offering a more straightforward analysis method over traditional numerical approaches. Our findings reveal conditions leading to both monostability and bistability, linking changes in the M-to-R ratio to factors like cell division timing and plasmid replication rates. These variations may link adjusting defense against phage infection, or the acquisition of new genes such as antibiotic resistance determinants, to changing physiological conditions. We also performed stochastic simulations to show that system regulation may significantly increase M-to-R ratio variability, providing an additional mechanism to generate heterogeneity in bacterial population.},
}

*Gene Transfer, Horizontal
*DNA Restriction-Modification Enzymes/genetics
Bacterial Proteins/genetics/metabolism
Gene Expression Regulation, Bacterial
Nonlinear Dynamics
Models, Genetic
Bacteria/genetics
Plasmids/genetics

@article {pmid39816412,
year = {2022},
author = {Arredondo-Hernandez, R and Siebe, C and Castillo-Rojas, G and Ponce de León, S and López-Vidal, Y},
title = {The synergistic interaction of systemic inflammation, dysbiosis and antimicrobial resistance promotes growth restriction in children with acute severe malnutrition: An emphasis on Escherichia coli.},
journal = {Frontiers in antibiotics},
volume = {1},
number = {},
pages = {1001717},
pmid = {39816412},
issn = {2813-2467},
abstract = {A healthy development is denied to millions of children worldwide as harsh life conditions manifest themselves in an altered inflammation-prone microbiome crosstalk environment. Keynote of this tragedy is that insufficient nutritious amino acid blocks lipids-intake to sustain diverse microbiota, and promotes the generalist strategy followed by Escherichia coli -besides other proteobacteria- of shifting gut metabolism, subverting the site specificity of first immune reaction. Furthermore, it could be hypothesized that selective success lies in their ability to induce inflammation, since this phenomenon also fuels horizontal gene transfer (HGT). In this review, we dilucidate how immune mechanisms of environmental enteric dysfunction affect overgrowth restriction, infectious morbidity rate, and acquired lifelong risks among severe acute malnourished children. Also, despite acknowledging complexities of antimicrobial resistant enrichment, we explore and speculate over the links between virulence regulation and HGT as an indissociable part in the quest for new inflammatory niches by open genome bacteria, particularly when both collide in the most vulnerable.},
}

@article {pmid39813956,
year = {2025},
author = {Yang, QE and Lin, Z and Gan, D and Li, M and Liu, X and Zhou, S and Walsh, TR},
title = {Microplastics mediates the spread of antimicrobial resistance plasmids via modulating conjugal gene expression.},
journal = {Environment international},
volume = {195},
number = {},
pages = {109261},
doi = {10.1016/j.envint.2025.109261},
pmid = {39813956},
issn = {1873-6750},
abstract = {Antimicrobial resistance (AMR) and environmental degradation are existential global public health threats. Linking microplastics (MPs) and AMR is particularly concerning as MPs pollution would have significant ramifications on controlling of AMR; however, the effects of MPs on the spread and genetic mechanisms of AMR bacteria remain unclear. Herein, we performed Simonsen end-point conjugation to investigate the impact of four commonly used MPs on transfer of clinically relevant plasmids. The transfer breadth of a representative pA/C_MCR-8 plasmid across bacterial communities was confirmed by the cell sorting and 16S rRNA gene amplicon sequencing. Our study shows that exposure to four commonly found MPs promotes the conjugation rates of four clinically relevant AMR plasmids by up to 200-fold, when compared to the non-exposed group and that the transfer rates are MP concentrations demonstrate a positive correlation with higher transfer rates. Furthermore, we show that MPs induce the expression of plasmid-borne conjugal genes and SOS-linked genes such as recA, lexA, dinB and dinD. High-throughput sequencing of the broad transmission of plasmid pA/C_MCR-8, shows distribution over two main phyla, Pseudomonadota (50.0 %-95.0 %) and Bacillota (0.4 %-2.0 %). These findings definitively link two global health emergencies - AMR and environmental degradation via MPs, and to tackle global AMR, we must also now consider plastic utilisation and waste management.},
}

@article {pmid39807864,
year = {2025},
author = {Nakatsu, G and Ko, D and Michaud, M and Franzosa, EA and Morgan, XC and Huttenhower, C and Garrett, WS},
title = {Virulence factor discovery identifies associations between the Fic gene family and Fap2[+] fusobacteria in colorectal cancer microbiomes.},
journal = {mBio},
volume = {},
number = {},
pages = {e0373224},
doi = {10.1128/mbio.03732-24},
pmid = {39807864},
issn = {2150-7511},
abstract = {Fusobacterium is a bacterium associated with colorectal cancer (CRC) tumorigenesis, progression, and metastasis. Fap2 is a fusobacteria-specific outer membrane galactose-binding lectin that mediates Fusobacterium adherence to and invasion of CRC tumors. Advances in omics analyses provide an opportunity to profile and identify microbial genomic features that correlate with the cancer-associated bacterial virulence factor Fap2. Here, we analyze genomes of Fusobacterium colon tumor isolates and find that a family of post-translational modification enzymes containing Fic domains is associated with Fap2 positivity in these strains. We demonstrate that Fic family genes expand with the presence of Fap2 in the fusobacterial pangenome. Through comparative genomic analysis, we find that Fap2[+] Fusobacteriota are highly enriched with Fic gene families compared to other cancer-associated and human gut microbiome bacterial taxa. Using a global data set of CRC shotgun metagenomes, we show that fusobacterial Fic and Fap2 genes frequently co-occur in the fecal microbiomes of individuals with late-stage CRC. We further characterize specific Fic gene families harbored by Fap2[+] Fusobacterium animalis genomes and detect recombination events and elements of horizontal gene transfer via synteny analysis of Fic gene loci. Exposure of a F. animalis strain to a colon adenocarcinoma cell line increases gene expression of fusobacterial Fic and virulence-associated adhesins. Finally, we demonstrate that Fic proteins are synthesized by F. animalis as Fic peptides are detectable in F. animalis monoculture supernatants. Taken together, our study uncovers Fic genes as potential virulence factors in Fap2[+] fusobacterial genomes.IMPORTANCEAccumulating data support that bacterial members of the intra-tumoral microbiota critically influence colorectal cancer progression. Yet, relatively little is known about non-adhesin fusobacterial virulence factors that may influence carcinogenesis. Our genomic analysis and expression assays in fusobacteria identify Fic domain-containing genes, well-studied virulence factors in pathogenic bacteria, as potential fusobacterial virulence features. The Fic family proteins that we find are encoded by fusobacteria and expressed by Fusobacterium animalis merit future investigation to assess their roles in colorectal cancer development and progression.},
}

@article {pmid39805347,
year = {2025},
author = {Sasikumar, J and Shaikh, HA and Naik, B and Laha, S and Das, SP},
title = {Emergence of fungal hybrids - Potential threat to humans.},
journal = {Microbial pathogenesis},
volume = {200},
number = {},
pages = {107278},
doi = {10.1016/j.micpath.2025.107278},
pmid = {39805347},
issn = {1096-1208},
abstract = {Fungal hybrids arise through the interbreeding of distinct species. This hybridization process fosters increased genetic diversity and the emergence of new traits. Mechanisms driving hybridization include the loss of heterozygosity, copy number variations, and horizontal gene transfer. Genetic mating barriers, changes in ploidy, chromosomal instability, and genomic diversity influence hybridization. These factors directly impact the fitness and adaptation of hybrid offspring. Epigenetic factors, including DNA methylation, histone modifications, non-coding RNAs, and chromatin remodelling, play a role in post-mating isolation in hybrids. In addition to all these mechanisms, successful hybridization in fungi is ensured by cellular mechanisms like mitochondrial inheritance, transposable elements, and other genome conversion mechanisms. These mechanisms support hybrid life and enhance the virulence and pathogenicity of fungal hybrids, which provoke diseases in host organisms. Recent advancements in sequencing have uncovered fungal hybrids in pathogens like Aspergillus, Candida, and Cryptococcus. Examples of these hybrids, such as Aspergillus latus, Candida metapsilosis, and Cryptococcus neoformans, induce severe human infections. Identifying fungal hybrids is challenging due to their altered genome traits. ITS sequencing has emerged as a promising method for diagnosing these hybrids. To prevent the emergence of novel hybrid fungal pathogens, it is crucial to develop effective diagnostic techniques and closely monitor pathogenic fungal populations for signs of hybridization. This comprehensive review delves into various facts about fungal hybridization, including its causes, genetic outcomes, barriers, diagnostic strategies, and examples of emerging fungal hybrids. The review emphasises the potential threat that fungal hybrids pose to human health and highlights their clinical significance.},
}

@article {pmid39803089,
year = {2024},
author = {Yadav, KS and Pawar, S and Datkhile, K and Patil, SR},
title = {Study on the Mobile Colistin Resistance (mcr-1) Gene in Gram-Negative Bacilli in a Rural Tertiary Care Hospital in Western Maharashtra.},
journal = {Cureus},
volume = {16},
number = {12},
pages = {e75569},
pmid = {39803089},
issn = {2168-8184},
abstract = {BACKGROUND: Colistin, a last-resort antibiotic for treating multidrug-resistant Gram-negative bacterial infections, has increased resistance as a result of the emergence of the mcr-1 gene. The mcr-1gene, which confers colistin resistance, is often carried on plasmids, facilitating its spread by horizontal gene transfer among bacterial populations. The rising prevalence of mcr-1-mediated resistance poses significant challenges for infection control and treatment efficacy. This study aimed to detect and investigate the prevalence of the mcr-1 gene among Gram-negative bacilli isolated from clinical specimens in a rural tertiary care hospital and to analyze the plasmid-mediated mechanisms of colistin resistance.

MATERIALS AND METHODS: A cross-sectional study was conducted over two years at Krishna Institute of Medical Sciences, Karad. Gram-negative bacilli were isolated from clinical specimens and identified using standard methodology. Antimicrobial susceptibility testing was performed by using the Vitek-2 Compact (bioMerieux, Marcy-l'Étoile, France) method and the colistin-resistance broth microdilution method (BMD). Polymerase chain reaction (PCR) was done for the presence of mcr-1 gene in colistin-resistant isolates.

RESULTS: Out of 359 Gram-negative bacilli isolates, 93 (25.90%) demonstrated resistance to colistin. Among these resistant strains, the mcr-1 gene was identified in 13 (13.97%) of the isolates. The gene was predominantly found in Pseudomonas aeruginosa (8, 61.53%), followed by Klebsiella pneumoniae (3, 23.07%), Acinetobacter baumannii (2, 15.38%) among the 13 isolates. Out of the various specimens received, mcr-1 gene was found in endotracheal tube (4, 30.76%), urine (4, 30.76%), pus (3, 23.07%), sputum (1, 7.69%), and blood (1, 7.69%). Colistin minimum inhibitory concentration (MIC) value for these resistant isolates ranged from 4 to 16 µg/ml.

CONCLUSION: The study highlights a significant prevalence of mcr-1 plasmid-mediated colistin resistance gene among Gram-negative bacilli in the hospital. This possibly highlights the frequent misuse of colistin in animal husbandry from this rural area. The findings underscore the importance of monitoring resistance patterns and implementing stringent infection control measures.},
}

@article {pmid39801834,
year = {2025},
author = {Bustamante, M and Mei, S and Daras, IM and van Doorn, GS and Falcao Salles, J and de Vos, MGJ},
title = {An eco-evolutionary perspective on antimicrobial resistance in the context of One Health.},
journal = {iScience},
volume = {28},
number = {1},
pages = {111534},
pmid = {39801834},
issn = {2589-0042},
abstract = {The One Health approach musters growing concerns about antimicrobial resistance due to the increased use of antibiotics in healthcare and agriculture, with all of its consequences for human, livestock, and environmental health. In this perspective, we explore the current knowledge on how interactions at different levels of biological organization, from genetic to ecological interactions, affect the evolution of antimicrobial resistance. We discuss their role in different contexts, from natural systems with weak selection, to human-influenced environments that impose a strong pressure toward antimicrobial resistance evolution. We emphasize the need for an eco-evolutionary approach within the One Health framework and highlight the importance of horizontal gene transfer and microbiome interactions for increased understanding of the emergence and spread of antimicrobial resistance.},
}

@article {pmid39786570,
year = {2025},
author = {Chen, J and Garfinkel, DJ and Bergman, CM},
title = {Horizontal Transfer and Recombination Fuel Ty4 Retrotransposon Evolution in Saccharomyces.},
journal = {Genome biology and evolution},
volume = {17},
number = {1},
pages = {},
doi = {10.1093/gbe/evaf004},
pmid = {39786570},
issn = {1759-6653},
support = {//University of Georgia Research Foundation/ ; R01GM124216/NH/NIH HHS/United States ; },
mesh = {*Gene Transfer, Horizontal ; *Retroelements ; *Saccharomyces/genetics ; *Evolution, Molecular ; *Recombination, Genetic ; Phylogeny ; Genome, Fungal ; },
abstract = {Horizontal transposon transfer (HTT) plays an important role in the evolution of eukaryotic genomes; however, the detailed evolutionary history and impact of most HTT events remain to be elucidated. To better understand the process of HTT in closely related microbial eukaryotes, we studied Ty4 retrotransposon subfamily content and sequence evolution across the genus Saccharomyces using short- and long-read whole genome sequence data, including new PacBio genome assemblies for two Saccharomyces mikatae strains. We find evidence for multiple independent HTT events introducing the Tsu4 subfamily into specific lineages of Saccharomyces paradoxus, Saccharomyces cerevisiae, Saccharomyces eubayanus, Saccharomyces kudriavzevii and the ancestor of the S. mikatae/Saccharomyces jurei species pair. In both S. mikatae and S. kudriavzevii, we identified novel Ty4 clades that were independently generated through recombination between resident and horizontally transferred subfamilies. Our results reveal that recurrent HTT and lineage-specific extinction events lead to a complex pattern of Ty4 subfamily content across the genus Saccharomyces. Moreover, our results demonstrate how HTT can lead to coexistence of related retrotransposon subfamilies in the same genome that can fuel evolution of new retrotransposon clades via recombination.},
}

*Gene Transfer, Horizontal
*Retroelements
*Saccharomyces/genetics
*Evolution, Molecular
*Recombination, Genetic
Phylogeny
Genome, Fungal

@article {pmid39750749,
year = {2025},
author = {Molari, M and Shaw, LP and Neher, RA},
title = {Quantifying the Evolutionary Dynamics of Structure and Content in Closely Related E. coli Genomes.},
journal = {Molecular biology and evolution},
volume = {42},
number = {1},
pages = {},
doi = {10.1093/molbev/msae272},
pmid = {39750749},
issn = {1537-1719},
support = {//University of Basel/ ; //Sir Henry Wellcome Postdoctoral Fellow/ ; 220422/Z/20/Z//Wellcome/ ; },
mesh = {*Escherichia coli/genetics ; *Genome, Bacterial ; *Evolution, Molecular ; *Phylogeny ; Synteny ; },
abstract = {Bacterial genomes primarily diversify via gain, loss, and rearrangement of genetic material in their flexible accessory genome. Yet the dynamics of accessory genome evolution are very poorly understood, in contrast to the core genome where diversification is readily described by mutations and homologous recombination. Here, we tackle this problem for the case of very closely related genomes. We comprehensively describe genome evolution within n=222 genomes of Escherichia coli ST131, which likely shared a common ancestor around 100 years ago. After removing putative recombinant diversity, the total length of the phylogeny is 6,000 core genome substitutions. Within this diversity, we find 22 modifications to core genome synteny and estimate around 2,000 structural changes within the accessory genome, i.e. one structural change for every three core genome substitutions. Sixty-three percent of loci with structural diversity could be resolved into individual gain and loss events with 10-fold more gains than losses, demonstrating a dominance of gains due to insertion sequences and prophage integration. Our results suggest the majority of synteny changes and insertions in our dataset are likely deleterious and only persist for a short time before being removed by purifying selection.},
}

*Escherichia coli/genetics
*Genome, Bacterial
*Evolution, Molecular
*Phylogeny
Synteny

@article {pmid39693608,
year = {2024},
author = {Laidlaw, A and Blondin-Brosseau, M and Shay, J and Dussault, F and Rao, M and Petronella, N and Tamber, S},
title = {Variation in plasmid conjugation among nontyphoidal Salmonella enterica serovars.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2024-0164},
pmid = {39693608},
issn = {1480-3275},
abstract = {Conjugation is a complex phenomenon involving multiple plasmid, bacterial, and environmental factors. Here we describe an IncI1 plasmid encoding multidrug antibiotic resistance to aminoglycosides, sulfonamides, and third-generation cephalosporins. This plasmid is widespread geographically among animal, human, and environmental sectors. We present data on the transmissibility of this plasmid from Salmonella enterica ser. Kentucky into 40 strains of S. enterica (10 strains each from serovars Enteritidis, Heidelberg, Infantis, and Typhimurium). Thirty seven out of 40 strains were able to take up the plasmid. Rates of conjugation were variable between strains ranging from 10[-8] to 10[-4]. Overall, serovars Enteritidis and Typhimurium demonstrated the highest rates of conjugation, followed by Heidelberg, and then Infantis. No relationships were observed between the recipient cell surface and rate of conjugation. Recipient cell numbers correlated positively with conjugation rate and strains with high conjugation rates had marginally but significantly higher growth parameters compared to strains that took up the plasmid at lower frequencies. Environmental conditions known to impact cell growth, such as temperature, nutrient availability, and the presence of antibiotics, had a modulating effect on conjugation. Collectively, these results will further understanding of plasmid transmission dynamics in Salmonella, which is a critical first step towards the development of mitigation strategies.},
}

@article {pmid39801293,
year = {2025},
author = {Marquiegui-Alvaro, A and Kottara, A and Chacón, M and Cliffe, L and Brockhurst, M and Dixon, N},
title = {Genetic Bioaugmentation-Mediated Bioremediation of Terephthalate in Soil Microcosms Using an Engineered Environmental Plasmid.},
journal = {Microbial biotechnology},
volume = {18},
number = {1},
pages = {e70071},
pmid = {39801293},
issn = {1751-7915},
support = {BB/P01738X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T005742/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/W012723/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; EP/S022856/1//Engineering and Physical Sciences Research Council/ ; },
mesh = {*Plasmids/genetics ; *Soil Microbiology ; *Biodegradation, Environmental ; *Soil Pollutants/metabolism ; *Phthalic Acids/metabolism ; Gene Transfer, Horizontal ; Pseudomonas putida/genetics/metabolism ; },
abstract = {Harnessing in situ microbial communities to clean-up polluted natural environments is a potentially efficient means of bioremediation, but often the necessary genes to breakdown pollutants are missing. Genetic bioaugmentation, whereby the required genes are delivered to resident bacteria via horizontal gene transfer, offers a promising solution to this problem. Here, we engineered a conjugative plasmid previously isolated from soil, pQBR57, to carry a synthetic set of genes allowing bacteria to consume terephthalate, a chemical component of plastics commonly released during their manufacture and breakdown. Our engineered plasmid caused a low fitness cost and was stably maintained in terephthalate-contaminated soil by the bacterium P. putida. Plasmid carriers efficiently bioremediated contaminated soil in model soil microcosms, achieving complete breakdown of 3.2 mg/g of terephthalate within 8 days. The engineered plasmid horizontally transferred the synthetic operon to P. fluorescens in situ, and the resulting transconjugants degraded 10 mM terephthalate during a 180-h incubation. Our findings show that environmental plasmids carrying synthetic catabolic operons can be useful tools for in situ engineering of microbial communities to perform clean-up even of complex environments like soil.},
}

*Plasmids/genetics
*Soil Microbiology
*Biodegradation, Environmental
*Soil Pollutants/metabolism
*Phthalic Acids/metabolism
Gene Transfer, Horizontal
Pseudomonas putida/genetics/metabolism

@article {pmid39799674,
year = {2025},
author = {Li, Y and Qin, W and Xin, X and Tang, C and Huang, Y and He, X and Chen, L and Yu, G and Yu, F},
title = {Dynamic impact of polyethylene terephthalate nanoplastics on antibiotic resistance and microplastics degradation genes in the rhizosphere of Oryza sativa L.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137173},
doi = {10.1016/j.jhazmat.2025.137173},
pmid = {39799674},
issn = {1873-3336},
abstract = {This study examined the effects of polyethylene terephthalate (PET) nanoplastics on the rhizosphere of Oryza sativa L., focusing on dynamic changes and interactions among microbial communities, antibiotic resistance genes (ARGs) and microplastic degradation genes (MDGs). PET exposure altered the structure and function of soil microbial, enabling specific microbial groups to thrive in polluted environments. High-dose PET treatments markedly increased the abundance and dissemination of ARGs, primarily via resistance mechanisms such as antibiotic efflux and target alteration. By providing additional carbon sources and surfaces for microbial attachment, PET stimulated the growth of microorganisms harboring MDGs, resulting in an increase in MDGs abundance. The elevated expression of MDGs facilitated the propagation of ARGs, with overlapping host microorganisms suggesting that certain microbial groups exhibit dual metabolic capabilities, enabling them to endure both antibiotic and microplastic pressures. Toxic byproducts of microplastic degradation, such as mono-ethylhexyl phthalate, further promoted ARGs dissemination by increasing horizontal gene transfer frequency. Structural equation modeling revealed that PET indirectly influenced ARGs and MDGs expression by altering soil C/N ratio, available phosphorus, and enzyme activities. Thus, nanoscale PET exacerbates ecological risks to soil microbial communities by driving co-propagation of ARGs and MDGs, highlighting the persistent threat of composite pollution to agroecosystems.},
}

@article {pmid39798650,
year = {2025},
author = {Zhang, X and Guo, W and Zhang, Z and Gao, P and Tang, P and Liu, T and Yao, X and Li, J},
title = {Insights into the mobility and bacterial hosts of antibiotic resistance genes under dinotefuran selection pressure in aerobic granular sludge based on metagenomic binning and functional modules.},
journal = {Environmental research},
volume = {268},
number = {},
pages = {120807},
doi = {10.1016/j.envres.2025.120807},
pmid = {39798650},
issn = {1096-0953},
abstract = {Dinotefuran (DIN) is toxic to non-target organisms and accelerates the evolution of antibiotic resistance, which poses a problem for the stable operation of the activated sludge process in wastewater treatment plants (WWTPs). However, the emergence and the transfer mechanism of antibiotic resistance genes (ARGs) in activated sludge systems under DIN stress remains unclear. Thus, in the study, the potential impact of DIN on ARGs and virulence factor genes (VFGs) in aerobic granular sludge (AGS) was investigated in depth using metagenomic binning and functional modules. It was found that DIN stress increased the total abundance of ARGs, mobile genetic elements (MGEs), and VFGs in the AGS system, with the highest abundance of fabG (4.6%), tnpA (55.6%) and LPS (39.0%), respectively. The proliferation of the enteric pathogens Salmonella enterica and Escherichia coli in the system indicates that DIN induces exposure of harmless bacteria to the infected environment. The genera Nitrospira (1169 ARG subtypes) and Dechloromonas (663 ARG subtypes) were identified as the potentially antibiotic-resistant bacteria carrying the most ARGs and MGEs in the metagenome-assembled genomes. Co-localization patterns of some ARGs, MGEs, and the SOS response-related gene lexA were observed on metagenome-assembled contigs under high levels of DIN exposure, suggesting DIN stimulated ROS production (101.8% increase over control), altered cell membrane permeability, and increased the potential for horizontal gene transfer (HGT). Furthermore, the DNA damage caused by DIN in AGS led to the activation of the antioxidant system and the SOS repair response, which in turn promoted the expression of the type IV secretion system and HGT through the flagellar channel. This study extends the previously unappreciated DIN understanding of the spread and associated risks of ARGs and VFGs in the AGS system of WWTPs. It elucidates how DIN facilitates HGT, offering a scientific basis for controlling emerging contaminant-induced resistance.},
}

@article {pmid39575680,
year = {2025},
author = {Wang, H and Xu, Z and Zhang, Z and Zhong, B},
title = {Horizontal transposon transfer during plant terrestrialization.},
journal = {Journal of integrative plant biology},
volume = {67},
number = {1},
pages = {15-18},
doi = {10.1111/jipb.13809},
pmid = {39575680},
issn = {1744-7909},
support = {32122010//National Natural Science Foundation of China/ ; 32370228//National Natural Science Foundation of China/ ; },
mesh = {*DNA Transposable Elements/genetics ; *Gene Transfer, Horizontal ; *Plants/genetics ; },
abstract = {During the move to land, plants acquired transposable elements by horizontal transfer from bacteria and fungi and land plants have many long non-coding RNAs derived from retrotransposons acquired by horizontal transposon transfer, including some that are highly expressed and involved in the response to drought stress and abscisic acid.},
}

*DNA Transposable Elements/genetics
*Gene Transfer, Horizontal
*Plants/genetics

@article {pmid39797530,
year = {2025},
author = {Liu, Y and Gong, C and Hu, Y and Han, H and Tian, T and Luo, Y and Yang, X and Xie, W and Wu, Q and Wang, S and Guo, Z and Zhang, Y},
title = {Silencing of the plant-derived horizontally transferred gene BtSC5DL effectively controls Bemisia tabaci MED.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.8638},
pmid = {39797530},
issn = {1526-4998},
support = {2021YFD1400600//National Key R&D Program of China/ ; 32221004//National Natural Science Foundation of China/ ; CARS-23//Earmarked Fund for CARS/ ; Y2023XK15//Central Public-Interest Scientific Institution Basal Research Fund of the Chinese Academy of Agricultural Sciences./ ; Y2024XK01//Central Public-Interest Scientific Institution Basal Research Fund of the Chinese Academy of Agricultural Sciences./ ; //Beijing Key Laboratory for Pest Control and Sustainable Cultivation of Vegetables/ ; CAAS-ASTIP-IVFCAAS//Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences/ ; },
abstract = {BACKGROUND: The whitefly Bemisia tabaci is a notorious agricultural pest known for its ability to cause significant crop damage through direct feeding and virus transmission. Its remarkable adaptability and reproductive capacity are linked to its ability to acquire and integrate horizontally transferred genes (HTGs) into its genome. These HTGs increase the physiological and metabolic capacities of this pest, including cholesterol synthesis, which is critical for its survival and reproductive success. Among these genes, we identified a plant-derived B. tabaci Δ7-sterol C5-desaturase-like gene (BtSC5DL), which plays a pivotal role in B. tabaci cholesterol metabolism and reproductive biology.

RESULTS: In this study, we cloned and identified the BtSC5DL gene from B. tabaci Mediterranean (MED). Bioinformatics and molecular analyses revealed that BtSC5DL was transferred from plants to B. tabaci millions of years ago and is now stably expressed in this species. Silencing BtSC5DL through dsRNA feeding resulted in significant reductions in egg production and cholesterol content in B. tabaci MED. Furthermore, virus-induced gene silencing (VIGS) experiments confirmed that long-term suppression of BtSC5DL had a notable ability to control whitefly populations.

CONCLUSION: Our results demonstrate the crucial role of BtSC5DL in cholesterol biosynthesis in B. tabaci MED and suggest that the acquisition of this gene significantly enhances the reproductive capacity of this species. These findings provide a theoretical basis for the development of RNA interference (RNAi)-based pest control strategies targeting BtSC5DL, offering a potential new approach for the effective management of whitefly populations in agricultural settings. © 2025 Society of Chemical Industry.},
}

@article {pmid39794121,
year = {2025},
author = {Liu, Y and Botelho, J and Iranzo, J},
title = {Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279300.124},
pmid = {39794121},
issn = {1549-5469},
abstract = {Prokaryotes have evolved a wide repertoire of defense systems to prevent invasion by mobile genetic elements (MGE). However, because MGE are vehicles for the exchange of beneficial accessory genes, defense systems could consequently impede rapid adaptation in microbial populations. Here, we study how defense systems impact horizontal gene transfer (HGT) in the short and long terms. By combining comparative genomics and phylogeny-aware statistical methods, we quantified the association between the presence of 7 widespread defense systems and the abundance of MGE in the genomes of 196 bacterial and 1 archaeal species. We also calculated the differences in the rates of gene gain and loss between lineages that possess and lack each defense system. Our results show that the impact of defense systems on HGT is highly taxon- and system-dependent, and in most cases not statistically significant. Timescale analysis reveals that defense systems must persist in a lineage for a relatively long time to exert an appreciable negative impact on HGT. In contrast, for shorter evolutionary timescales, frequent co-acquisition of MGE and defense systems results in a net positive association of the latter with HGT. Given the high turnover rates experienced by defense systems, we propose that the inhibitory effect of most defense systems on HGT is masked by their strong linkage with MGE. These findings help explain the contradictory conclusions of previous research by pointing at mobility and within-host retention times as key factors that determine the impact of defense systems on genome plasticity.},
}

@article {pmid39793087,
year = {2025},
author = {Zhang, Y and Tu, C and Bai, J and Li, X and Sun, Z and Xu, L},
title = {Metabolic enhancement contributed by horizontal gene transfer is essential for dietary specialization in leaf beetles.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {1},
pages = {e2415717122},
doi = {10.1073/pnas.2415717122},
pmid = {39793087},
issn = {1091-6490},
support = {32370523//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {Animals ; *Coleoptera/genetics/metabolism ; *Gene Transfer, Horizontal ; *Plant Leaves/parasitology/metabolism/genetics ; *Larva/metabolism/genetics/growth & development ; *Cellulose/metabolism ; Diet ; },
abstract = {Horizontal gene transfer (HGT) from bacteria to insects is widely reported and often associated with the adaptation and diversification of insects. However, compelling evidence demonstrating how HGT-conferred metabolic adjustments enable species to adapt to surrounding environment remains scarce. Dietary specialization is an important ecological strategy adopted by animals to reduce inter- and intraspecific competition for limited resources. Adults of the leaf beetle Plagiodera versicolora (Coleoptera) preferentially consume new leaves; nevertheless, we found that they selectively oviposit on mature leaves, thereby establishing a distinct dietary niche separation between adults and larvae. Based on the de novo assembled chromosome-level genome, we identified two horizontally transferred genes with cellulose degradation potential, belonging to the glycosyl hydrolase 48 family (GH48-1 and GH48-2). Prokaryotic expression of the HGTs confirmed the cellulose degradation capability of the two genes. Knockdown of GH48 significantly hampered the growth and survival rate of larvae feeding on mature leaves compared to wild-type larvae, with no similar effect observed in adults. Replenishing the GH48-expressing bacteria compensated for the knockdown of these two genes and recurred larval adaptability to mature leaves. Taken together, our results highlight the advantage and metabolic enhancement conferred by the two cellulose-degrading HGTs in P. versicolora larvae, enabling their development on cellulose-enriched mature leaves and underscoring the indispensable role of HGTs in facilitating the adaptation of leaf beetles to plants.},
}

Animals
*Coleoptera/genetics/metabolism
*Gene Transfer, Horizontal
*Plant Leaves/parasitology/metabolism/genetics
*Larva/metabolism/genetics/growth & development
*Cellulose/metabolism
Diet

@article {pmid39791879,
year = {2025},
author = {Kohlmeier, MG and O'Hara, GW and Ramsay, JP and Terpolilli, JJ},
title = {Closed genomes of commercial inoculant rhizobia provide a blueprint for management of legume inoculation.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0221324},
doi = {10.1128/aem.02213-24},
pmid = {39791879},
issn = {1098-5336},
abstract = {UNLABELLED: Rhizobia are soil bacteria capable of establishing symbiosis within legume root nodules, where they reduce atmospheric N2 into ammonia and supply it to the plant for growth. Australian soils often lack rhizobia compatible with introduced agricultural legumes, so inoculation with exotic strains has become a common practice for over 50 years. While extensive research has assessed the N2-fixing capabilities of these inoculants, their genomics, taxonomy, and core and accessory gene phylogeny are poorly characterized. Furthermore, in some cases, inoculant strains have been developed from isolations made in Australia. It is unknown whether these strains represent naturalized exotic organisms, native rhizobia with a capacity to nodulate introduced legumes, or recombinant strains arising from horizontal transfer between introduced and native bacteria. Here, we describe the complete, closed genome sequences of 42 Australian commercial rhizobia. These strains span the genera, Bradyrhizobium, Mesorhizobium, Methylobacterium, Rhizobium, and Sinorhizobium, and only 23 strains were identified to species level. Within inoculant strain genomes, replicon structure and location of symbiosis genes were consistent with those of model strains for each genus, except for Rhizobium sp. SRDI969, where the symbiosis genes are chromosomally encoded. Genomic analysis of the strains isolated from Australia showed they were related to exotic strains, suggesting that they may have colonized Australian soils following undocumented introductions. These genome sequences provide the basis for accurate strain identification to manage inoculation and identify the prevalence and impact of horizontal gene transfer (HGT) on legume productivity.

IMPORTANCE: Inoculation of cultivated legumes with exotic rhizobia is integral to Australian agriculture in soils lacking compatible rhizobia. The Australian inoculant program supplies phenotypically characterized high-performing strains for farmers but in most cases, little is known about the genomes of these rhizobia. Horizontal gene transfer (HGT) of symbiosis genes from inoculant strains to native non-symbiotic rhizobia frequently occurs in Australian soils and can impact the long-term stability and efficacy of legume inoculation. Here, we present the analysis of reference-quality genomes for 42 Australian commercial rhizobial inoculants. We verify and classify the genetics, genome architecture, and taxonomy of these organisms. Importantly, these genome sequences will facilitate the accurate strain identification and monitoring of inoculants in soils and plant nodules, as well as enable detection of horizontal gene transfer to native rhizobia, thus ensuring the efficacy and integrity of Australia's legume inoculation program.},
}

@article {pmid39789078,
year = {2025},
author = {Lee, D and Muir, P and Lundberg, S and Lundholm, A and Sandegren, L and Koskiniemi, S},
title = {A CRISPR-Cas9 system protecting E. coli against acquisition of antibiotic resistance genes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {1545},
pmid = {39789078},
issn = {2045-2322},
mesh = {*CRISPR-Cas Systems ; *Escherichia coli/genetics/drug effects ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Plasmids/genetics ; Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; },
abstract = {Antimicrobial resistance (AMR) is an increasing problem worldwide, and new treatment options for bacterial infections are direly needed. Engineered probiotics show strong potential in treating or preventing bacterial infections. However, one concern with the use of live bacteria is the risk of the bacteria acquiring genes encoding for AMR or virulence factors through horizontal gene transfer (HGT), and the transformation of the probiotic into a superbug. Therefore, we developed an engineered CRISPR-Cas9 system that protects bacteria from horizontal gene transfer. We synthesized a CRISPR locus targeting eight AMR genes and cloned this with the Cas9 and transacting tracrRNA on a medium copy plasmid. We next evaluated the efficiency of the system to block HGT through transformation, transduction, and conjugation. Our results show that expression of the CRISPR-Cas9 system successfully protects E. coli MG1655 from acquiring the targeted resistance genes by transformation or transduction with 2-3 logs of protection depending on the system for transfer and the target gene. Furthermore, we show that the system blocks conjugation of a set of clinical plasmids, and that the system is also able to protect the probiotic bacterium E. coli Nissle 1917 from acquiring AMR genes.},
}

*CRISPR-Cas Systems
*Escherichia coli/genetics/drug effects
Drug Resistance, Bacterial/genetics
Gene Transfer, Horizontal
Plasmids/genetics
Anti-Bacterial Agents/pharmacology
Conjugation, Genetic

@article {pmid39623141,
year = {2025},
author = {Bhattacharya, S and Bejerano-Sagie, M and Ravins, M and Zeroni, L and Kaur, P and Gopu, V and Rosenshine, I and Ben-Yehuda, S},
title = {Flagellar rotation facilitates the transfer of a bacterial conjugative plasmid.},
journal = {The EMBO journal},
volume = {44},
number = {2},
pages = {587-611},
pmid = {39623141},
issn = {1460-2075},
support = {810186//EC | European Research Council (ERC)/ ; SPP2389//Deutsche Forschungsgemeinschaft (DFG)/ ; },
mesh = {*Plasmids/genetics/metabolism ; *Flagella/genetics/metabolism ; *Conjugation, Genetic ; *Bacillus subtilis/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Bacterial Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; Promoter Regions, Genetic ; },
abstract = {Conjugation-mediated DNA delivery is the primary mode for antibiotic resistance spread in bacteria; yet, molecular mechanisms regulating the conjugation process remain largely unexplored. While conjugative plasmids typically require bacterial attachment to solid surfaces for facilitation of donor-to-recipient proximity, the pLS20 conjugative plasmid, prevalent among Gram-positive Bacillus spp., uniquely requires fluid environments to enhance its transfer. Here, we show that pLS20, carried by Bacillus subtilis, induces multicellular clustering, which can accommodate various species, hence offering a stable platform for DNA delivery in a liquid milieu. We further discovered that induction of pLS20 promoters, governing crucial conjugative genes, is dependent on the presence of donor cell flagella, the major bacterial motility organelle. Moreover, the pLS20 regulatory circuit is controlled by a mechanosensing signal transduction pathway responsive to flagella rotation, thus activating conjugation gene expression exclusively during the host motile phase. This flagella-conjugation coupling strategy may allow the dissemination of the plasmid to remote destinations, allowing infiltration into new niches.},
}

*Plasmids/genetics/metabolism
*Flagella/genetics/metabolism
*Conjugation, Genetic
*Bacillus subtilis/genetics/metabolism
Gene Expression Regulation, Bacterial
Bacterial Proteins/genetics/metabolism
Gene Transfer, Horizontal
Promoter Regions, Genetic

@article {pmid39788974,
year = {2025},
author = {Scarpa, A and Pianezza, R and Gellert, HR and Haider, A and Kim, BY and Lai, EC and Kofler, R and Signor, S},
title = {Double trouble: two retrotransposons triggered a cascade of invasions in Drosophila species within the last 50 years.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {516},
pmid = {39788974},
issn = {2041-1723},
support = {P35093//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; P30 CA008748/CA/NCI NIH HHS/United States ; P34965//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; R01 HD108914/HD/NICHD NIH HHS/United States ; NSF-EPSCoR-2032756//National Science Foundation (NSF)/ ; R01 GM083300/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Retroelements/genetics ; *Gene Transfer, Horizontal ; *Phylogeny ; *Evolution, Molecular ; Drosophila/genetics ; Genome, Insect ; Drosophila melanogaster/genetics ; Introduced Species ; },
abstract = {Horizontal transfer of genetic material in eukaryotes has rarely been documented over short evolutionary timescales. Here, we show that two retrotransposons, Shellder and Spoink, invaded the genomes of multiple species of the melanogaster subgroup within the last 50 years. Through horizontal transfer, Spoink spread in D. melanogaster during the 1980s, while both Shellder and Spoink invaded D. simulans in the 1990s. Possibly following hybridization, D. simulans infected the island endemic species D. mauritiana (Mauritius) and D. sechellia (Seychelles) with both TEs after 1995. In the same approximate time-frame, Shellder also invaded D. teissieri, a species confined to sub-Saharan Africa. We find that the donors of Shellder and Spoink are likely American Drosophila species from the willistoni, cardini, and repleta groups. Thus, the described cascade of TE invasions could only become feasible after D. melanogaster and D. simulans extended their distributions into the Americas 200 years ago, likely aided by human activity. Our work reveals that cascades of TE invasions, likely initiated by human-mediated range expansions, could have an impact on the genomic and phenotypic evolution of geographically dispersed species. Within a few decades, TEs could invade many species, including island endemics, with distributions very distant from the donor of the TE.},
}

Animals
*Retroelements/genetics
*Gene Transfer, Horizontal
*Phylogeny
*Evolution, Molecular
Drosophila/genetics
Genome, Insect
Drosophila melanogaster/genetics
Introduced Species

@article {pmid39788725,
year = {2025},
author = {Robinson, LR and McDevitt, CJ and Regan, MR and Quail, SL and Wadsworth, CB},
title = {In vitro evolution of ciprofloxacin resistance in Neisseria commensals and derived mutation population dynamics in natural Neisseria populations.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnae107},
pmid = {39788725},
issn = {1574-6968},
abstract = {Commensal Neisseria are members of a healthy human oropharyngeal microbiome; however, they also serve as a reservoir of antimicrobial resistance for their pathogenic relatives. Despite their known importance as sources of novel genetic variation for pathogens, we still do not understand the full suite of resistance mutations commensal species can harbor. Here, we use in vitro selection to assess the mutations that emerge in response to ciprofloxacin selection in commensal Neisseria by passaging 4 replicates of 4 different species in the presence of a selective antibiotic gradient for 20 days; then categorized derived mutations with whole genome sequencing. 10/16 selected cells lines across the 4 species evolved ciprofloxacin resistance (≥ 1 ug/ml); with resistance-contributing mutations primarily emerging in DNA gyrase subunit A and B (gyrA and gyrB), topoisomerase IV subunits C and E (parC and parE), and the multiple transferable efflux pump repressor (mtrR). Of note, these derived mutations appeared in the same loci responsible for ciprofloxacin reduced susceptibility in the pathogenic Neisseria, suggesting conserved mechanisms of resistance across the genus. Additionally, we tested for zoliflodacin cross-resistance in evolved strain lines and found 6 lineages with elevated zoliflodacin minimum inhibitory concentrations. Finally, to interrogate the likelihood of experimentally derived mutations emerging and contributing to resistance in natural Neisseria, we used a population-based approach and identified GyrA 91I as a substitution circulating within commensal Neisseria populations and ParC 85C in a single gonococcal isolate. A small cluster of gonococcal isolates shared commensal alleles at parE, suggesting recent cross-species recombination events.},
}

@article {pmid39787839,
year = {2025},
author = {Zhao, W and Hou, Y and Wei, L and Wei, W and Zhang, K and Duan, H and Ni, BJ},
title = {Chlorination-induced spread of antibiotic resistance genes in drinking water systems.},
journal = {Water research},
volume = {274},
number = {},
pages = {123092},
doi = {10.1016/j.watres.2025.123092},
pmid = {39787839},
issn = {1879-2448},
abstract = {Chlorine, the most widely utilized disinfectant for drinking water globally, has recently been implicated in facilitating the spread of antibiotic resistance genes (ARGs), raising concerns about its underestimated environmental and ecological risks. However, given the current fragmented research focus and results, a comprehensive understanding of the potential mechanisms and influencing factors behind chlorination-promoted ARGs transmission in drinking water systems is crucial. This work is the first to systematically review the variations in abundance, transmission mechanisms, influencing factors, and mitigation strategies related to ARGs during the chlorination process. The results indicated that chlorination could induce genetic mutations and promote horizontal gene transfer through multiple pathways, including increased reactive oxygen species, enhanced membrane permeability, stimulation of the SOS response, and activation of efflux pumps. In addition, this work delves into significant discoveries regarding the factors affecting ARG transmission in drinking water, such as chlorine concentration, reaction time, disinfection byproducts, pipe materials, biofilms, and the water matrix. A series of effective strategies from water source to point-of-use were proposed aimed at mitigating ARGs transmission risks in the drinking water system. Finally, we address existing challenges and outline future research directions to overcome these bottlenecks. Overall, this review aims to advance our understanding of the role of chlorination in the dissemination of ARGs and to inspire innovative research ideas for optimizing disinfection techniques, minimizing the risks of antibiotic resistance transmission, and enhancing the safety of drinking water.},
}

@article {pmid39780077,
year = {2025},
author = {Lv, C and Abdullah, M and Su, CL and Chen, W and Zhou, N and Cheng, Z and Chen, Y and Li, M and Simpson, KW and Elsaadi, A and Zhu, Y and Lipkin, SM and Chang, YF},
title = {Genomic characterization of Escherichia coli with a polyketide synthase (pks) island isolated from ulcerative colitis patients.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {19},
pmid = {39780077},
issn = {1471-2164},
mesh = {Humans ; *Polyketide Synthases/genetics ; *Colitis, Ulcerative/microbiology/genetics ; *Escherichia coli/genetics/isolation & purification ; *Phylogeny ; *Genomic Islands ; Genome, Bacterial ; Genomics ; Gene Transfer, Horizontal ; Virulence Factors/genetics ; Escherichia coli Infections/microbiology ; Peptides ; Polyketides ; },
abstract = {The E. coli strains harboring the polyketide synthase (pks) island encode the genotoxin colibactin, a secondary metabolite reported to have severe implications for human health and for the progression of colorectal cancer. The present study involves whole-genome-wide comparison and phylogenetic analysis of pks harboring E. coli isolates to gain insight into the distribution and evolution of these organisms. Fifteen E. coli strains isolated from patients with ulcerative colitis (UC) were sequenced, 13 of which harbored pks islands. In addition, 2,654 genomes from the public database were also screened for pks harboring E. coli genomes, 158 of which were pks-positive (pks[+]) isolates. Whole-genome-wide comparison and phylogenetic analysis revealed that 171 (158 + 13) pks[+] isolates belonged to phylogroup B2, and most of the isolates belong to sequence types ST73 and ST95. One isolate from a UC patient was of the sequence type ST8303. The maximum likelihood tree based on the core genome of pks[+] isolates revealed horizontal gene transfer across sequence types and serotypes. Virulome and resistome analyses revealed the0020preponderance of virulence genes and a reduced number of antimicrobial genes in pks[+] isolates. This study significantly contributes to understanding the evolution of pks islands in E. coli.},
}

Humans
*Polyketide Synthases/genetics
*Colitis, Ulcerative/microbiology/genetics
*Escherichia coli/genetics/isolation & purification
*Phylogeny
*Genomic Islands
Genome, Bacterial
Genomics
Gene Transfer, Horizontal
Virulence Factors/genetics
Escherichia coli Infections/microbiology
Peptides
Polyketides

@article {pmid39778056,
year = {2025},
author = {Silva, JK and Hervé, V and Mies, US and Platt, K and Brune, A},
title = {A Novel Lineage of Endosymbiotic Actinomycetales: Genome Reduction and Acquisition of New Functions in Bifidobacteriaceae Associated With Termite Gut Flagellates.},
journal = {Environmental microbiology},
volume = {27},
number = {1},
pages = {e70010},
pmid = {39778056},
issn = {1462-2920},
support = {//Max-Planck-Gesellschaft/ ; },
mesh = {*Symbiosis ; Animals ; *Isoptera/microbiology ; *Genome, Bacterial ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; *Actinomycetales/genetics/metabolism ; Gene Transfer, Horizontal ; Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology/parasitology ; Metagenome ; },
abstract = {Cellulolytic flagellates are essential for the symbiotic digestion of lignocellulose in the gut of lower termites. Most species are associated with host-specific consortia of bacterial symbionts from various phyla. 16S rRNA-based diversity studies and taxon-specific fluorescence in situ hybridization revealed a termite-specific clade of Actinomycetales that colonise the cytoplasm of Trichonympha spp. and other gut flagellates, representing the only known case of intracellular Actinomycetota in protists. Comparative analysis of eleven metagenome-assembled genomes from lower termites allowed us to describe them as new genera of Bifidobacteriaceae. Like the previously investigated Candidatus Ancillula trichonymphae, they ferment sugars via the bifidobacterium shunt but, unlike their free-living relatives, experienced significant genome erosion. Additionally, they acquired new functions by horizontal gene transfer from other gut bacteria, including the capacity to produce hydrogen. Members of the genus Ancillula (average genome size 1.56 ± 0.2 Mbp) retained most pathways for the synthesis of amino acids, including a threonine/serine exporter, providing concrete evidence for the basis of the mutualistic relationship with their host. By contrast, Opitulatrix species (1.23 ± 0.1 Mbp) lost most of their biosynthetic capacities, indicating that an originally mutualistic symbiosis is on the decline.},
}

*Symbiosis
Animals
*Isoptera/microbiology
*Genome, Bacterial
*RNA, Ribosomal, 16S/genetics
*Phylogeny
*Actinomycetales/genetics/metabolism
Gene Transfer, Horizontal
Gastrointestinal Microbiome
Gastrointestinal Tract/microbiology/parasitology
Metagenome

@article {pmid39777960,
year = {2025},
author = {Perez, MF and Angelov, A and Übelacker, M and Torres Tejerizo, GA and Farias, ME and Liebl, W and Dib, JR},
title = {Linear Plasmids in Micrococcus: Insights Into a Common Ancestor and Transfer by Conjugation.},
journal = {Environmental microbiology},
volume = {27},
number = {1},
pages = {e70020},
pmid = {39777960},
issn = {1462-2920},
support = {PICT 2018 N° 2545 PRESTAMO BID//Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación/ ; PIUNT A618/2//Universidad Nacional de Tucumán/ ; },
mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Micrococcus/genetics ; *Conjugation, Genetic ; Evolution, Molecular ; Phylogeny ; Open Reading Frames ; DNA, Bacterial/genetics ; Base Composition ; },
abstract = {Actinobacteria have frequently been reported in the Andean Puna, including strains of the genus Micrococcus. These strains demonstrate resistance to high levels of UV radiation, arsenic, and multiple antibiotics, and possess large linear plasmids. A comparative analysis of the sequences and putative functions of these plasmids was conducted. The presence of large regions with high sequence identity (exceeding 30 kb in total) in all three studied Micrococcus megaplasmids indicates a clear evolutionary link among these elements. Genes related to essential plasmid functions were primarily found within these conserved regions, while genes associated with resistance to metals and antibiotics resided in accessory regions. Moreover, the abundance of open reading frames related to transposition and recombination, along with local deviations from the average GC content, provides evidence for the mosaic nature and considerable genetic plasticity of these plasmids. This study presents evidence of a common ancestor for linear plasmids in Micrococcus and suggests that horizontal gene transfer likely occurs frequently within Andean lakes, providing the native microbial community with a beneficial gene pool to withstand extreme conditions. Additionally, the successful transfer of the linear plasmid pLMA1 by a DNase-insensitive, conjugation-type mechanism and its potential use as a genetic vector is demonstrated.},
}

*Plasmids/genetics
*Gene Transfer, Horizontal
*Micrococcus/genetics
*Conjugation, Genetic
Evolution, Molecular
Phylogeny
Open Reading Frames
DNA, Bacterial/genetics
Base Composition

@article {pmid39777461,
year = {2025},
author = {Blanchais, C and Pages, C and Campos, M and Boubekeur, K and Contarin, R and Orlando, M and Siguier, P and Laaberki, MH and Cornet, F and Charpentier, X and Rousseau, P},
title = {Interplay between the Xer recombination system and the dissemination of antibioresistance in Acinetobacter baumannii.},
journal = {Nucleic acids research},
volume = {53},
number = {1},
pages = {},
pmid = {39777461},
issn = {1362-4962},
support = {//University of Toulouse III Paul Sabatier/ ; ANR-AAPG2021-InXS//Agence Nationale de la Recherche/ ; ANR-11-LABX-0048//LabEx Ecofect/ ; ANR-11-IDEX-0007//Université de Lyon/ ; EQU202303016268//Fondation pour la Recherche Médicale/ ; ANR-AAPG2021-InXS//Agence Nationale de la Recherche/ ; },
mesh = {*Acinetobacter baumannii/genetics/drug effects ; *Plasmids/genetics ; *Recombination, Genetic ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Recombinases/metabolism/genetics ; Escherichia coli/genetics/drug effects ; },
abstract = {Antibiotic-resistant infections are a pressing clinical challenge. Plasmids are known to accelerate the emergence of resistance by facilitating horizontal gene transfer of antibiotic resistance genes between bacteria. We explore this question in Acinetobacter baumannii, a globally emerging nosocomial pathogen responsible for a wide range of infections with a worrying accumulation of resistance, particularly involving plasmids. In this species, plasmids of the Rep_3 family harbor antibiotic resistance genes within variable regions flanked by potential site-specific recombination sites recognized by the XerCD recombinase. We first show that the Xer system of A. baumannii functions as described in Escherichia coli, resolving chromosome dimers at the dif site and recombining plasmid-carried sites. However, the multiple Xer recombination sites found in Rep_3 plasmids do not allow excision of plasmid fragments. Rather, they recombine to cointegrate plasmids, which could then evolve to exchange genes. Cointegrates represent a significant fraction of the plasmid population and their formation is controlled by the sequence of recombination sites, which determines the compatibility between recombination sites. We conclude that plasmids in A. baumannii frequently recombine by Xer recombination, allowing a high level of yet controlled plasticity in the acquisition and combination of antibiotic resistance genes.},
}

*Acinetobacter baumannii/genetics/drug effects
*Plasmids/genetics
*Recombination, Genetic
Gene Transfer, Horizontal
Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
Recombinases/metabolism/genetics
Escherichia coli/genetics/drug effects

@article {pmid39776180,
year = {2025},
author = {Shimuta, K and Ohama, Y and Ito, S and Hoshina, S and Takahashi, H and Igawa, G and Dorin Yamamoto, M and Akeda, Y and Ohnishi, M},
title = {Emergence of ceftriaxone-resistant Neisseria gonorrhoeae through horizontal gene transfer among Neisseria spp.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf008},
pmid = {39776180},
issn = {1537-6613},
abstract = {OBJECTIVES: It has been suggested that the emergence of ceftriaxone-resistant strains of Neisseria gonorrhoeae involves the incorporation of the penA gene from commensal Neisseria spp. that are resistant to ceftriaxone. However, the mechanism of this mosaic penA generation is unknown.

METHODS: We obtained 10 strains of commensal Neisseria spp. showing ceftriaxone MIC >0.5 mg/L. The similarity of the penA gene region of these commensal Neisseria spp. strains and some ceftriaxone-resistant N. gonorrhoeae strains was investigated. To obtain transformants, commensal Neisseria spp., Neisseria lactamica, gDNA was used as donor DNA and a N. gonorrhoeae strain as the recipient.

RESULTS: The sequence similarity in certain regions of penA-murE between some of the commensal Neisseria spp. strains and the N. gonorrhoeae FC428 strain was very high. The sequence of these regions was very similar among some ceftriaxone-resistant strains of Neisseria spp. The PenA of the transformants matched the full PenA 60 of the original FC428 strain. Furthermore, our findings indicated that the source of resistance could have been a penA fragment derived from Neisseria spp. that originally carried the same sequence.

CONCLUSIONS: We suggest that FC428 developed ceftriaxone resistance by acquiring part of the penA-murE gene region from N. lactamica through horizontal gene transfer. The ceftriaxone-resistant N. lactamica shown here may also have emerged by acquiring part of penA from other Neisseria spp. From this work, our data provide insights into the understanding of the mechanism underlying the evolution of drug-resistant gonorrhea-causing strains.},
}

@article {pmid39772912,
year = {2025},
author = {Figueroa, D and Ruiz, D and Tellini, N and De Chiara, M and Kessi-Pérez, EI and Martínez, C and Liti, G and Querol, A and Guillamón, JM and Salinas, F},
title = {Optogenetic control of horizontally acquired genes prevent stuck fermentations in yeast.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0179424},
doi = {10.1128/spectrum.01794-24},
pmid = {39772912},
issn = {2165-0497},
abstract = {Nitrogen limitations in the grape must be the main cause of stuck fermentations during the winemaking process. In Saccharomyces cerevisiae, a genetic segment known as region A, which harbors 12 protein-coding genes, was acquired horizontally from a phylogenetically distant yeast species. This region is mainly present in the genome of wine yeast strains, carrying genes that have been associated with nitrogen utilization. Despite the putative importance of region A in yeast fermentation, its contribution to the fermentative process is largely unknown. In this work, we used a wine yeast strain to evaluate the contribution of region A to the fermentation process. To do this, we first sequenced the genome of the wine yeast strain using long-read sequencing and determined that region A is present in a single copy. We then implemented an optogenetic system in this wine yeast strain to precisely regulate the expression of each gene, generating a collection of 12 strains that allow for light-activated gene expression. To evaluate the role of these genes during fermentation, we assayed this collection using microculture and fermentation experiments in synthetic must with varying amounts of nitrogen concentration. Our results show that changes in gene expression for genes within this region can impact growth parameters and fermentation rate. We additionally found that the expression of various genes in region A is necessary to complete the fermentation process and prevent stuck fermentations under low nitrogen conditions. Altogether, our optogenetics-based approach demonstrates the importance of region A in completing fermentation under nitrogen-limited conditions.IMPORTANCEStuck fermentations due to limited nitrogen availability in grape must represent one of the main problems in the winemaking industry. Nitrogen limitation in grape must reduces yeast biomass and fermentation rate, resulting in incomplete fermentations with high levels of residual sugar, undesired by-products, and microbiological instability. Here, we used an optogenetic approach to demonstrate that expression of genes within region A is necessary to complete fermentations under low nitrogen availability. Overall, our results suggest that region A is a genetic signature for adaptation to low nitrogen conditions.},
}

@article {pmid39771135,
year = {2024},
author = {Li, Z and Yuan, D},
title = {Metagenomic Analysis Reveals the Effects of Microplastics on Antibiotic Resistance Genes in Sludge Anaerobic Digestion.},
journal = {Toxics},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/toxics12120920},
pmid = {39771135},
issn = {2305-6304},
support = {No. 52170097//the National Natural Science Foundation of China/ ; },
abstract = {Sewage sludge is recognized as both a source and a reservoir for antibiotic resistance genes (ARGs). Within an anaerobic digestion (AD) system, the presence of microplastics (MPs) has been observed to potentially facilitate the proliferation of these ARGs. Understanding the influence of MPs on microbial behavior and horizontal gene transfer (HGT) within the AD system is crucial for effectively managing the dissemination of ARGs in the environment. This study utilized metagenomic approaches to analyze the dynamics of various types of ARGs and potential microbial mechanisms under exposure to MPs during the AD process. The findings indicated that MPs in the AD process can enhance the proliferation of ARGs, with the extent of this enhancement increasing with the dosage of MPs: polyethylene (PE), polyethylene terephthalate (PET), and polylactic acid (PLA) MPs increased the abundance of ARGs in the anaerobic digestion system by up to 29.90%, 18.64%, and 14.15%, respectively. Additionally, the presence of MPs increased the relative abundance of mobile genetic elements (MGEs) during the AD process. Network correlation analysis further revealed that plasmids represent the predominant category of MGEs involved in the HGT of ARGs. Propionibacterium and Alicycliphilus were identified as the primary potential hosts for these ARGs. The results of gene function annotation indicated that exposure to MPs led to an increased the relative abundance of genes related to the production of reactive oxygen species (ROS), alterations in membrane permeability, ATP synthesis, and the secretion of extracellular polymeric substances (EPS). These genes play crucial roles in influencing the HGT of ARGs.},
}

@article {pmid39566460,
year = {2025},
author = {Xia, L and Wang, J and Chen, M and Li, G and Wang, W and An, T},
title = {Biofilm formation mechanisms of mixed antibiotic-resistant bacteria in water: Bacterial interactions and horizontal transfer of antibiotic-resistant plasmids.},
journal = {Journal of hazardous materials},
volume = {481},
number = {},
pages = {136554},
doi = {10.1016/j.jhazmat.2024.136554},
pmid = {39566460},
issn = {1873-3336},
mesh = {*Biofilms/drug effects/growth & development ; *Plasmids/genetics ; *Gene Transfer, Horizontal ; *Escherichia coli/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Water Microbiology ; Bacteria/drug effects/genetics/metabolism ; Microbial Interactions ; },
abstract = {Over 95 % of bacteria on water supply pipeline surfaces exist in biofilms, which are hotspots for antibiotic resistance gene (ARG) transmission. This study established mixed biofilm culture systems on a metal iron substrate using Escherichia coli: antibiotic-sensitive bacteria (ASB) and antibiotic-resistant bacteria (ARB). The growth rate and extracellular polymeric substances (EPS) content of mixed biofilm surpassed single-species biofilms due to synergistic interactions among different bacteria. However, the composition of mixed biofilms formed by ASB and ARB became unstable after 72 h, linked to reduced polysaccharide proportions in EPS and inter-bacterial competition. The bacterial composition and conjugative transfer frequency of ARGs in mixed biofilms indicate that biofilm formation significantly enhances horizontal transfer of ARGs. Notably, the conjugative transfer frequency of the mixed biofilm formed by two ARB increased 100-fold within five days. In contrast, the conjugative transfer frequency in the mixed biofilm formed by ASB and ARB was unstable; inter-bacterial competition led to plasmid loss associated with horizontal transfer of ARGs, ultimately resulting in biofilm shedding. Furthermore, genes associated with ARG transfer and biofilm growth up-regulated by 1.5 - 6 and 2 - 7 times, respectively, in mixed biofilm. These findings highlight a mutually reinforcing relationship between biofilm formation and horizontal ARG transmission, with significant environmental implications.},
}

*Biofilms/drug effects/growth & development
*Plasmids/genetics
*Gene Transfer, Horizontal
*Escherichia coli/drug effects/genetics
Anti-Bacterial Agents/pharmacology
Drug Resistance, Bacterial/genetics
Water Microbiology
Bacteria/drug effects/genetics/metabolism
Microbial Interactions

@article {pmid39770765,
year = {2024},
author = {Cangioli, L and Tabacchioni, S and Visca, A and Fiore, A and Aprea, G and Ambrosino, P and Ercole, E and Sørensen, S and Mengoni, A and Bevivino, A},
title = {Genome Insights into Beneficial Microbial Strains Composing SIMBA Microbial Consortia Applied as Biofertilizers for Maize, Wheat and Tomato.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/microorganisms12122562},
pmid = {39770765},
issn = {2076-2607},
support = {862695//European Union's Horizon 2020/ ; },
abstract = {For the safe use of microbiome-based solutions in agriculture, the genome sequencing of strains composing the inoculum is mandatory to avoid the spread of virulence and multidrug resistance genes carried by them through horizontal gene transfer to other bacteria in the environment. Moreover, the annotated genomes can enable the design of specific primers to trace the inoculum into the soil and provide insights into the molecular and genetic mechanisms of plant growth promotion and biocontrol activity. In the present work, the genome sequences of some members of beneficial microbial consortia that have previously been tested in greenhouse and field trials as promising biofertilizers for maize, tomato and wheat crops have been determined. Strains belong to well-known plant-growth-promoting bacterial genera such as Bacillus, Burkholderia, Pseudomonas and Rahnella. The genome size of strains ranged from 4.5 to 7.5 Mbp, carrying many genes spanning from 4402 to 6697, and a GC content of 0.04% to 3.3%. The annotation of the genomes revealed the presence of genes that are implicated in functions related to antagonism, pathogenesis and other secondary metabolites possibly involved in plant growth promotion and gene clusters for protection against oxidative damage, confirming the plant-growth-promoting (PGP) activity of selected strains. All the target genomes were found to possess at least 3000 different PGP traits, belonging to the categories of nitrogen acquisition, colonization for plant-derived substrate usage, quorum sensing response for biofilm formation and, to a lesser extent, bacterial fitness and root colonization. No genes putatively involved in pathogenesis were identified. Overall, our study suggests the safe application of selected strains as "plant probiotics" for sustainable agriculture.},
}

@article {pmid39770663,
year = {2024},
author = {Ben Natan, M and Masasa, M and Shashar, N and Guttman, L},
title = {Antibiotic Resistance in Vibrio Bacteria Associated with Red Spotting Disease in Sea Urchin Tripneustes gratilla (Echinodermata).},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/microorganisms12122460},
pmid = {39770663},
issn = {2076-2607},
support = {3-0000-17701//The Israeli Ministry of Health/ ; },
abstract = {The red spotting disease harms sea urchins to the extent of mass mortality in the ocean and echinocultures, accompanied by environmental damage and economic losses. The current study emphasizes the antimicrobial resistance of three isolated bacteria, closely related to Vibrio harveyi, Vibrio owensii, and Vibrio fortis, associated with red spotting in the cultured sea urchin Tripneustes gratilla. In vitro trials examined the susceptibility of these bacterial isolates to various antibiotics. In addition, using an in silico examination, we revealed the arsenal of antimicrobial resistance genes in available genomes of various pathogenic Vibrio associated with diseases in sea urchins, fish, shellfish, and corals. These two approaches enabled the discussion of the similarities and differences between aquatic pathogenic Vibrio and their antibiotic resistance. Among them, we revealed a core resistance to tetracyclines and penams by the in vitro examined strains. At the same time, the in silico study also supported this core resistance by the presence of the adeF and CRP genes in the bacterial genomes. Nevertheless, variability and specific resistance were evident at the species and strain levels in the Vibrio bacteria and genomes. The in vitro trials highlighted the diverse resistance of the Vibrio harveyi-like isolate to all examined antibiotics, while the other two isolates were found susceptible to nitrofurantoin and sulfamethoxazole. The resistance of the Vibrio harveyi-like isolate could not have been obtained in the genome of the proposed relative of Vibrio harveyi VHJR7 that lacks the oqxA and oqxB genes, which enables such a resistance. A unique sensitivity of the Vibrio fortis-like isolate to erythromycin is proposed when compared to other isolated Vibrio and Vibrio genomes that seem capable of resisting this drug. According to the results, we propose nitrofurantoin or sulfamethoxazole for treating two of the red-spotting-associated isolates (Vibrio fortis and Vibrio owensii-like), but not Vibrio harveyi-like. We assume that a shared resistance to some antibiotics by Vibrios is gained by a horizontal gene transfer while previous exposures of a bacterial strain to a specific drug may induce the development of a unique resistance. Finally, we discuss the novel knowledge on antibiotic resistance in Vibrio from the current research in light of the potential risks when using drugs for disease control in aquaculture.},
}

@article {pmid39770308,
year = {2024},
author = {Islam, MM and Jung, DE and Shin, WS and Oh, MH},
title = {Colistin Resistance Mechanism and Management Strategies of Colistin-Resistant Acinetobacter baumannii Infections.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {12},
pages = {},
doi = {10.3390/pathogens13121049},
pmid = {39770308},
issn = {2076-0817},
support = {Grant Nos. 2022R1F1A1071415 and NRF-RS-2023-00275307 and Grant No. 2019R1A6C1010033//National Research Foundation of Korea (NRF) funded by the Ministry of Education & Basic Science Research Capacity Enhancement Project through Korea Basic Science Institute (National research Facilities and Equipment Center) grant funded by the Ministry o/ ; },
mesh = {*Acinetobacter baumannii/drug effects/genetics ; *Colistin/pharmacology/therapeutic use ; Humans ; *Acinetobacter Infections/drug therapy ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics/drug effects ; Drug Resistance, Bacterial/genetics/drug effects ; Animals ; },
abstract = {The emergence of antibiotic-resistant Acinetobacter baumannii (A. baumannii) is a pressing threat in clinical settings. Colistin is currently a widely used treatment for multidrug-resistant A. baumannii, serving as the last line of defense. However, reports of colistin-resistant strains of A. baumannii have emerged, underscoring the urgent need to develop alternative medications to combat these serious pathogens. To resist colistin, A. baumannii has developed several mechanisms. These include the loss of outer membrane lipopolysaccharides (LPSs) due to mutation of LPS biosynthetic genes, modification of lipid A (a constituent of LPSs) structure through the addition of phosphoethanolamine (PEtN) moieties to the lipid A component by overexpression of chromosomal pmrCAB operon genes and eptA gene, or acquisition of plasmid-encoded mcr genes through horizontal gene transfer. Other resistance mechanisms involve alterations of outer membrane permeability through porins, the expulsion of colistin by efflux pumps, and heteroresistance. In response to the rising threat of colistin-resistant A. baumannii, researchers have developed various treatment strategies, including antibiotic combination therapy, adjuvants to potentiate antibiotic activity, repurposing existing drugs, antimicrobial peptides, nanotechnology, photodynamic therapy, CRISPR/Cas, and phage therapy. While many of these strategies have shown promise in vitro and in vivo, further clinical trials are necessary to ensure their efficacy and widen their clinical applications. Ongoing research is essential for identifying the most effective therapeutic strategies to manage colistin-resistant A. baumannii. This review explores the genetic mechanisms underlying colistin resistance and assesses potential treatment options for this challenging pathogen.},
}

*Acinetobacter baumannii/drug effects/genetics
*Colistin/pharmacology/therapeutic use
Humans
*Acinetobacter Infections/drug therapy
*Anti-Bacterial Agents/therapeutic use/pharmacology
Drug Resistance, Multiple, Bacterial/genetics/drug effects
Drug Resistance, Bacterial/genetics/drug effects
Animals

@article {pmid39766551,
year = {2024},
author = {Li, R and Dai, H and Wang, W and Peng, R and Yu, S and Zhang, X and Huo, ZY and Yuan, Q and Luo, Y},
title = {Local Electric Field-Incorporated In-Situ Copper Ions Eliminating Pathogens and Antibiotic Resistance Genes in Drinking Water.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {12},
pages = {},
doi = {10.3390/antibiotics13121161},
pmid = {39766551},
issn = {2079-6382},
support = {2022YFC3205400//National Key R&D Program of China/ ; 42377436 & 52200079//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND/OBJECTIVES: Pathogen inactivation and harmful gene destruction from water just before drinking is the last line of defense to protect people from waterborne diseases. However, commonly used disinfection methods, such as chlorination, ultraviolet irradiation, and membrane filtration, experience several challenges such as continuous chemical dosing, the spread of antibiotic resistance genes (ARGs), and intensive energy consumption.

METHODS: Here, we perform a simultaneous elimination of pathogens and ARGs in drinking water using local electric fields and in-situ generated trace copper ions (LEF-Cu) without external chemical dosing. A 100-μm thin copper wire placed in the center of a household water pipe can generate local electric fields and trace copper ions near its surface after an external low voltage is applied.

RESULTS: The local electric field rapidly damages the outer structure of microorganisms through electroporation, and the trace copper ions can effectively permeate the electroporated microorganisms, successfully damaging their nucleic acids. The LEF-Cu disinfection system achieved complete inactivation (>6 log removal) of Escherichia coli O157:H7, Pseudomonas aeruginosa PAO1, and bacteriophage MS2 in drinking water at 2 V for 2 min, with low energy consumption (10[-2] kWh/m[3]). Meanwhile, the system effectively damages both intracellular (0.54~0.64 log) and extracellular (0.5~1.09 log) ARGs and blocks horizontal gene transfer.

CONCLUSIONS: LEF-Cu disinfection holds promise for preventing horizontal gene transfer and providing safe drinking water for household applications.},
}

@article {pmid39766521,
year = {2024},
author = {de Andrade, FCC and Carvalho, MF and Figueiredo, AMS},
title = {Survival Strategies of Staphylococcus aureus: Adaptive Regulation of the Anti-Restriction Gene ardA-H1 Under Stress Conditions.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {12},
pages = {},
doi = {10.3390/antibiotics13121131},
pmid = {39766521},
issn = {2079-6382},
support = {443804/2018-4 and 307672/2019-0//Conselho Nacional de Desenvolvimento Científico e tecnológico (CNPq)/ ; E-26/210.875/2016, E-26/211.554/2019, E-26.200.952/2020, and E-26/203.941/2024//Fundação Carlos Chagas Filho de Amparo à Pesquisa (FAPERJ)/ ; 001//Fundação Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)/ ; INV-007641/GATES/Bill & Melinda Gates Foundation/United States ; },
abstract = {Background/Objective: The anti-restriction protein ArdA-H1, found in multiresistant Staphylococcus aureus (MRSA) strains from the ST239-SCCmecIII lineage, inhibits restriction-modification systems, fostering horizontal gene transfer (HGT) and supporting genetic adaptability and resistance. This study investigates the regulatory mechanisms controlling ardA-H1 expression in S. aureus under various stress conditions, including acidic pH, iron limitation, and vancomycin exposure, and explores the roles of the Agr quorum sensing system. Methods: The expression of ardA-H1 was analyzed in S. aureus strains exposed to environmental stressors using real-time quantitative reverse transcription PCR. Comparisons were made between Agr-functional and Agr-deficient strains. In addition, Agr inhibition was achieved using a heterologous Agr autoinducing peptide. Results: The Agr system upregulated ardA-H1 expression in acidic and iron-limited conditions. However, vancomycin induced ardA-H1 activation specifically in the Agr-deficient strain GV69, indicating that an alternative regulatory pathway controls ardA-H1 expression in the absence of agr. The vancomycin response in GV69 suggests that diminished quorum sensing may offer a survival advantage by promoting persistence and HGT-related adaptability. Conclusion: Overall, our findings provide new insights into the intricate relationships between quorum-sensing, stress responses, bacterial virulence, and genetic plasticity, enhancing our understanding of S. aureus adaptability in challenging environments.},
}

@article {pmid39765217,
year = {2025},
author = {Niault, T and van Houte, S and Westra, E and Swarts, DC},
title = {Evolution and ecology of anti-defence systems in phages and plasmids.},
journal = {Current biology : CB},
volume = {35},
number = {1},
pages = {R32-R44},
doi = {10.1016/j.cub.2024.11.033},
pmid = {39765217},
issn = {1879-0445},
mesh = {*Plasmids/genetics ; *Bacteriophages/genetics/physiology ; *Bacteria/virology/genetics ; Archaea/genetics/virology ; Evolution, Molecular ; Biological Evolution ; Interspersed Repetitive Sequences ; },
abstract = {Prokaryotes (Bacteria and Archaea) encode a highly diversified arsenal of defence systems that protect them against mobile genetic elements, such as phages and plasmids. In turn, mobile genetic elements encode anti-defence systems that allow them to escape the activity of these defence systems. This has resulted in an evolutionary arms race in which defence systems and anti-defence systems evolve and adapt continuously, driving intriguing innovation and enormous diversification on both sides. Over 150 prokaryotic defence systems have been identified to date. Anti-defence systems are known for only a subset of these, but more are being discovered at a steady rate. Despite an increasing understanding of the highly diverse molecular mechanisms of anti-defence systems, their diverse evolutionary origins, the selective pressures they are subjected to, and their ecological importance and implications often remain obscure. In this review, we describe the diverse strategies that phage and plasmid anti-defence systems employ to escape host defence systems. We explore the evolutionary origins of anti-defence systems and describe different factors that exert selective pressure, affecting their maintenance and diversification. We describe how, in turn, defence systems themselves evolved to act upon anti-defence mechanisms, thereby adding a new layer to the co-evolutionary battle between prokaryotes and their mobile genetic elements. We discuss how the continuous selective pressures found in dynamic microbial communities promote the retention and diversification of these anti-defence systems. Finally, we consider the ecological implications for both hosts and their mobile genetic elements, noting how the balance of defence and anti-defence strategies can shape microbial community composition, influence horizontal gene transfer, and impact ecosystem stability.},
}

*Plasmids/genetics
*Bacteriophages/genetics/physiology
*Bacteria/virology/genetics
Archaea/genetics/virology
Evolution, Molecular
Biological Evolution
Interspersed Repetitive Sequences

@article {pmid39763003,
year = {2025},
author = {Feng, Y and Lu, X and Zhao, J and Li, H and Xu, J and Li, Z and Wang, M and Peng, Y and Tian, T and Yuan, G and Zhang, Y and Liu, J and Zhang, M and Zhu La, AT and Qu, G and Mu, Y and Guo, W and Wu, Y and Zhang, Y and Wang, D and Hu, Y and Kan, B},
title = {Regional antimicrobial resistance gene flow among the One Health sectors in China.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {3},
pmid = {39763003},
issn = {2049-2618},
support = {2022YFC2303900//National Key Research and Development Program of China/ ; 22193064//major projects of the National Natural Science Foundation of China/ ; },
mesh = {Humans ; China ; *Gene Transfer, Horizontal ; *One Health ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Anti-Bacterial Agents/pharmacology ; *Gene Flow ; Feces/microbiology ; Drug Resistance, Bacterial/genetics ; Food Microbiology ; Metagenomics/methods ; Genes, Bacterial/genetics ; },
abstract = {BACKGROUND: Antimicrobial resistance poses a significant threat to global health, with its spread intricately linked across human, animal, and environmental sectors. Revealing the antimicrobial resistance gene (ARG) flow among the One Health sectors is essential for better control of antimicrobial resistance.

RESULTS: In this study, we investigated regional ARG transmission among humans, food, and the environment in Dengfeng, Henan Province, China by combining large-scale metagenomic sequencing with culturing of resistant bacterial isolates in 592 samples. A total of 40 ARG types and 743 ARG subtypes were identified, with a predominance of multidrug resistance genes. Compared with microbes from human fecal samples, those from food and environmental samples showed a significantly higher load of ARGs. We revealed that dietary habits and occupational exposure significantly affect ARG abundance. Pseudomonadota, particularly Enterobacteriaceae, were identified as the main ARG carriers shaping the resistome. The resistome in food samples was found more affected by mobile genetic elements (MGEs), whereas in environmental samples, it was more associated with the microbial composition. We evidenced that horizontal gene transfer (HGT) mediated by plasmids and phages, together with strain transmission, particularly those associated with the Enterobacteriaceae members, drive regional ARG flow. Lifestyle, dietary habits, and occupational exposure are all correlated with ARG dissemination and flies and food are important potential sources of ARGs to humans. The widespread mobile carbapenemase gene, OXA-347, carried by non-Enterobacteriaceae bacteria in the human gut microbiota, requires particular attention. Finally, we showed that machine learning models based on microbiome profiles were effective in predicting the presence of carbapenem-resistant strains, suggesting a valuable approach for AMR surveillance.

CONCLUSIONS: Our study provides a full picture of regional ARG transmission among the One Health sectors in a county-level city in China, which facilitates a better understanding of the complex routes of ARG transmission and highlights new points of focus for AMR surveillance and control. Video Abstract.},
}

Humans
China
*Gene Transfer, Horizontal
*One Health
*Bacteria/genetics/classification/drug effects/isolation & purification
*Anti-Bacterial Agents/pharmacology
*Gene Flow
Feces/microbiology
Drug Resistance, Bacterial/genetics
Food Microbiology
Metagenomics/methods
Genes, Bacterial/genetics

@article {pmid39756571,
year = {2025},
author = {Heneghan, PG and Salzberg, LI and Wolfe, KH},
title = {Zymocin-like killer toxin gene clusters in the nuclear genomes of filamentous fungi.},
journal = {Fungal genetics and biology : FG & B},
volume = {},
number = {},
pages = {103957},
doi = {10.1016/j.fgb.2024.103957},
pmid = {39756571},
issn = {1096-0937},
abstract = {Zymocin-like killer toxins are anticodon nucleases secreted by some budding yeast species, which kill competitor yeasts by cleaving tRNA molecules. They are encoded by virus-like elements (VLEs), cytosolic linear DNA molecules that are also called killer plasmids. To date, toxins of this type have been found only in budding yeast species (Saccharomycotina). Here, we show that the nuclear genomes of many filamentous fungi (Pezizomycotina) contain small clusters of genes coding for a zymocin-like ribonuclease (γ-toxin), a chitinase (toxin α/β-subunit), and in some cases an immunity protein. The γ-toxins from Fusarium oxysporum and Colletotrichum siamense abolished growth when expressed intracellularly in S. cerevisiae. Phylogenetic analysis of glycoside hydrolase 18 (GH18) domains shows that the chitinase genes in the gene clusters are members of the previously described C-II subgroup of Pezizomycotina chitinases. We propose that the Pezizomycotina gene clusters originated by integration of a yeast-like VLE into the nuclear genome, but this event must have been ancient because (1) phylogenetically, the Pezizomycotina C-II chitinases and the Saccharomycotina VLE-encoded toxin α/β subunit chitinases are sister clades with neither of them nested inside the other, and (2) many of the Pezizomycotina toxin cluster genes contain introns, whereas VLEs do not. One of the toxin gene clusters in Fusarium graminearum is a locus that has previously been shown to be under diversifying selection in North American populations of this plant pathogen. We also show that two genera of agaric mushrooms (Basidiomycota) have acquired toxin gene clusters by horizontal transfers from different Pezizomycotina donors.},
}

@article {pmid39754881,
year = {2025},
author = {Li, X and Zhang, Z and Liu, H and Wen, H and Wang, Q},
title = {The fate of intracellular and extracellular antibiotic resistance genes during ultrafiltration-ultraviolet-chlorination in a full-scale wastewater tretament plant.},
journal = {Journal of hazardous materials},
volume = {486},
number = {},
pages = {137088},
doi = {10.1016/j.jhazmat.2024.137088},
pmid = {39754881},
issn = {1873-3336},
abstract = {Effluent from wastewater treatment plants (WWTPs) is recognized as a significant source of antibiotic resistance genes (ARGs) in the environment. Advanced treatment processes such as ultrafiltration (UF), ultraviolet (UV) light disinfection, and chlorination have emerged as promising approaches for ARG removal. However, the efficacy of sequential disinfection processes, such as UF-UV-chlorination on intracellular (iARGs) and extracellular ARGs (eARGs), remains largely unknown. This study investigates the impact of this sequential disinfection process on the fate of iARGs, eARGs, and a crucial mobile genetic element (intI1) within a full-scale WWTP. Our findings revealed that the UF-UV-chlorination process effectively reduced the overall absolute abundance of detected ARGs in the effluent by 1.93 log, and intI1 by 0.86 log, compared to secondary effluent. The majority of these removals was achieved due to the UF and UV disinfection, while chlorination showed negligible impact on the absolute abundance of ARGs in the final effluent. Notably, five genera were identified as potential hosts for intI1 and eight iARGs, including aac(6')-Ib-cr, drfA1, sul1, sul2, ermB, mefA, tetA, and tetX, suggesting a high potential for horizontal gene transfer involving these ARGs. Overall, this study demonstrated that UF-UV-chlorination is a highly effective method for reducing ARGs in effluent from WWTPs.},
}

@article {pmid39752084,
year = {2025},
author = {Heiss, J and Huson, DH and Steel, M},
title = {Transformations to Simplify Phylogenetic Networks.},
journal = {Bulletin of mathematical biology},
volume = {87},
number = {2},
pages = {20},
pmid = {39752084},
issn = {1522-9602},
support = {23-UOC-003//Marsden Fund/ ; },
mesh = {*Phylogeny ; *Mathematical Concepts ; *Models, Genetic ; Biological Evolution ; Evolution, Molecular ; },
abstract = {The evolutionary relationships between species are typically represented in the biological literature by rooted phylogenetic trees. However, a tree fails to capture ancestral reticulate processes, such as the formation of hybrid species or lateral gene transfer events between lineages, and so the history of life is more accurately described by a rooted phylogenetic network. Nevertheless, phylogenetic networks may be complex and difficult to interpret, so biologists sometimes prefer a tree that summarises the central tree-like trend of evolution. In this paper, we formally investigate methods for transforming an arbitrary phylogenetic network into a tree (on the same set of leaves) and ask which ones (if any) satisfy a simple consistency condition. This consistency condition states that if we add additional species into a phylogenetic network (without otherwise changing this original network) then transforming this enlarged network into a rooted phylogenetic tree induces the same tree on the original set of species as transforming the original network. We show that the LSA (lowest stable ancestor) tree method satisfies this consistency property, whereas several other commonly used methods (and a new one we introduce) do not. We also briefly consider transformations that convert arbitrary phylogenetic networks to another simpler class, namely normal networks.},
}

*Phylogeny
*Mathematical Concepts
*Models, Genetic
Biological Evolution
Evolution, Molecular

@article {pmid39749146,
year = {2024},
author = {Chaves, CRS and Salamandane, A and Vieira, EJF and Salamandane, C},
title = {Antibiotic Resistance in Fermented Foods Chain: Evaluating the Risks of Emergence of Enterococci as an Emerging Pathogen in Raw Milk Cheese.},
journal = {International journal of microbiology},
volume = {2024},
number = {},
pages = {2409270},
pmid = {39749146},
issn = {1687-918X},
abstract = {Fermented foods, particularly fermented dairy products, offer significant health benefits but also present serious concerns. Probiotic bacteria, such as lactic acid bacteria (LAB), found in these foods have been strongly linked to the selection and dissemination of antibiotic resistance genes (ARGs). This study aims to examine the potential risks associated with fermented foods, despite their importance in human nutrition, by analyzing the entire production chain from raw material acquisition to storage. Focusing on cheese production as a key fermented food, the study will investigate various aspects, including dairy farm management, milk acquisition, milk handling, and the application of good manufacturing practices (GMP) and good hygiene practices (GHP) in cheese production. The findings of this review highlight that ARGs found in LAB are similar to those observed in hygiene indicator bacteria like E. coli and pathogens like S. aureus. The deliberate use of antibiotics in dairy farms and the incorrect use of disinfectants in cheese factories contribute to the prevalence of antibiotic-resistant bacteria in cheeses. Cheese factories, with their high frequency of horizontal gene transfer, are environments where the microbiological diversity of raw milk can enhance ARG transfer. The interaction between the raw milk microbiota and other environmental microbiotas, facilitated by cross-contamination, increases metabolic communication between bacteria, further promoting ARG transfer. Understanding these bacterial and ARG interactions is crucial to ensure food safety for consumers.},
}

@article {pmid39747694,
year = {2025},
author = {Hsu, TY and Nzabarushimana, E and Wong, D and Luo, C and Beiko, RG and Langille, M and Huttenhower, C and Nguyen, LH and Franzosa, EA},
title = {Profiling lateral gene transfer events in the human microbiome using WAAFLE.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39747694},
issn = {2058-5276},
support = {K23DK125838//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R24DK110499//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; Research Scholars Award//American Gastroenterological Association (AGA)/ ; Career Development Award//Crohn's and Colitis Foundation (Crohn's & Colitis Foundation)/ ; T32CA009001//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; U54DE023798//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; },
abstract = {Lateral gene transfer (LGT), also known as horizontal gene transfer, facilitates genomic diversification in microbial populations. While previous work has surveyed LGT in human-associated microbial isolate genomes, the landscape of LGT arising in personal microbiomes is not well understood, as there are no widely adopted methods to characterize LGT from complex communities. Here we developed, benchmarked and validated a computational algorithm (WAAFLE or Workflow to Annotate Assemblies and Find LGT Events) to profile LGT from assembled metagenomes. WAAFLE prioritizes specificity while maintaining high sensitivity for intergenus LGT. Applying WAAFLE to >2,000 human metagenomes from diverse body sites, we identified >100,000 high-confidence previously uncharacterized LGT (~2 per microbial genome-equivalent). These were enriched for mobile elements, as well as restriction-modification functions associated with the destruction of foreign DNA. LGT frequency was influenced by biogeography, phylogenetic similarity of involved pairs (for example, Fusobacterium periodonticum and F. nucleatum) and donor abundance. These forces manifest as networks in which hub taxa donate unequally with phylogenetic neighbours. Our findings suggest that human microbiome LGT may be more ubiquitous than previously described.},
}

@article {pmid39460620,
year = {2025},
author = {Zhu, Q and Chen, Q and Gao, S and Li, Z and Zhou, H and Cui, Z and Fan, G and Liu, X and Wu, X and Ma, J and Kan, B and Hu, S and Wu, L and Lu, X},
title = {PIPdb: a comprehensive plasmid sequence resource for tracking the horizontal transfer of pathogenic factors and antimicrobial resistance genes.},
journal = {Nucleic acids research},
volume = {53},
number = {D1},
pages = {D169-D178},
pmid = {39460620},
issn = {1362-4962},
support = {2021YFF0703805//National Key Research and Development Program of China/ ; XDB0830000//Chinese Academy of Sciences/ ; 2022YFC2602301//National Key Research and Development Program of China/ ; 22193064//National Natural Science Foundation of China/ ; SRPG22007//Self-supporting Program of Guangzhou National Laboratory/ ; },
mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Virulence Factors/genetics ; *Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Humans ; Databases, Genetic ; Genome, Bacterial ; },
abstract = {Plasmids, as independent genetic elements, carrying resistance or virulence genes and transfer them among different pathogens, posing a significant threat to human health. Under the 'One Health' approach, it is crucial to control the spread of plasmids carrying such genes. To achieve this, a comprehensive characterization of plasmids in pathogens is essential. Here we present the Plasmids in Pathogens Database (PIPdb), a pioneering resource that includes 792 964 plasmid segment clusters (PSCs) derived from 1 009 571 assembled genomes across 450 pathogenic species from 110 genera. To our knowledge, PIPdb is the first database specifically dedicated to plasmids in pathogenic bacteria, offering detailed multi-dimensional metadata such as collection date, geographical origin, ecosystem, host taxonomy, and habitat. PIPdb also provides extensive functional annotations, including plasmid type, insertion sequences, integron, oriT, relaxase, T4CP, virulence factors genes, heavy metal resistance genes and antibiotic resistance genes. The database features a user-friendly interface that facilitates studies on plasmids across diverse host taxa, habitats, and ecosystems, with a focus on those carrying antimicrobial resistance genes (ARGs). We have integrated online tools for plasmid identification and annotation from assembled genomes. Additionally, PIPdb includes a risk-scoring system for identifying potentially high-risk plasmids. The PIPdb web interface is accessible at https://nmdc.cn/pipdb.},
}

*Plasmids/genetics
*Gene Transfer, Horizontal
*Virulence Factors/genetics
*Bacteria/genetics/drug effects
*Drug Resistance, Bacterial/genetics
Humans
Databases, Genetic
Genome, Bacterial

@article {pmid39373502,
year = {2025},
author = {Liu, G and Li, X and Guan, J and Tai, C and Weng, Y and Chen, X and Ou, HY},
title = {oriTDB: a database of the origin-of-transfer regions of bacterial mobile genetic elements.},
journal = {Nucleic acids research},
volume = {53},
number = {D1},
pages = {D163-D168},
pmid = {39373502},
issn = {1362-4962},
support = {2023YFC2307103//National Key Research and Development Program of China/ ; 32070572//National Natural Science Foundation of China/ ; SHDC2022CRD039//Shanghai Hospital Development Center Foundation/ ; GWV1-11.2-XD01//Talent Program on Public Health System Construction of Shanghai/ ; 20240818//Shanghai Jiao Tong University School of Medicine/ ; },
mesh = {*Interspersed Repetitive Sequences ; Gene Transfer, Horizontal ; Plasmids/genetics ; Conjugation, Genetic ; Bacteria/genetics/classification ; Databases, Genetic ; Genome, Bacterial ; Bacterial Proteins/genetics/metabolism ; Databases, Nucleic Acid ; DNA, Bacterial/genetics ; },
abstract = {Conjugation and mobilization are two important pathways of horizontal transfer of bacterial mobile genetic elements (MGEs). The origin-of-transfer (oriT) region is crucial for this process, serving as a recognition site for relaxase and containing the DNA nicking site (nic site), which initiates the conjugation or mobilization. Here, we present a database of the origin-of-transfer regions of bacterial MGEs, oriTDB (https://bioinfo-mml.sjtu.edu.cn/oriTDB2/). Incorporating data from text mining and genome analysis, oriTDB comprises 122 experimentally validated and 22 927 predicted oriTs within bacterial plasmids, Integrative and Conjugative Elements, and Integrative and Mobilizable Elements. Additionally, oriTDB includes details about associated relaxases, auxiliary proteins, type IV coupling proteins, and a gene cluster encoding the type IV secretion system. The database also provides predicted secondary structures of oriT sequences, dissects oriT regions into pairs of inverted repeats, nic sites, and their flanking conserved sequences, and offers an interactive visual representation. Furthermore, oriTDB includes an enhanced oriT prediction pipeline, oriTfinder2, which integrates a functional annotation module for cargo genes in bacterial MGEs. This resource is intended to support research on bacterial conjugative or mobilizable elements and promote an understanding of their cargo gene functions.},
}

*Interspersed Repetitive Sequences
Gene Transfer, Horizontal
Plasmids/genetics
Conjugation, Genetic
Bacteria/genetics/classification
Databases, Genetic
Genome, Bacterial
Bacterial Proteins/genetics/metabolism
Databases, Nucleic Acid
DNA, Bacterial/genetics

@article {pmid39742307,
year = {2024},
author = {Lian, ZH and Salam, N and Tan, S and Yuan, Y and Li, MM and Li, YX and Liu, ZT and Hu, CJ and Lv, AP and OuYang, YT and Lu, CY and Zhang, JY and Chen, Y and Chen, LB and Luo, ZH and Ma, B and Hua, ZS and Jiao, JY and Li, WJ and Liu, L},
title = {Metagenomic analysis sheds light on the mixotrophic lifestyle of bacterial phylum Zhuqueibacterota.},
journal = {iMeta},
volume = {3},
number = {6},
pages = {e249},
pmid = {39742307},
issn = {2770-596X},
abstract = {Zhuqueibacterota is a novel bacterial phylum proposed based on hot spring metagenomes and public metagenome-assembled genomes, classified within the Fibrobacterota-Chlorobiota-Bacteroidota superphylum. This globally distributed phylum consists of one class and five orders, with the majority of its members being facultative anaerobes. Notably, the order Zhuqueibacterales utilizes hydrogen as an electron donor for carbon fixation through the Calvin Benson Bassham cycle. Phylogenetic and metabolic analyses reveal the phylum's key role in the carbon cycle, with frequent horizontal gene transfer events influencing its evolutionary trajectory.},
}

@article {pmid39740178,
year = {2024},
author = {Zahir, A and Okorie, PA and Nwobasi, VN and David, EI and Nwankwegu, RO and Azi, F},
title = {Harnessing Microbial Signal Transduction Systems in Natural and Synthetic Consortia for Biotechnological Applications.},
journal = {Biotechnology and applied biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1002/bab.2707},
pmid = {39740178},
issn = {1470-8744},
abstract = {Signal transduction is crucial for communication and cellular response in microbial communities. Consortia rely on it for effective communication, responding to changing environmental conditions, establishing community structures, and performing collective behaviors. Microbial signal transduction can be through quorum sensing (QS), two-component signal transduction systems, biofilm formation, nutrient sensing, chemotaxis, horizontal gene transfer stress response, and so forth. The consortium uses small signaling molecules in QS to regulate gene expression and coordinate intercellular communication and behaviors. Biofilm formation allows cells to adhere and aggregate, promoting species interactions and environmental stress resistance. Chemotaxis enables directional movement toward or away from chemical gradients, promoting efficient resource utilization and community organization within the consortium. In recent years, synthetic microbial consortia have gained attention for their potential applications in biotechnology and bioremediation. Understanding signal transduction in natural and synthetic microbial consortia is important for gaining insights into community dynamics, evolution, and ecological function. It can provide strategies for biotechnological innovation for enhancing biosensors, biodegradation, bioenergy efficiency, and waste reduction. This review provides compelling insight that will advance our understanding of microbial signal transduction dynamics and its role in orchestrating microbial interactions, which facilitate coordination, cooperation, gene expression, resource allocation, and trigger specific responses that determine community success.},
}

@article {pmid39737801,
year = {2024},
author = {Singh, S and Selvakumar, S and Swaminathan, P},
title = {In silico targeting of AmpC beta-lactamases in Enterobacter cloacae: unveiling Piperenol B as a potent antimicrobial lead.},
journal = {Journal of biomolecular structure & dynamics},
volume = {},
number = {},
pages = {1-18},
doi = {10.1080/07391102.2024.2446661},
pmid = {39737801},
issn = {1538-0254},
abstract = {Antimicrobial Resistance poses a major threat to human health worldwide. Microorganisms develop multi-drug resistance due to intrinsic factors, evolutionary chromosomal alterations, and horizontal gene transfer. Enterobacter cloacae, a common nosocomial bacterium, can cause various infections and is classified as multidrug-resistant. This species produces AmpC enzymes, serine beta-lactamases that hydrolyze beta-lactam antibiotics by cleaving their beta-lactam ring, contributing to its resistance. Traditionally, many phytoconstituents have been used for their antibacterial properties against microorganisms. This study explores phytocompounds to mitigate the effects of beta-lactamase enzymes. In this study, we selected 12592 phytoconstituents with antibacterial properties from Dr. Duke's Ethnobotanical and Phytochemical Database for the virtual screening process. Initial hits were selected based on highest docking scores and then filtered using the ADMET property. Among these, a promising compound Piperenol B showed the highest docking score of -9.1 kcal/mol. A 240 ns molecular dynamics simulation showed that Piperenol B maintained stable conformation and showed consistent results in multiple runs with AmpC protein. Piperenol B complex had a binding free energy score of -61.75 ± 8.0 kJ/mol, whereas the known AmpC inhibitor Clavulanic acid showed -46.64 ± 3.2 kJ/mol. Non-covalent contacts in protein-ligand interactions and specific subunit interfaces were examined using the Protein Contacts Atlas. The STRING database was used to construct the Protein-Protein interaction for AmpC and its interacting proteins. The findings of this study suggested that Piperenol B could be an effective inhibitor of the targeted AmpC protein in Enterobacter cloacae which requires validation in in vitro studies.},
}

@article {pmid39736215,
year = {2024},
author = {Wang, Y and Ge, J and Xian, W and Tang, Z and Xue, B and Yu, J and Yao, YF and Liu, H and Qiu, J and Liu, X},
title = {Phosphorylation of the prokaryotic histone-like protein H-NS modulates bacterial virulence in Salmonella Typhimurium.},
journal = {Microbiological research},
volume = {292},
number = {},
pages = {128041},
doi = {10.1016/j.micres.2024.128041},
pmid = {39736215},
issn = {1618-0623},
abstract = {H-NS is a prokaryotic histone-like protein that binds to bacterial chromosomal DNA with important regulatory roles in gene expression. Unlike histone proteins, hitherto post-translational modifications of H-NS are still largely uncharacterized, especially in bacterial pathogens. Salmonella Typhimurium is a primary enteric pathogen and its virulence is mainly dependent on specialized type III secretion systems (T3SSs), which were evolutionarily acquired via horizontal gene transfer. Previous studies have shown that H-NS plays a critical role in silencing foreign T3SS genes. Here, we found that H-NS is phosphorylated at multiple residues in S. Typhimurium, including S45, Y61, S78, S84, T86, and T106. Notably, we demonstrated that phosphorylation of H-NS S78 promotes its dissociation from DNA via a mechanism dependent on dimer formation, thereby leading to transcriptional activation of target genes. Functionally, phosphoryl-H-NS contributes to the expression of T3SS-associated proteins and hence increases bacterial virulence during infection. Therefore, our study reveals a novel mechanism by which covalent modifications of prokaryotic histone-like proteins regulate bacterial virulence of an important human pathogen.},
}

@article {pmid39733752,
year = {2024},
author = {Feng, B and Chen, J and Wang, C and Wang, P and You, G and Lin, J and Gao, H},
title = {Removal of ofloxacin and inhibition of antibiotic resistance gene spread during the aerobic biofilm treatment of rural domestic sewage through the micro-nano aeration technology.},
journal = {Journal of hazardous materials},
volume = {486},
number = {},
pages = {137020},
doi = {10.1016/j.jhazmat.2024.137020},
pmid = {39733752},
issn = {1873-3336},
abstract = {Micro-nano aeration (MNA) has great potential for emerging contaminant removal. However, the mechanism of antibiotic removal and antibiotic resistance gene (ARG) spread, and the impact of the different aeration conditions remain unclear. This study investigated the adsorption and biodegradation of ofloxacin (OFL) and the spread of ARGs in aerobic biofilm systems under MNA and conventional aeration (CVA) conditions. Results showed that the MNA increased OFL removal by 17.27 %-40.54 % and decreased total ARG abundance by 36.37 %-54.98 %, compared with CVA. MNA-induced biofilm rough morphology, high zeta potential, and reduced extracellular polymeric substance (EPS) secretion enhanced OFL adsorption. High dissolved oxygen and temperature, induced by MNA-enriched aerobic bacteria and their carrying OFL-degrading genes, enhanced OFL biodegradation. MNA inhibited the enrichment of ARG host bacteria, which acquired ARGs possibly via horizontal gene transfer (HGT). Functional profiles involved in the HGT process, including reactive oxygen species production, membrane permeability, mobile genetic elements (MGEs), adenosine triphosphate synthesis, and EPS secretion, were down-regulated by MNA, inhibiting ARG spread. Partial least-squares path modeling revealed that MGEs might be the main factor inhibiting ARG spread. This study provides insights into the mechanisms by which MNA enhances antibiotic removal and inhibits ARG spread in aerobic biofilm systems.},
}

@article {pmid39733355,
year = {2024},
author = {Kumar, G and Balakrishna, K and Mukhopadhyay, C and Kalwaje Eshwara, V},
title = {Characterization and comparative analysis of antimicrobial resistance in Escherichia coli from hospital and municipal wastewater treatment plants.},
journal = {Journal of water and health},
volume = {22},
number = {12},
pages = {2276-2288},
pmid = {39733355},
issn = {1477-8920},
support = {Intramural Fund//Manipal Academy of Higher Education/ ; },
mesh = {*Escherichia coli/drug effects/genetics/isolation & purification ; *Wastewater/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Integrons ; Hospitals ; Drug Resistance, Bacterial ; Waste Disposal, Fluid ; },
abstract = {The spread of antimicrobial resistance (AMR) poses global health threats, with wastewater treatment plants (WWTPs) as hotspots for its development. Horizontal gene transfer facilitates acquisition of resistance genes, particularly through integrons in Escherichia coli. Our study investigates E. coli isolates from hospital and municipal WWTPs, focusing on integrons, their temporal correlation and phenotypic and molecular characterization of AMR. Samples from hospital and municipal WWTPs were collected over two seasons, pre-monsoon (March-May) and post-monsoon (December-February). From the hospital (hWWTP) and municipal (mWWTP) influents, 45 and 172 E. coli isolates were obtained, respectively. E. coli from hWWTP exhibited significantly higher resistance rates than mWWTP to most tested antimicrobials except tetracycline. The hWWTP isolates showed a higher prevalence (86.7%) of multidrug resistance (MDR) compared with mWWTP (48.3%). The proportion of MDR isolates from mWWTP nearly doubled in the post-monsoon season. Integron positivity was 17.7% (hWWTP) and 19.7% (mWWTP) with common gene cassettes conferring resistance to trimethoprim and aminoglycosides. Phylogroup analysis showed a predominance of group A in hWWTP and group B1 in mWWTP. The study highlights the role of hospital and municipal wastewater in disseminating AMR, with high rates of MDR E. coli and class 1 integrons detected.},
}

*Escherichia coli/drug effects/genetics/isolation & purification
*Wastewater/microbiology
*Anti-Bacterial Agents/pharmacology
*Integrons
Hospitals
Drug Resistance, Bacterial
Waste Disposal, Fluid

@article {pmid39731890,
year = {2024},
author = {Zhang, Y and Zhu, D and Zhou, S and Gong, H and Dai, X},
title = {Antibiotic resistome during two-stage partial nitritation/anammox process for sludge anaerobic digestion reject water treatment.},
journal = {Journal of hazardous materials},
volume = {486},
number = {},
pages = {136967},
doi = {10.1016/j.jhazmat.2024.136967},
pmid = {39731890},
issn = {1873-3336},
abstract = {Anaerobic digestion (AD) reject water serves as a significant reservoir for antibiotic resistance genes (ARGs), underscoring the importance of understanding ARGs dynamics during treatment processes. Partial nitritation /anammox (PN/A) has become an increasingly adopted process, while comprehensive investigation on ARG behavior within this system, especially in full-scale, remains limited. This study explores the distribution of ARGs in a full-scale two-stage PN/A system, with an anaerobic/anoxic/oxic (AAO) system for comparison. The sludge in partial nitritation (PN) stage exhibited higher ARG abundance (0.82 copy/cell) compared to that in anammox stage (0.21-0.26 copy/cell). In anammox sludge samples, 95.8-99.1 % of the mobile genetic elements (MGEs) were identified as tnpA, while the PN stage showing greater diversity. Some ARGs co-occur in the same contigs, and some of these ARGs belong to different ARGs types, which is related to multi-antibiotic resistance, with the highest frequency observed in the PN stage. The abundance of contigs with ARG-MGE co-occurrence, suggesting the possibility of horizontal gene transfer (HGT), was most prevalent in the AAO system. Potential ARG hosts were identified by metagenomic binning, and some functional bacteria, like Nitrosomonas, were regarded as ARGs host. This study offers a comprehensive analysis of the complexities of ARGs distribution within full-scale two-stage PN/A systems treating AD reject water.},
}

@article {pmid39731837,
year = {2024},
author = {Yang, R and Tang, J and Niu, J and Hou, B and Zhang, L},
title = {Dissemination mechanisms of unique antibiotic resistance genes from flowback water to soil revealed by combined Illumina and Nanopore sequencing.},
journal = {Water research},
volume = {273},
number = {},
pages = {123030},
doi = {10.1016/j.watres.2024.123030},
pmid = {39731837},
issn = {1879-2448},
abstract = {As a byproduct of shale gas extraction, flowback water (FW) is produced in large quantities globally. Due to the unique interactions between pollutants and microorganisms, FW always harbor multiple antibiotic resistance genes (ARGs) that have been confirmed in our previous findings, potentially serving as a point source for ARGs released into the environment. However, whether ARGs in FW can disseminate or integrate into the environmental resistome remains unclear. In this study, unique ARGs from FW were identified, and the ARG profiles in soil and FW-spiked soil were compared using a combination of Illumina and Nanopore sequencing. The results indicated that the total abundance of the soil resistome increased by 30.8 % in soil contaminated with FW. Of this increase, 11.1 % was attributable to the integration of exogenous ARGs from FW into the soil resistome. Sequence alignment at the gene level further confirmed the successful integration of 20 unique ARG sequences classified as multidrug and vancomycin resistance genes into the soil resistome. These 20 ARG sequences were detected only in the FW. Multiple lines of evidence indicated that horizontal gene transfer dominated ARG dissemination in soil contaminated by FW. This conclusion is supported by the discrepancy between changes in mobile ARGs and host abundance, the upregulation of oxidative stress-related genes (SOD1 and SOD2) and the SOS response (lexA and recA), as well as the upregulation of genes related to quorum sensing (virD4, virB9, and virB3) and naked DNA uptake (pilD, pilT, and pilQ).},
}

@article {pmid39731060,
year = {2024},
author = {Shen, SP and Lin, HC and Chen, JF and Wang, HS and Huang, YY and Hsia, KC and Lin, JH and Kuo, YW and Li, CM and Hsu, YC and Tsai, SY and Ho, HH},
title = {Assessment of the safety and gut microbiota modulation ability of an infant formula containing Bifidobacterium animalis ssp. lactis CP-9 or Lactobacillus salivarius AP-32 and the effects of the formula on infant growth outcomes: insights from a four-month clinical study in infants under two months old.},
journal = {BMC pediatrics},
volume = {24},
number = {1},
pages = {840},
pmid = {39731060},
issn = {1471-2431},
mesh = {Humans ; *Infant Formula ; *Gastrointestinal Microbiome ; *Probiotics ; Infant ; Male ; Female ; *Bifidobacterium animalis ; *Ligilactobacillus salivarius ; Infant, Newborn ; Child Development ; Milk, Human/microbiology ; },
abstract = {BACKGROUND: Breast milk is a natural treasure for infants, and its microbiota contains a rich array of bacterial species. When breastfeeding is not possible, infant formula with probiotics can be used as a sole source or as a breast milk supplement. The main aim of this study was to evaluate the growth outcomes and tolerance of infants consuming an infant formula containing Bifidobacterium animalis ssp. lactis CP-9 (B. animalis CP-9) or Lactobacillus salivarius AP-32 (L. salivarius AP-32), which were isolated from breast milk and the guts of healthy infants. The safety of these strains in terms of antibiotic resistance and their ability to modulate the gut microbiota were also evaluated.

METHODS: One hundred eighty healthy infants were included in this study and separated into three groups: the control group, the L. salivarius AP-32 group, and the B. animalis CP-9 group. In this clinical study, adverse events, growth effects, and the incidence of allergies and gastrointestinal disorders in infants consuming infant formula containing B. animalis CP-9 or L. salivarius AP-32 were evaluated. Finally, the impact of the probiotic infant formula on the gut microbiota was elucidated via next-generation sequencing (NGS) analysis.

RESULTS: The 4-month interventional study revealed that body weight, recumbent length, and head circumference were similar among the three groups. No adverse events related to the intervention were observed. The microbiota composition was more diverse on day 0 and became more uniform by month 4. B. animalis CP-9 and L. salivarius AP-32 were found to be susceptible to streptomycin, tetracycline, erythromycin, clindamycin, chloramphenicol, and ampicillin.

CONCLUSIONS: The use of infant formula containing B. animalis CP-9 and L. salivarius AP-32 was considered safe and well tolerated, with no adverse events observed during the study. While these strains showed low antibiotic resistance and no immediate concerns related to antibiotic resistance genes, further research is needed to comprehensively assess their long-term safety and efficacy and the potential risk of horizontal gene transfer in broader contexts.

TRIAL REGISTRATION: The trial was registered with the US Library of Medicine (clinicaltrials.gov) with the number NCT03993301 on 20/06/2019.},
}

Humans
*Infant Formula
*Gastrointestinal Microbiome
*Probiotics
Infant
Male
Female
*Bifidobacterium animalis
*Ligilactobacillus salivarius
Infant, Newborn
Child Development
Milk, Human/microbiology

@article {pmid39730778,
year = {2024},
author = {Cotta, SR and Dias, ACF and Mendes, R and Andreote, FD},
title = {Role of horizontal gene transfer and cooperation in rhizosphere microbiome assembly.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {39730778},
issn = {1678-4405},
support = {2018/24049-2//Fapesp/ ; 485116/2013-8//CNPq/ ; 405163/2018-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
abstract = {Microbes employ a variety of mechanisms, encompassing chemical signaling (e.g., quorum-sensing molecules) and genetic processes like horizontal gene transfer (HGT), to engage in interactions. HGT, in particular, holds a pivotal role as it facilitates the generation of metabolic diversity, thus directly or indirectly influencing microorganisms' interactions and functioning within their habitat. In this study, we investigate the correlations between enhanced metabolic diversity through HGT and cooperative behavior in the rhizosphere. Despite the potential drawbacks of cooperative behavior, which renders it susceptible to exploitation by cheaters based on evolutionary theory, HGT emerges as a mitigating factor. It serves as a valuable and adaptive tool for survival in competitive environments, notably the rhizosphere. By initiating a comprehensive discussion on these processes combined, we anticipate achieving a profound understanding of the rhizosphere microbiome, ultimately enhancing soil microbiology management and the exploitation of this ecological niche.},
}

@article {pmid39729844,
year = {2024},
author = {Ku, H and Kelk, D and Bauer, DC and Sidhu, JPS},
title = {Plasmid hybrids as vectors for antibiotic resistance in environmental Escherichia coli.},
journal = {The Science of the total environment},
volume = {959},
number = {},
pages = {178157},
doi = {10.1016/j.scitotenv.2024.178157},
pmid = {39729844},
issn = {1879-1026},
abstract = {This study investigated the potential role of phages in the dissemination of antimicrobial resistance genes (ARGs) and virulence factor genes (VFGs) in Escherichia coli (E. coli). A comprehensive in silico analysis of 18,410 phage sequences retrieved from the National Center for Biotechnology Information database (NCBI) revealed distinct carriage patterns for ARGs and VFGs between lytic, temperate, and chronic phage types. Notably, 57 temperate phages carried ARGs, particularly associated with multidrug and aminoglycoside resistance. Temperate phages (8.97 %, 635/7081) and chronic phages (8.09 %, 14/173) exhibited a significantly higher prevalence of VFGs (Chi-Square, p ≤ 0.05), particularly associated with exotoxin-related genes, compared to lytic phages (0.05 %, 6/11,156). This underscores the role phages play as reservoirs and potential vectors for the dissemination of ARGs and VFGs in bacteria. Our environmental E. coli isolates (n = 60) were found to carry 179 intact prophages containing polymyxin, macrolide, tetracycline, and multidrug resistance genes as well as various VFGs. This study documents the presence of phage-plasmids (P-Ps) in environmental E. coli isolates, offering new insights into horizontal gene transfer (HGT) mechanisms. Notably, the blaCTX-M-15 gene, associated with beta-lactam resistance, was identified in two P-Ps, suggesting a potentially novel route for the dissemination of beta-lactam resistance. The diverse replicon types observed in P-Ps suggest a broader integration capacity compared to traditional plasmids, potentially enabling the blaCTX-M-15 gene dissemination across diverse bacterial species. This study provides valuable insights into the multifaceted role of phages in shaping the antimicrobial resistance landscape. Further research is necessary to fully understand the intricate mechanisms underlying phage-mediated ARG and VFG dissemination.},
}

@article {pmid39729729,
year = {2024},
author = {Wang, M and Yao, Y and Yang, Y and Zhu, D and Wang, M and Jia, R and Chen, S and Zhao, X and Yang, Q and Wu, Y and Zhang, S and Huang, J and Ou, X and Tian, B and Sun, D and Zhang, L and Yu, Y and He, Y and Wu, Z and Cheng, A and Liu, M},
title = {The characterization of outer membrane vesicles (OMVs) and their role in mediating antibiotic-resistance gene transfer through natural transformation in Riemerella anatipestifer.},
journal = {Poultry science},
volume = {104},
number = {2},
pages = {104730},
doi = {10.1016/j.psj.2024.104730},
pmid = {39729729},
issn = {1525-3171},
abstract = {Riemerella anatipestifer (R. anatipestifer, RA) is the etiological agent of duck serositis, an acute multisystemic disease in ducks that is globally distributed and causes serious economic losses in the duck industry. Despite exhibiting multidrug resistance, the transmission mechanism of its antibiotic resistance genes (ARGs) remains incompletely identified. To contribute to addressing this gap, in this study, outer membrane vesicles (OMVs) from the RA strain CH-1 were isolated and characterized to investigate their involvement in ARG transfer in RA. Sequencing and data analysis revealed that RA CH-1 OMVs had ∼2.04 Mb genomic size, representing 88.3 % of the RA CH-1 genomic length. Proteomic analysis showed that OMVs contained 577 proteins, representing 27.2 % of the bacterial proteins. Subsequent investigations demonstrated that OMVs from antibiotic-resistant strains transferred ARG fragments and plasmids to the sensitive strain RA ATCC11845, relying on the natural transformation system, and the transformants exhibited corresponding resistance. Overall, OMV-mediated horizontal transfer of ARGs serving as a significant mechanism for acquiring multiple resistance genes in R. anatipestifer.},
}

@article {pmid39729001,
year = {2024},
author = {Elbir, H},
title = {Updating the Relationship Between the Threshold Value of Average Nucleotide Identity and Digital DNA-DNA Hybridization for Reliable Taxonomy of Corynebacterium.},
journal = {Veterinary sciences},
volume = {11},
number = {12},
pages = {},
doi = {10.3390/vetsci11120661},
pmid = {39729001},
issn = {2306-7381},
abstract = {Currently, bacterial classification at the species level relies on the 95-96% average nucleotide identity (ANI) value that is known to be equivalent to a 70% digital DNA-DNA hybridization (dDDH) value. However, during the routine identification of bacteria in the uteri of camels with a history of conception failure, we found that four out of the seven strains (2298A, 2569A, 2652, 2571B, 1103A, 2571A, and 335C) could not be assigned to any valid Corynebacterium species. Furthermore, a 70% dDDH value did not correspond to a 95-96% ANI value in strain 2569A. Thus, we aimed to classify these strains and explain the mechanisms underlying gene repertoire diversity and the disagreement we found between the ANI and dDDH cutoff values. For this study, we extracted information from the genomes of 150 Corynebacterium-type species and seven sequenced genomes of uterine Corynebacterium isolates. We found that the 96.67% OrthoANI value should be used in place of the generally accepted 95-96% ANI threshold in order to obtain an equivalent 70% dDDH value. Phylogenomic analysis determined the evolutionary position of each uterine strain. Then, strains 2652 and 2571B were classified as C. camporealensis based on the ANI value (98.44% and 98.72%) and dDDH value (85.8% and 88.5%). Strain 2569A had a 96.58% ANI and a 69.4% dDDH value and was classified as C. urogenitale. The strains 335C, 1103A, 2571A, and 2298A were classified as novel Corynebacterium based on the ANI value (77.12, 94.01%, 94.26%, and 94.03%) and dDDH value (21.3%, 54.1%, 54.9%, and 51.3%), respectively. Genes for menaquinone biosynthesis and the saturation of chains were detected in uterine strains and their closely related type strains. Gene gain predominates as a source of variation in the gene repertoire. Most of these genes are gained by horizontal gene transfer, driven by genomic islands and prophage. In summary, we refined the ANI cutoff value for an accurate diagnosis of Corynebacterium. Moreover, we clarified the mechanism underlying the diversity of the gene repertoire and expanded the number of Corynebacterium species isolated from the camel uterus.},
}

@article {pmid39727166,
year = {2024},
author = {},
title = {Correction to 'GutMetaNet: an integrated database for exploring horizontal gene transfer and functional redundancy in the human gut microbiome'.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae1307},
pmid = {39727166},
issn = {1362-4962},
}

@article {pmid39727139,
year = {2024},
author = {Wang, Q and Qiu, JH and Sun, Y and Ni, N and Sun, SJ and Li, XL and Yang, SJ and Liu, YR and Cui, YY},
title = {[Research progress on the effect of estuary microplastics on antibiotic resistance genes].},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {35},
number = {10},
pages = {2916-2924},
doi = {10.13287/j.1001-9332.202410.028},
pmid = {39727139},
issn = {1001-9332},
mesh = {*Microplastics ; *Water Pollutants, Chemical/analysis ; *Estuaries ; Biofilms/drug effects/growth & development ; Drug Resistance, Microbial/genetics ; Environmental Monitoring ; Gene Transfer, Horizontal ; },
abstract = {Estuaries are transitional zones between rivers and marine environments, with intensive human activities. Pollutants pose a threat to the ecological systems of estuaries. Among these pollutants, microplastics and antibiotic resistant genes have gained significant attention due to their potential impacts on estuarine organisms and human health. Microplastics can form unique biofilms, adsorb pollutants from the surrounding environment, and provide potential hosts for antibiotic resistant genes, with positive consequence on horizontal gene transfer of antibiotic resistance. We provided an overview of the pollution status of microplastics and antibiotic resistant genes in estua-rine areas, with a particular emphasis on the influence of biofilms formed on microplastics on the enrichment, transport, and transfer of antibiotic resistant genes. We also highlighted the limitations in current research, regarding microplastic sampling, analysis methods, and inconsistent reporting units. Furthermore, we proposed prospects for the biodegradation of microplastics and potential risk assessment of microplastic biofilms.},
}

*Microplastics
*Water Pollutants, Chemical/analysis
*Estuaries
Biofilms/drug effects/growth & development
Drug Resistance, Microbial/genetics
Environmental Monitoring
Gene Transfer, Horizontal

@article {pmid39725890,
year = {2024},
author = {Javier-López, R and Geliashvili, N and Birkeland, NK},
title = {Comparative genomics of Fervidobacterium: a new phylogenomic landscape of these wide-spread thermophilic anaerobes.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1248},
pmid = {39725890},
issn = {1471-2164},
support = {328955//Norges Forskningsråd/ ; 328955//Norges Forskningsråd/ ; 862555//ERA-NET Cofund on Food Systems and Climate (FOSC)/ ; 862555//ERA-NET Cofund on Food Systems and Climate (FOSC)/ ; 862555//ERA-NET Cofund on Food Systems and Climate (FOSC)/ ; CPEA-LT-2017/10061//Norwegian Directorate for Higher Education and Skills/ ; CPEA-LT-2017/10061//Norwegian Directorate for Higher Education and Skills/ ; },
mesh = {*Phylogeny ; *Genome, Bacterial ; *Genomics ; RNA, Ribosomal, 16S/genetics ; Base Composition ; },
abstract = {BACKGROUND: Fervidobacterium is a genus of thermophilic anaerobic Gram-negative rod-shaped bacteria belonging to the phylum Thermotogota. They can grow through fermentation on a wide range of sugars and protein-rich substrates. Some can also break down feather keratin, which has significant biotechnological potential. Fervidobacteria genomes have undergone several horizontal gene transfer events, sharing DNA with unrelated microbial taxa. Despite increasing biotechnological and evolutionary interest in this genus, only seven species have been described to date. Here, we present and describe six new and complete Fervidobacterium genomes, including the type strains Fervidobacterium gondwanense CBS-1[ T], F. islandicum H-21[ T] and F. thailandense FC2004[T], one novel isolate from Georgia (strain GSH) and two strains (DSM 21710 and DSM 13770) that have not been previously described along with an evolutionary and phylogenomic analysis of the genus.

RESULTS: The complete genomes were around 2 Mb with approximately 2,000 CDS identified and annotated in each of them and a G + C content ranging from 38.9 mol% to 45.8 mol%. Phylogenomic comparisons of all currently available Fervidobacterium genomes, including OrthoANI and TYGS analyses, as well as a phylogenetic analysis based on the 16S rRNA gene, identified six species and nine subspecies clusters across the genus, with a consistent topology and a distant and separately branching species, Fervidobacterium thailandense. F. thailandense harbored the highest number of transposases, CRISPR clusters, pseudo genes and horizontally transferred regions The pan genome of the genus showed that 44% of the genes belong to the cloud pangenome, with most of the singletons found also in F. thailandense.

CONCLUSIONS: The additional genome sequences described in this work and the comparison with all available Fervidobacterium genome sequences provided new insights into the evolutionary history of this genus and supported a phylogenetic reclassification. The phylogenomic results from OrthoANI and TYGS analyses revealed that F. riparium and F. gondwanense belong to the same genome species, and includes Fervidobacterium sp. 13770, while "F. pennivorans" strain DYC belongs to a separate genome species, whereas Fervidobacterium sp. 21710 and Fervidobacterium sp. GSH within the Fervidobacterium pennivorans clade represent two subspecies. F. changbaicum is reclassified as F. islandicum.},
}

*Phylogeny
*Genome, Bacterial
*Genomics
RNA, Ribosomal, 16S/genetics
Base Composition

@article {pmid39725200,
year = {2024},
author = {Song, M and Wang, K and Xie, Y and Wen, X and Tu, Y and Teng, T and Luo, C and Zhang, D},
title = {Impacts of anthropogenic disturbances on antibiotic resistomes in biological soil crusts on the Qinghai-Tibetan Plateau.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {367},
number = {},
pages = {125582},
doi = {10.1016/j.envpol.2024.125582},
pmid = {39725200},
issn = {1873-6424},
abstract = {Biological soil crusts (BSCs) are the main landscape on the Qinghai-Tibetan Plateau and an ecological indicator of human disturbance. Information about antibiotic resistomes in BSCs on the Qinghai-Tibetan Plateau can provide baseline for the risk assessment and management of resistomes and yet to be explored. This work investigated the profiles and geographic patterns of antibiotic resistomes in BSCs along the Lhasa River and their response to anthropogenic activities for the first time. Various antibiotic resistance genes (ARGs) were widely distributed in BSCs, but had relatively lower detection frequency and abundance comparing to soils from human disturbed sites. ARGs profiles in BSCs were separated by altitude from 3860 to 3880 m, possibly attributing to the difference in anthropogenic activities. Above 3860 m, resistomes exhibited lower abundance including total ARGs, aadA, blaSFO and tnpA-04 owing to the rare human activities; at human disturbed sites with altitude <3860 m, the detection frequency and relative abundance of tetG02, oprJ, qacEdelta1-01, and ARGs with the mechanism of efflux pump were higher and viewed as potential indicators of human activities. Anthropogenic activities potentially promoted the horizontal gene transfer of ARGs in BSCs at human disturbed sites from co-occurrence network analysis. Our findings provided fundamental information of antibiotic resistomes in BSCs on the Qinghai-Tibetan Plateau, and unraveled possible mechanisms of human disturbance in shaping antibiotic resistomes.},
}

@article {pmid39724227,
year = {2024},
author = {Shahid, U and Hooi, SL and Lim, SY and Mohd Aris, A and Khor, BC and Ayub, Q and Tan, HS},
title = {Metagenomic surveillance of microbial community and antibiotic resistant genes associated with Malaysian wastewater during the COVID-19 pandemic.},
journal = {Current genetics},
volume = {71},
number = {1},
pages = {1},
pmid = {39724227},
issn = {1432-0983},
mesh = {*Wastewater/microbiology ; *COVID-19/epidemiology ; Malaysia/epidemiology ; *Metagenomics/methods ; *SARS-CoV-2/genetics ; Humans ; Drug Resistance, Microbial/genetics ; Pandemics ; Microbiota/genetics ; Metagenome ; Bacteria/genetics/classification/drug effects ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; },
abstract = {Wastewater is a reservoir of pathogens and hotspots for disseminating antibiotic resistance genes across species. The metagenomic surveillance of wastewater provides insight into the native microbial community, antibiotic-resistance genes (ARGs) and mobile genetic elements. t. The COVID-19 pandemic has caused wider dissemination of ARGs and resistant bacteria in wastewater. Although immensely significant, no research has been performed on the Malaysian wastewater microbial community and ARGs or their correlation with COVID-19 infections. This study utilised a 16S metagenomics approach to characterise the microbial community in Malaysian wastewater during high and low-case phases of the pandemic. Bacteria belonging to Bacteriodales, Bacillales, Actinomycetales and opportunistic pathogens-Arcobacters, Flavobacteria, and Campylobacterales, Neisseriales, were enriched during higher COVID-19 pandemic (active cases). Additionally, copy number profiling of ARGs in water samples showed the prevalence of elements conferring resistance to antibiotics like sulphonamides, cephalosporins, and colistin. The high prevalence of intI1 and other ion-based transporters in samples highlights an extensive risk of horizontal gene transfer to previously susceptible species. Our study emphasises the importance of wastewater surveillance in understanding microbial community dynamics and ARG dissemination, particularly during public health crises like the COVID-19 pandemic.},
}

*Wastewater/microbiology
*COVID-19/epidemiology
Malaysia/epidemiology
*Metagenomics/methods
*SARS-CoV-2/genetics
Humans
Drug Resistance, Microbial/genetics
Pandemics
Microbiota/genetics
Metagenome
Bacteria/genetics/classification/drug effects
Anti-Bacterial Agents/pharmacology
Drug Resistance, Bacterial/genetics
Gene Transfer, Horizontal

@article {pmid39724170,
year = {2024},
author = {Farrell, AA and Nesbø, CL and Zhaxybayeva, O},
title = {Bacterial growth temperature as a horizontally acquired polygenic trait.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae277},
pmid = {39724170},
issn = {1759-6653},
abstract = {Evolutionary events leading to organismal preference for a specific growth temperature, as well as genes whose products are needed for a proper function at that temperature, are poorly understood. Using 64 bacteria from phylum Thermotogota as a model system, we examined how optimal growth temperature changed throughout Thermotogota history. We inferred that Thermotogota's last common ancestor was a thermophile and that some Thermotogota evolved the mesophilic and hyperthermophilic lifestyles secondarily. By modeling gain and loss of genes throughout Thermotogota history and by reconstructing their phylogenies, we demonstrated that adaptations to lower and higher growth temperature involve both the acquisition of necessary genes and loss of unnecessary genes. Via a pangenome-wide association study, we correlated presence/absence of 68 genes with specific optimal growth temperature intervals. While some of these genes are poorly characterized, most are involved in metabolism of amino acids, nucleotides, carbohydrates, and lipids, as well as in signal transduction and regulation of transcription. Most of the 68 genes have a history of horizontal gene transfer with other bacteria and archaea that often grow at similar temperatures, suggesting that parallel acquisitions of genes likely promote independent adaptations of different Thermotogota species to specific growth temperatures.},
}

@article {pmid39723821,
year = {2024},
author = {Sanchez, VA and Renner, T and Baker, LJ and Hendry, TA},
title = {Genome evolution following an ecological shift in nectar-dwelling Acinetobacter.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0101024},
doi = {10.1128/msphere.01010-24},
pmid = {39723821},
issn = {2379-5042},
abstract = {UNLABELLED: The bacterial genus Acinetobacter includes species found in environmental habitats like soil and water, as well as taxa adapted to be host-associated or pathogenic. High genetic diversity may allow for this habitat flexibility, but the specific genes underlying switches between habitats are poorly understood. One lineage of Acinetobacter has undergone a substantial habitat change by evolving from a presumed soil-dwelling ancestral state to thrive in floral nectar. Here, we compared the genomes of floral-dwelling and pollinator-associated Acinetobacter, including newly described species, with genomes from relatives found in other environments to determine the genomic changes associated with this ecological shift. Following one evolutionary origin of floral nectar adaptation, nectar-dwelling Acinetobacter taxa have undergone reduction in genome size compared with relatives and have experienced dynamic gene gains and losses as they diversified. Gene content changes suggest a shift to metabolism of monosaccharides rather than diverse carbohydrates, and scavenging of nitrogen sources, which we predict to be beneficial in nectar environments. Gene gains appear to result from duplication events, evolutionary divergence, and horizontal gene transfer. Most notably, nectar-dwelling Acinetobacter acquired the ability to degrade pectin from plant pathogens, and the genes underlying this ability have duplicated and are under selection within the clade. We hypothesize that this ability was a key trait for adaptation to floral nectar, as it could improve access to nutrients in the nutritionally unbalanced habitat of nectar. These results identify the genomic changes and traits coinciding with a dramatic habitat switch from soil to floral nectar.

IMPORTANCE: Many bacteria, including the genus Acinetobacter, commonly evolve to exploit new habitats. However, the genetic changes that underlie habitat switches are often unknown. Floral nectar is home to specialized microbes that can grow in this nutritionally unbalanced habitat. Several specialized Acinetobacter species evolved from soil-dwelling relatives to become common and abundant in floral nectar. Here, we investigate the genomic adaptations required to successfully colonize a novel habitat like floral nectar. We performed comparative genomics analyses between nectar-dwelling Acinetobacter and Acinetobacter species from other environments, like soil and water. We find that although gene loss coincided with the switch to living in nectar, gains of specific genes from other bacteria may have been particularly important for this ecological change. Acinetobacter living in nectar gained genes for degrading pectin, a plant polysaccharide, which may improve access to nutrients in their environment. These findings shed light on how evolutionary novelty evolves in bacteria.},
}

@article {pmid39721637,
year = {2025},
author = {Zhou, JZ and Sun, QN and Li, A and Wang, XJ and Zhao, JF},
title = {[Simultaneous Removal of Antibiotic-resistant Bacteria, Genes, and Inhibition of Horizontal Transfer using Vis-rGO-CNCF-enhanced Peroxymonosulfate Activation Process].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {1},
pages = {305-317},
doi = {10.13227/j.hjkx.202401171},
pmid = {39721637},
issn = {0250-3301},
mesh = {*Graphite/chemistry ; *Drug Resistance, Bacterial/genetics ; Peroxides/chemistry ; Copper/chemistry ; Gene Transfer, Horizontal ; Ferric Compounds/chemistry ; Anti-Bacterial Agents/pharmacology/chemistry ; Water Purification/methods ; Bacteria/genetics/drug effects ; Oxidation-Reduction ; Drug Resistance, Microbial/genetics ; },
abstract = {As emerging contaminants, antibiotic-resistant bacteria （ARBs） and antibiotic-resistant genes （ARGs） pose a serious threat to human health and ecological security. Here, a reduced graphene oxide and g-C3N4 co-doped copper ferrite （rGO-CNCF） were synthesized. The composite material was characterized using XRD, FTIR, XPS, SEM-EDS, TEM, and DRS analysis methods, and a visible-light-assisted rGO-CNCF-activated PMS system was constructed for the removal of ARB and ARGs in water. The results showed that the complete inactivation of 8.01 log SA-ARB could be achieved within 30 min when the catalyst dosage was 0.2 g·L[-1], The PMS dosage was 0.3 g·L[-1], and the initial pH value of the solution was 7.0. The Vis-rGO-CNCF/PMS system was able to effectively reduce the horizontal transfer of SA-ARGs, and this system had a good destructive ability for intracellular and extracellular SA-ARGs. The destruction ability of the advanced oxidation process for the two pollutants together, SMT and SA-ARB, was maintained at a high level. This system could destroy the cell membrane structure of resistant bacteria, causing cell fragmentation, and quenching experiments showed that singlet oxygen （[1]O2） played a major role in the system. This study can provide a promising method for controlling ARB and ARG pollution in water and controlling the horizontal transfer of ARGs.},
}

*Graphite/chemistry
*Drug Resistance, Bacterial/genetics
Peroxides/chemistry
Copper/chemistry
Gene Transfer, Horizontal
Ferric Compounds/chemistry
Anti-Bacterial Agents/pharmacology/chemistry
Water Purification/methods
Bacteria/genetics/drug effects
Oxidation-Reduction
Drug Resistance, Microbial/genetics

@article {pmid39719706,
year = {2024},
author = {Zhang, AN and Gaston, JM and Cárdenas, P and Zhao, S and Gu, X and Alm, EJ},
title = {CRISPR-Cas spacer acquisition is a rare event in human gut microbiome.},
journal = {Cell genomics},
volume = {},
number = {},
pages = {100725},
doi = {10.1016/j.xgen.2024.100725},
pmid = {39719706},
issn = {2666-979X},
abstract = {Host-parasite relationships drive the evolution of both parties. In microbe-phage dynamics, CRISPR functions as an adaptive defense mechanism, updating immunity via spacer acquisition. Here, we investigated these interactions within the human gut microbiome, uncovering low frequencies of spacer acquisition at an average rate of one spacer every ∼2.9 point mutations using isolates' whole genomes and ∼2.7 years using metagenome time series. We identified a highly prevalent CRISPR array in Bifidobacterium longum spreading via horizontal gene transfer (HGT), with six spacers found in various genomic regions in 15 persons from the United States and Europe. These spacers, targeting two prominent Bifidobacterium phages, comprised 76% of spacer occurrence of all spacers targeting these phages in all B. longum populations. This result suggests that HGT of an entire CRISPR-Cas system introduced three times more spacers than local CRISPR-Cas acquisition in B. longum. Overall, our findings identified key ecological and evolutionary factors in prokaryote adaptive immunity.},
}

@article {pmid39717269,
year = {2024},
author = {Zhang, S and Shu, Y and Yang, Z and Zhong, Z and Wang, M and Jia, R and Chen, S and Liu, M and Zhu, D and Zhao, X and Wu, Y and Yang, Q and Huang, J and Ou, X and Sun, D and Tian, B and Wu, Z and He, Y and Cheng, A},
title = {Decoding the enigma: unveiling the transmission characteristics of waterfowl-associated bla NDM-5-positive Escherichia coli in select regions of China.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1501594},
pmid = {39717269},
issn = {1664-302X},
abstract = {Escherichia coli (E. coli) serves as a critical indicator microorganism for assessing the prevalence and dissemination of antibiotic resistance, notably harboring various antibiotic-resistant genes (ARGs). Among these, the emergence of the bla NDM gene represents a significant threat to public health, especially since carbapenem antibiotics are vital for treating severe infections caused by Gram-negative bacteria. This study aimed to characterize the antibiotic resistance features of bla NDM-5-positive E. coli strains isolated from waterfowl in several regions of China and elucidate the dissemination patterns of the bla NDM-5 gene. We successfully isolated 103 bla NDM-5-positive E. coli strains from 431 intestinal fecal samples obtained from waterfowl across five provincial-level units in China, with all strains exhibiting multidrug resistance (MDR). Notably, the bla NDM-5 gene was identified on plasmids, which facilitate efficient and stable horizontal gene transfer (HGT). Our adaptability assays indicated that while the bla NDM-5-positive plasmid imposed a fitness cost on the host bacteria, the NDM-5 protein was successfully induced and purified, exhibiting significant enzymatic activity. One strain, designated DY51, exhibited a minimum inhibitory concentration (MIC) for imipenem of 4 mg/L, which escalated to 512 mg/L following exposure to increasing imipenem doses. This altered strain demonstrated stable resistance to imipenem alongside improved adaptability, correlating with elevated relative expression levels of the bla NDM-5 and overexpression of efflux pumps. Collectively, this study highlights the horizontal dissemination of the bla NDM-5 plasmid among E. coli strains, confirms the associated fitness costs, and provides insights into the mechanisms underlying the stable increase in antibiotic resistance to imipenem. These findings offer a theoretical framework for understanding the dissemination dynamics of bla NDM-5 in E. coli, which is essential for developing effective strategies to combat carbapenem antibiotic resistance.},
}

@article {pmid39716502,
year = {2024},
author = {Zheng, J and Li, YY and Lu, YS and Wang, D and Liu, C and Peng, HL and Shi, CH and Xie, KZ and Zhang, K and Sun, LL and Zhou, CM and Gu, WJ},
title = {Impact of different continuous fertilizations on the antibiotic resistome associated with a subtropical triple-cropping system over one decade.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125564},
doi = {10.1016/j.envpol.2024.125564},
pmid = {39716502},
issn = {1873-6424},
abstract = {The prevalence of antibiotic resistance genes (ARGs) in agricultural soils has garnered significant attention. However, the long-term impacts of various nitroge (N)-substitution fertilization regimes on the distribution of soil ARGs and their dominant drivers in a subtropical triple-cropping system remain largely unexplored. This study employed a metagenomic approach to analyze soil ARGs, microbial communities, mobile genetic elements (MGEs), and viruses from a maize-maize-cabbage rotation field experiment with five different fertilization regimes. Soil samples were collected in 2012 and 2021. A total of 615 unique ARG subtypes were identified, with multidrug, bacitracin, and rifamycin resistance genes being the most abundant. Notably, ARG types. the continuous application of fresh chicken manure (CM) over 10 years significantly increased both the count of unique ARG subtypes and the total ARG abundance compared to other fertilization regimes, such as inorganic fertilizer and composted chicken manure. Specifically, the abundance of genes associated with antibiotic target replacement (e.g., sul1 and sul2) in the CM-treated soil rose by 8.83-fold from 2021 to 2012. Our random forest analysis revealed that the abundance of three MGEs (QacEdelta, plasmids, and IstB), two viral families (Myoviridae and Podoviridae), two bacterial phyla (Chloroflexi and Planctomycetes), and two environmental factors (pH and soil organic matter (SOM)) significantly influenced the distribution of ARGs. Furthermore, variance decomposition analysis underscored the critical roles of the three MGEs and the two viral families in the dissemination of ARGs, suggesting that horizontal gene transfer (HGT) may play a key role in ARG spread. These findings enhance our understanding of how different fertilization practices influence ARG dissemination in subtropical triple-cropping agroecosystems over the long term and provide valuable insights for optimizing fertilization management strategies.},
}

@article {pmid39708795,
year = {2024},
author = {Tarnopol, RL and Tamsil, JA and Cinege, G and Ha, JH and Verster, KI and Ábrahám, E and Magyar, LB and Kim, BY and Bernstein, SL and Lipinszki, Z and Andó, I and Whiteman, NK},
title = {Experimental horizontal transfer of phage-derived genes to Drosophila confers innate immunity to parasitoids.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.11.071},
pmid = {39708795},
issn = {1879-0445},
abstract = {Metazoan parasites have played a major role in shaping innate immunity in animals. Insect hosts and parasitoid wasps are excellent models for illuminating how animal innate immune systems have evolved to neutralize these enemies. One such strategy relies on symbioses between insects and intracellular bacteria that express phage-encoded toxins. In some cases, the genes that encode these toxins have been horizontally transferred to the genomes of the insects. Here, we used genome editing in Drosophila melanogaster to recapitulate the evolution of two toxin genes-cytolethal distending toxin B (cdtB) and apoptosis inducing protein of 56kDa (aip56)-that were horizontally transferred likely from phages of endosymbiotic bacteria to insects millions of years ago. We found that a cdtB::aip56 fusion gene (fusionB), which is conserved in D. ananassae subgroup species, dramatically promoted fly survival and suppressed parasitoid wasp development when heterologously expressed in D. melanogaster immune tissues. We found that FusionB was a functional nuclease and was secreted into the host hemolymph where it targeted the parasitoid embryo's serosal tissue. Although the mechanism of toxicity remains unknown, when expressed ubiquitously, fusionB resulted in delayed development of late-stage fly larvae and eventually killed pupating flies. These results point to the salience of regulatory constraint in mitigating autoimmunity during the domestication process following horizontal transfer. Our findings demonstrate how horizontal gene transfer can instantly provide new, potent innate immune modules in animals.},
}

@article {pmid39708598,
year = {2024},
author = {Sun, D and Shi, X and Shen, Y and Liu, Y and Luo, S and Jin, Y and Zhai, W and Liu, L and Deng, Z and Sun, C and Liu, D and Yang, X and Xie, Y and Krüger-Haker, H and Wu, C and Schwarz, S and Shen, J and Chen, Y and Ma, S and Wang, Y},
title = {Comparative efficacy of anaerobic digestion systems in removing antimicrobial resistance genes from swine wastewater.},
journal = {Journal of hazardous materials},
volume = {485},
number = {},
pages = {136868},
doi = {10.1016/j.jhazmat.2024.136868},
pmid = {39708598},
issn = {1873-3336},
abstract = {Swine farm wastewater is a major reservoir of antimicrobial resistance genes (ARGs). Anaerobic digestion (AD), widely implemented in farms, has been extensively studied for ARG removal. However, a comparative study on ARG removal efficiency across the four principal AD systems - up-flow anaerobic sludge blanket (UASB), continuous stirred tank reactor (CSTR), buried biogas digester (BBD), and septic tank (SPT) - is lacking. Herein, we employed metagenomic sequencing, ultra-performance liquid chromatography-tandem mass spectrometry, as well as atomic absorption spectrometry/atomic fluorescence spectrophotometry, and revealed that UASB and CSTR achieved higher removal efficiencies for both ARGs (67% and 57%) and antibiotic residues (100% and 90%) compared to BBD and SPT. Acinetobacter, Escherichia, Pseudomonas and Streptococcus were the primary ARG hosts, comprising over 65% of the total abundance in influent samples. UASB and CSTR systems demonstrated superior removal efficiencies for both mobile genetic elements (MGEs) and antibiotic residues, both of which had essential impacts on ARG profiles. In addition, heavy metals might contribute to variation in ARGs through horizontal gene transfer. Collectively, the variation in microbial communities and better removal of both MGEs and antibiotic residues contribute to the remarkable ARG removal efficiency of UASB and CSTR, therefore, advocating for the widespread adoption of these two AD systems in swine farms.},
}

@article {pmid39706477,
year = {2024},
author = {Bientz, L and Guyet, U and Guiraud, J and Metifiot, M and Moulieras, M and Aillerie, S and Coulange-Mayonnove, L and Abdou, BB and Groppi, A and Nikolski, M and Bébéar, C and Pereyre, S and Dubois, V},
title = {Mobilization of an ICEclc-like element as a potential mechanism for the spread of IMP-13 carbapenemase in Pseudomonas aeruginosa.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2024.12.006},
pmid = {39706477},
issn = {2213-7173},
abstract = {Carbapenem-resistant Pseudomonas aeruginosa is a global public health concern. IMP-13 is a carbapenemase that was described for the first time in 2001 but is often underestimated due to poor hydrolysis of carbapenems and a lack of molecular detection. The aim of this study was to characterize the genetic support of blaIMP-13 in P. aeruginosa and to assess the ability of mobile genetic elements to disseminate this resistance. A retrospective analysis conducted between 2010 and 2020 revealed eight multiresistant P. aeruginosa isolates by their production of the carbapenemase IMP-13 in Bordeaux. Additionally, three of the studied isolates exhibited high-level resistance to imipenem and imipenem-relebactam that was linked to an insertion sequence in the oprD gene. Successful mating was achieved, and transconjugants and parental clinical isolate genomes were sequenced. All clinical isolates were found to be ST621 strains. The data revealed that blaIMP-13 was carried on an Integrative and Conjugative Element (ICEclc-like) of 88589 bp with a 62% GC content harboring 85 CDSs, and was inserted at the tRNA[Gly] locus PA0729.1. The ICE was identical in the eight studied clinical isolates and in all the ST621 strains found in the databases. The conjugation rate was low, at approximately 10[-8] transconjugants per donor and ICE transfer appeared to mobilize some adjacent parental genes located immediately downstream of the ICE. In conclusion, these results suggest that even if the spread of blaIMP-13 is mainly due to an epidemic ST621 clone, the mobilization of a blaIMP-13-carrying ICEclc-like element is possible and should not be underestimated.},
}

@article {pmid39706021,
year = {2024},
author = {Dinesh, R and Sreena, CP and Sheeja, TE and Srinivasan, V and Subila, KP and Sona, C and Kumar, IPV and Anusree, M and Alagupalamuthirsolai, M and Jayarajan, K and Sajith, V},
title = {Co-resistance is the dominant mechanism of co-selection and dissemination of antibiotic resistome in nano zinc oxide polluted soil.},
journal = {Journal of hazardous materials},
volume = {485},
number = {},
pages = {136885},
doi = {10.1016/j.jhazmat.2024.136885},
pmid = {39706021},
issn = {1873-3336},
abstract = {The broader soil bacterial community responses at ecotoxicologically relevant levels of nano ZnO (nZnO) focussing on co-selection of antibiotic resistance (AR) were investigated. nZnO imposed a stronger influence than the bulk counterpart (bZnO) on antibiotic resistance genes (ARGs) with multidrug resistance (MDR) systems being predominant (63 % of total ARGs). Proliferation of biomarker ARGs especially for last resort antibiotic like vancomycin was observed and Streptomyces hosted multiple ARGs. nZnO was the major driver of the resistome with efflux systems dominating the AR mechanism. Environmental risk associated with nZnO was mediated through metal driven co-selection of ARGs and their probable transfer to eukaryotic hosts through horizontal gene transfer (HGT) via mobile genetic elements (MGEs). Novel resistance genes tetA, mdtA, int and tnpA validated in our study can be used as biomarkers for rapid detection of nZnO toxicity in soils. qRT-PCR validation of resistome in the rhizosphere soil microbiome of turmeric indicated that Zn levels decreased by 16 % compared to bulk soil with 80 % bioaccumulation in rhizomes at 1000 mg Zn kg[-1] and subsequent down regulation of ARGs. Expression of key biosynthetic genes for curcumin in turmeric rhizomes showed an increase up to 500 mg Zn kg[-1] as nZnO. Validation of co-selection phenomenon in microcosm with 10 mg kg[-1] tetracycline without added Zn indicated 20 % upregulation of Zn resistance genes (ZRGs) like czcA, yiip and zntA.},
}

@article {pmid39699696,
year = {2024},
author = {Yagisawa, F and Fujiwara, T and Yamashita, S and Hirooka, S and Tamashiro, K and Izumi, J and Kanesaki, Y and Onuma, R and Misumi, O and Nakamura, S and Yoshikawa, H and Kuroiwa, H and Kuroiwa, T and Miyagishima, SY},
title = {A fusion protein of polyphosphate kinase 1 (PPK1) and a Nudix hydrolase is involved in inorganic polyphosphate accumulation in the unicellular red alga Cyanidioschyzon merolae.},
journal = {Plant molecular biology},
volume = {115},
number = {1},
pages = {9},
pmid = {39699696},
issn = {1573-5028},
support = {22K06299//Japan Society for the Promotion of Science/ ; 22K06396//Japan Society for the Promotion of Science/ ; 22K15166//Japan Society for the Promotion of Science/ ; 22H02657//Japan Society for the Promotion of Science/ ; 24H00579//Japan Society for the Promotion of Science/ ; JPMJMI22E1//JST-Mirai Program/ ; NIG-JOINT 68A2024//National Institute of Genetics/ ; S1311017//Ministry of Education, Culture, Sports, Science and Technology/ ; Spatiotemporal Genomics Project//University of the Ryukyus/ ; Researcher exchange promotion program//Research Organization of Information and Systems/ ; },
mesh = {*Rhodophyta/genetics/enzymology/metabolism ; *Polyphosphates/metabolism ; *Phosphotransferases (Phosphate Group Acceptor)/metabolism/genetics ; *Phylogeny ; *Nudix Hydrolases ; Pyrophosphatases/metabolism/genetics ; Recombinant Fusion Proteins/metabolism/genetics ; },
abstract = {Inorganic polyphosphate (polyP) is a linear polymer of phosphate that plays various roles in cells, including in phosphate and metal homeostasis. Homologs of the vacuolar transporter chaperone 4 (VTC4), catalyzing polyP synthesis in many eukaryotes, are absent in red algae, which are among the earliest divergent plant lineages. We identified homologs of polyphosphate kinase 1 (PPK1), a conserved polyP synthase in bacteria, in 42 eukaryotic genomes, including 31 species detected in this study and 12 species of red algae. Phylogenetic analysis suggested that most eukaryotic PPK1 homologs originated from horizontal gene transfer from a prokaryote to a plant before the divergence of red algae and Viridiplantae. In red algae, the homologs were fused to a nucleoside diphosphate-linked moiety X (Nudix) hydrolase of the diphosphoinositol polyphosphate phosphohydrolase (DIPP) family. We characterized the fusion protein CmPPK1 in the unicellular red alga Cyanidioschyzon merolae, which has been used in studies on basic features of eukaryotes. In the knockout strain ∆CmPPK1, polyP was undetectable, suggesting a primary role for CmPPK1 in polyP synthesis. In addition, ∆CmPPK1 showed altered metal balance. Mutations in the catalytically important residues of the Nudix hydrolase domain (NHD) either increased or decreased polyP contents. Both high and low polyP NHD mutants were susceptible to phosphate deprivation, indicating that adequate NHD function is necessary for normal phosphate starvation responses. The results reveal the unique features of PPK1 in red algae and promote further investigation of polyP metabolism and functions in red algae and eukaryotic evolution.},
}

*Rhodophyta/genetics/enzymology/metabolism
*Polyphosphates/metabolism
*Phosphotransferases (Phosphate Group Acceptor)/metabolism/genetics
*Phylogeny
*Nudix Hydrolases
Pyrophosphatases/metabolism/genetics
Recombinant Fusion Proteins/metabolism/genetics

@article {pmid39696916,
year = {2024},
author = {Prabhu, C and Satyaprasad, AU and Deekshit, VK},
title = {Understanding Bacterial Resistance to Heavy Metals and Nanoparticles: Mechanisms, Implications, and Challenges.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e2400596},
doi = {10.1002/jobm.202400596},
pmid = {39696916},
issn = {1521-4028},
support = {//This work was funded by the Indian Council of Medical Research (grant no. AMR/DHR/GIA/3/ECD-II/2020)./ ; },
abstract = {Antimicrobial resistance is a global health problem as it contributes to high mortality rates in several infectious diseases. To address this issue, engineered nanoparticles/nano-formulations of antibiotics have emerged as a promising strategy. Nanoparticles are typically defined as materials with dimensions up to 100 nm and are made of different materials such as inorganic particles, lipids, polymers, etc. They are widely dispersed in the environment through various consumer products, and their clinical applications are diverse, ranging from contrast agents in imaging to carriers for gene and drug delivery. Nanoparticles can also act as antimicrobial agents either on their own or in combination with traditional antibiotics to produce synergistic effects, earning them the label of "next-generation therapeutics." They have also shown great effectiveness against multidrug-resistant pathogens responsible for nosocomial infections. However, overexposure or prolonged exposure to sublethal doses of nanoparticles can promote the development of resistance in human pathogens. The resistance can arise from various factors such as genetic mutation, horizontal gene transfer, production of reactive oxygen species, changes in the outer membrane of bacteria, efflux-induced resistance, cross-resistance from intrinsic antibiotic resistance determinants, plasmid-mediated resistance, and many more. Continuous exposure to nanoparticles can also transform an antibiotic-susceptible bacterial pathogen into multidrug resistance. Considering all these, the current review focuses on the mode of action of different heavy metals and nanoparticles and possible mechanisms through which bacteria attain resistance towards these heavy metals and nanoparticles.},
}

@article {pmid39696539,
year = {2024},
author = {Pianezza, R and Haider, A and Kofler, R},
title = {GenomeDelta: detecting recent transposable element invasions without repeat library.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {315},
pmid = {39696539},
issn = {1474-760X},
support = {P35093//Austrian Science Fund (FWF)/ ; },
mesh = {*DNA Transposable Elements ; Animals ; *Drosophila melanogaster/genetics ; Software ; Ascomycota/genetics ; Gene Library ; },
abstract = {We present GenomeDelta, a novel tool for identifying sample-specific sequences, such as recent transposable element (TE) invasions, without requiring a repeat library. GenomeDelta compares high-quality assemblies with short-read data to detect sequences absent from the short reads. It is applicable to both model and non-model organisms and can identify recent TE invasions, spatially heterogeneous sequences, viral insertions, and hotizontal gene transfers. GenomeDelta was validated with simulated and real data and used to discover three recent TE invasions in Drosophila melanogaster and a novel TE with geographic variation in Zymoseptoria tritici.},
}

*DNA Transposable Elements
Animals
*Drosophila melanogaster/genetics
Software
Ascomycota/genetics
Gene Library

@article {pmid39695425,
year = {2024},
author = {Yu, L and Zhao, Y and Zhang, S and Ni, W and Zhang, L and Xue, C and Wang, P and Zhang, X},
title = {Antimicrobial resistance and virulence factors analysis of a multidrug-resistant Acinetobacter baumannii isolated from chickens using whole-genome sequencing.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {526},
pmid = {39695425},
issn = {1471-2180},
support = {32202810//National Natural Science Foundation of China/ ; ZR2022QC115//Natural Science Foundation of Shandong Province/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Acinetobacter baumannii/genetics/drug effects/pathogenicity/isolation & purification ; *Virulence Factors/genetics ; *Drug Resistance, Multiple, Bacterial/genetics ; *Whole Genome Sequencing ; *Acinetobacter Infections/microbiology/veterinary ; *Genome, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *Poultry Diseases/microbiology ; Microbial Sensitivity Tests ; Virulence/genetics ; Plasmids/genetics ; },
abstract = {Multidrug-resistant (MDR) Acinetobacter baumannii (A. baumannii) is currently recognized not only as a significant nosocomial pathogen but also is an emerging bacterial infection in food-producing animals, posing a critical threat to global health. However, this is a hindrance to detailed bioinformatic studies of MDR A. baumannii of chicken origin due to the lack of its complete genome sequence. Here, we report whole-genome sequencing analysis of MDR A. baumannii Y03 isolated from chickens. The Y03 genome consists of 1 circular chromosome and 4 circular plasmids, The Y03 chromosome harbors 41 antimicrobial resistance genes conferring resistance to major classes of antibiotics, including β-lactams, phenicols, macrolides, lincosamides, aminoglycosides, and nitrofurans, as well as 135 virulence factors involved in effector delivery system, immune modulation, adherence, stress survival, biofilm, exotoxin, and nutritional/metabolic factor. The in vivo infection experiments certificated that Y03 was virulent to chickens. Meanwhile, we used PCR amplification method to detect 10 antimicrobial resistance genes including abeM, adeB, adeH, adeK, blaapmC, blaOXA-90, catB9, macB, folP, and parE, as well as 14 virulence genes including lpxC, pilO, fimT, ompA, basA, bauA, gspL, csu, pgaC, plc2, tssA, tviB, bap, and vgrG. Whole-genome sequencing analysis revealed that Y03 contained 46 horizontal gene transfer elements, including 11 genomic islands, 30 transposons, and 5 prophages, as well as 518 mutations associated with reduced virulence and 44 mutations resulting in loss of pathogenicity. Furthermore, there were 22 antibiotic targets and 28 lethal mutations on the Y03 chromosome that could be used as potential targets to prevent, control, and treat infections caused by MDR A. baumannii Y03. Therefore, this study contributes to the development of strategies for the prevention, control, and treatment of A. baumannii infections and their spread in chickens.},
}

Animals
*Chickens/microbiology
*Acinetobacter baumannii/genetics/drug effects/pathogenicity/isolation & purification
*Virulence Factors/genetics
*Drug Resistance, Multiple, Bacterial/genetics
*Whole Genome Sequencing
*Acinetobacter Infections/microbiology/veterinary
*Genome, Bacterial/genetics
*Anti-Bacterial Agents/pharmacology
*Poultry Diseases/microbiology
Microbial Sensitivity Tests
Virulence/genetics
Plasmids/genetics

@article {pmid39694196,
year = {2024},
author = {Panigrahi, M and Rajawat, D and Nayak, SS and Jain, K and Nayak, A and Rajput, AS and Sharma, A and Dutt, T},
title = {A Comprehensive Review on Genomic Insights and Advanced Technologies for Mastitis Prevention in Dairy Animals.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107233},
doi = {10.1016/j.micpath.2024.107233},
pmid = {39694196},
issn = {1096-1208},
abstract = {Mastitis, is a multi-etiological disease that significantly impacts milk production and reproductive efficiency. This is highly prevalent in dairy populations subjected to intensive selection for higher milk yield and where inbreeding is common. The issue is amplified by climate change and poor hygiene management, making disease control challenging. Key obstacles include antibiotic resistance, maximum residue levels, horizontal gene transfer, and limited success in breeding for resistance. Predictive genomics offers a promising solution for mastitis prevention by identifying genetic traits linked with susceptibility to mastitis. This review compiles the research and findings on genomics and its allied approaches such as pan-genomics, epigenetics, proteomics, and transcriptomics for diagnosing, understanding, and treating mastitis. In dairy production, artificial intelligence (AI), particularly deep learning (DL) techniques like convolutional neural networks (CNNs), has demonstrated significant potential to enhance milk production and improve farm profitability. It highlights the integration of advanced technologies like machine learning (ML), CRISPR, and pan-genomics to enhance our knowledge of mastitis epidemiology, pathogen evolution, and the development of more effective diagnostic, preventive, and therapeutic strategies for dairy herds. Genomic advancements provide critical insights into the complexities of mastitis, offering new avenues for understanding its dynamics. Integrating these findings with key predisposing factors can drive targeted prevention and more effective disease management.},
}

@article {pmid39692564,
year = {2024},
author = {Sloan, DB and Broz, AK and Kuster, SA and Muthye, V and Peñafiel-Ayala, A and Marron, JR and Lavrov, DV and Brieba, LG},
title = {Expansion of the MutS gene family in plants.},
journal = {The Plant cell},
volume = {},
number = {},
pages = {},
doi = {10.1093/plcell/koae277},
pmid = {39692564},
issn = {1532-298X},
abstract = {The widely distributed MutS gene family functions in recombination, DNA repair, and protein translation. Multiple evolutionary processes have expanded this gene family in plants relative to other eukaryotes. Here, we investigate the origins and functions of these plant-specific genes. Cyanobacterial-like MutS1 and MutS2 genes were ancestrally gained via plastid endosymbiotic gene transfer. MutS1 was subsequently lost in seed plants, whereas MutS2 was duplicated in Viridiplantae (i.e., land plants and green algae). Viridiplantae also have two anciently duplicated copies of the eukaryotic MSH6 gene and acquired MSH1 via horizontal gene transfer - potentially from a nucleocytovirus. Despite sharing a name, "plant MSH1" is not directly related to the MSH1 gene in some fungi and animals, which may be an ancestral eukaryotic gene acquired via mitochondrial endosymbiosis and subsequently lost in most eukaryotes. There has been substantial progress in understanding the functions of plant MSH1 and MSH6 genes, but the cyanobacterial-like MutS1 and MutS2 genes remain uncharacterized. Known functions of bacterial homologs and predicted protein structures, including fusions to diverse nuclease domains, provide hypotheses about potential molecular mechanisms. Because most plant-specific MutS proteins are mitochondrial and/or plastid-targeted, the expansion of this family has played a large role in shaping plant organelle genetics.},
}

@article {pmid39690351,
year = {2024},
author = {Ullah, H and Hassan, SHA and Yang, Q and Salama, ES and Liu, P and Li, X},
title = {Dynamic interaction of antibiotic resistance between plant microbiome and organic fertilizers: sources, dissemination, and health risks.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {1},
pages = {4},
pmid = {39690351},
issn = {1573-0972},
support = {lzujbky-2024-ey12//Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Microbiota/drug effects ; *Fertilizers/analysis ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Plants/microbiology ; *Soil Microbiology ; *Bacteria/drug effects/genetics/classification ; *Manure/microbiology ; Gene Transfer, Horizontal ; Agriculture/methods ; Drug Resistance, Bacterial ; Sewage/microbiology ; Drug Resistance, Microbial/genetics ; Wastewater/microbiology ; Animals ; Soil/chemistry ; },
abstract = {Antibiotic resistance is a global health problem driven by the irrational use of antibiotics in different areas (such as agriculture, animal farming, and human healthcare). Sub-lethal concentrations of antibiotic residues impose selective pressure on environmental, plant-associated, and human microbiome leading to the emergence of antibiotic-resistant bacteria (ARB). This review summarizes all sources of antibiotic resistance in agricultural soils (including manure, sewage sludge, wastewater, hospitals/pharmaceutical industry, and bioinoculants). The factors (such as the physicochemical properties of soil, root exudates, concentration of antibiotic exposure, and heavy metals) that facilitate the transmission of resistance in plant microbiomes are discussed. Potential solutions for effective measures and control of antibiotic resistance in the environment are also hypothesized. Manure exhibits the highest antibiotics load, followed by hospital and municipal WW. Chlortetracycline, tetracycline, and sulfadiazine have the highest concentrations in the manure. Antibiotic resistance from organic fertilizers is transmitted to the plant microbiome via horizontal gene transfer (HGT). Plant microbiomes serve as transmission routes of ARB and ARGS to humans. The ingestion of ARB leads to human health risks (such as ineffectiveness of medication, increased morbidity, and mortality).},
}

*Microbiota/drug effects
*Fertilizers/analysis
Humans
*Anti-Bacterial Agents/pharmacology
*Plants/microbiology
*Soil Microbiology
*Bacteria/drug effects/genetics/classification
*Manure/microbiology
Gene Transfer, Horizontal
Agriculture/methods
Drug Resistance, Bacterial
Sewage/microbiology
Drug Resistance, Microbial/genetics
Wastewater/microbiology
Animals
Soil/chemistry

@article {pmid39689477,
year = {2024},
author = {Li, S and Wang, K and Wang, D and Wang, H and Zhao, H and Pu, J and Wang, K and Li, C},
title = {Distribution and environmental dissemination of antibiotic resistance genes in poultry farms and surrounding ecosystems.},
journal = {Poultry science},
volume = {104},
number = {1},
pages = {104665},
doi = {10.1016/j.psj.2024.104665},
pmid = {39689477},
issn = {1525-3171},
abstract = {Antibiotic resistance poses a significant threat to human and animal health worldwide, with farms serving as crucial reservoirs of Antibiotic Resistance Genes (ARGs) and Antibiotic-resistant bacteria. However, the distribution of ARGs in poultry farms and their transmission patterns in the environment remain poorly understood. This study collected samples of aerosol microorganisms, cloacal matter, soil, and vegetables from poultry farms and surrounding environments at three different distances. We used 16S rRNA gene sequencing and HT-qPCR to analyze the characteristics of aerosol microbial communities and the abundance of ARGs. At the phylum level, Proteobacteria, Firmicutes, and Bacteroidetes were dominant in cloacal samples, aerosol samples, and vegetable samples, while Proteobacteria Actinobacteriota and Acidobacteria dominated soil. Pseudomonas was dominant in cloacal samples at the genus level, whereas Fusobacterium was prevalent in soil. The diversity and richness of bacterial communities were more similar between cloacal samples than those observed between either sample type compared with soil. Our results showed that tetracycline and aminoglycoside ARG relative abundance was high across all sample types but significantly increased within feces/air compared to soils/vegetables. Association analysis revealed five potential host genera for ARG/MGE presence among various microbiota populations studied here. Our findings confirm that farms are important sources for the environmental dissemination of pathogens and ARGs.},
}

@article {pmid39686544,
year = {2024},
author = {Stott, C and Diop, A and Raymann, K and Bobay, LM},
title = {Co-evolution and Gene Transfers Drive Speciation Patterns in Host-Associated Bacteria.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msae256},
pmid = {39686544},
issn = {1537-1719},
abstract = {Microbial communities that maintain symbiotic relationships with animals evolve by adapting to the specific environmental niche provided by their host, yet understanding their patterns of speciation remains challenging. Whether bacterial speciation occurs primarily through allopatric or sympatric processes remains an open question. In addition, patterns of DNA transfers, which are pervasive in bacteria, are more constrained in a closed host-gut system. Eusocial bees have co-evolved with their specialized microbiota for over 85 million years, constituting a simple and valuable system to study the complex dynamics of host-associated microbial interactions. Here we studied the patterns of speciation and evolution of seven specialized gut bacteria from three clades of eusocial bee species: western honey bees, eastern honey bees and bumblebees. We conducted genomic analyses to infer species delineation relative to the patterns of homologous recombination (HR), and horizontal gene transfer (HGT). The studied bacteria presented various modes of evolution and speciation relative to their hosts, but some trends were consistent across all of them. We observed a clear interruption of homologous recombination between bacteria inhabiting different bee hosts, which is consistent with a mechanism of allopatric speciation, but we also identified interruptions of homologous recombination within hosts, suggesting recent or ongoing sympatric speciation. In contrast to HR, we observed that HGT events were not constrained by species borders. Overall, our findings show that in host-associated bacterial populations, patterns of HR and HGT have different impacts on speciation patterns, which are driven by both allopatric and sympatric speciation processes.},
}

@article {pmid39684674,
year = {2024},
author = {Wiśniewski, P and Chajęcka-Wierzchowska, W and Zadernowska, A},
title = {High-Pressure Processing Influences Antibiotic Resistance Gene Transfer in Listeria monocytogenes Isolated from Food and Processing Environments.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
pmid = {39684674},
issn = {1422-0067},
support = {2018/29/B/NZ9/00645 (OPUS-15)//National Science Center/ ; },
mesh = {*Listeria monocytogenes/genetics/drug effects ; *Food Microbiology ; *Anti-Bacterial Agents/pharmacology ; Food Handling/methods ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; Pressure ; Daucus carota/microbiology/genetics ; },
abstract = {The study aimed to assess the high-pressure processing (HPP) impact on antibiotic resistance gene transfer in L. monocytogenes from food and food processing environments, both in vitro (in microbiological medium) and in situ (in carrot juice), using the membrane filter method. Survival, recovery, and frequency of antibiotic resistance gene transfer analyses were performed by treating samples with HPP at different pressures (200 MPa and 400 MPa). The results showed that the higher pressure (400 MPa) had a significant effect on increasing the transfer frequency of genes such as fosX, encoding fosfomycin resistance, and tet_A1, tet_A3, tetC, responsible for tetracycline resistance, both in vitro and in situ. In contrast, the Lde gene (the gene encoding ciprofloxacin resistance) was not transferred under any conditions. In the food matrix (carrot juice), greater variability in results was observed, suggesting that food matrices may have a protective effect on bacteria and modify HPP efficacy. In general, an increase in MIC values for antibiotics was noted in transconjugants compared to donors. Genotypic analysis of transconjugants showed differences in genetic structure, especially after exposure to 400 MPa pressure, indicating genotypic changes induced by pressure stress. The study confirms the possibility of antibiotic resistance genes transfer in the food environment, even from strains showing initial susceptibility to antibiotics carrying so-called silent antibiotic resistance genes, highlighting the public health risk of the potential spread of antibiotic-resistant strains through the food chain. The findings suggest that high-pressure processing can increase and decrease the frequency of resistance gene transfer depending on the strain, antibiotic combination, and processing conditions.},
}

*Listeria monocytogenes/genetics/drug effects
*Food Microbiology
*Anti-Bacterial Agents/pharmacology
Food Handling/methods
Gene Transfer, Horizontal
Drug Resistance, Bacterial/genetics
Microbial Sensitivity Tests
Pressure
Daucus carota/microbiology/genetics

@article {pmid39671179,
year = {2024},
author = {Chen, X and Urban, JM and Wurlitzer, J and Wei, X and Han, J and E O'Connor, S and Rudolf, JD and Köllner, TG and Chen, F},
title = {Canonical terpene synthases in arthropods: Intraphylum gene transfer.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {51},
pages = {e2413007121},
doi = {10.1073/pnas.2413007121},
pmid = {39671179},
issn = {1091-6490},
mesh = {Animals ; *Alkyl and Aryl Transferases/genetics/metabolism ; *Gene Transfer, Horizontal ; *Arthropods/genetics/enzymology ; *Phylogeny ; Male ; Female ; Evolution, Molecular ; Terpenes/metabolism ; },
abstract = {Insects employ terpenoids for communication both within and between species. While terpene synthases derived from isoprenyl diphosphate synthase have been shown to catalyze terpenoid biosynthesis in some insects, canonical terpene synthases (TPS) commonly found in plants, fungi, and bacteria were previously unidentified in insects. This study reveals the presence of TPS genes in insects, likely originating via horizontal gene transfer from noninsect arthropods. By examining 361 insect genomes, we identified TPS genes in five species of the Sciaridae family (fungus gnats). Additionally, TPS genes were found in Collembola (springtails) and Acariformes (mites) among diverse noninsect arthropods. Selected TPS enzymes from Sciaridae, Collembola, and Acariformes display monoterpene, sesquiterpene, and/or diterpene synthase activities. Through comprehensive protein database search and phylogenetic analysis, the TPS genes in Sciaridae were found to be most closely related to those in Acariformes, suggesting transfer of TPS genes from Acariformes to Sciaridae. In the model Sciaridae Bradysia coprophila, all five TPS genes are most highly expressed in adult males, suggesting a sex- and developmental stage-specific role of their terpenoid products. The finding of TPS genes in insects and their possible evolutionary origin through intraphylum gene transfer within arthropods sheds light on metabolic innovation in insects.},
}

Animals
*Alkyl and Aryl Transferases/genetics/metabolism
*Gene Transfer, Horizontal
*Arthropods/genetics/enzymology
*Phylogeny
Male
Female
Evolution, Molecular
Terpenes/metabolism

@article {pmid39670763,
year = {2024},
author = {Dalia, TN and Dalia, AB},
title = {SbcB facilitates natural transformation in Vibrio cholerae in an exonuclease-independent manner.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0041924},
doi = {10.1128/jb.00419-24},
pmid = {39670763},
issn = {1098-5530},
abstract = {UNLABELLED: Natural transformation (NT) is a conserved mechanism of horizontal gene transfer in bacterial species. During this process, DNA is taken up into the cytoplasm where it can be integrated into the host genome by homologous recombination. We have previously shown that some cytoplasmic exonucleases inhibit NT by degrading ingested DNA prior to its successful recombination. However, one exonuclease, SbcB, counterintuitively promotes NT in Vibrio cholerae. Here, through a systematic analysis of the distinct steps of NT, we show that SbcB acts downstream of DNA uptake into the cytoplasm, but upstream of recombinational branch migration. Through mutational analysis, we show that SbcB promotes NT in a manner that does not rely on its exonuclease activity. Finally, we provide genetic evidence that SbcB directly interacts with the primary bacterial recombinase, RecA. Together, these data advance our molecular understanding of horizontal gene transfer in V. cholerae and reveal that SbcB promotes homologous recombination during NT in a manner that does not rely on its canonical exonuclease activity.

IMPORTANCE: Horizontal gene transfer by natural transformation contributes to the spread of antibiotic resistance and virulence factors in bacterial species. Here, we study how one protein, SbcB, helps facilitate this process in the facultative bacterial pathogen Vibrio cholerae. SbcB is a well-known for its exonuclease activity (i.e., the ability to degrade the ends of linear DNA). Through this study, we uncover that while SbcB is important for natural transformation, it does not facilitate this process using its exonuclease activity. Thus, this work helps further our understanding of the molecular events required for this conserved evolutionary process and uncovers a function for SbcB beyond its canonical exonuclease activity.},
}

@article {pmid39668116,
year = {2025},
author = {Fagerquist, CK and Shi, Y and Park, J},
title = {Colicin Immunity Proteins of Pathogenic Bacteria Detected by Antibiotic-Induced SOS Response, Plasmid Sequencing, MALDI-TOF-TOF Mass Spectrometry, and Top-Down Proteomic Analysis.},
journal = {Rapid communications in mass spectrometry : RCM},
volume = {39},
number = {5},
pages = {e9964},
doi = {10.1002/rcm.9964},
pmid = {39668116},
issn = {1097-0231},
support = {ARS project number 0500-00093-001-00-D//USDA-ARS/ ; USDA-ARS project numbers: 2030-42000-055-000-D//USDA-ARS/ ; 0500-00093-001-00-D//USDA-ARS/ ; 2030-42000-055-000-D//USDA-ARS/ ; },
mesh = {*Colicins/genetics/chemistry ; *Proteomics/methods ; *Plasmids/genetics ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; *Anti-Bacterial Agents/pharmacology ; *SOS Response, Genetics ; Escherichia coli Proteins/genetics ; Shiga-Toxigenic Escherichia coli/genetics ; Sequence Analysis, DNA ; },
abstract = {RATIONALE: Plasmids can play a major role in the survival of pathogenic bacteria. Plasmids are acquired through horizontal gene transfer resulting in their spread across various strains, species and genera of bacteria. Colicins are bacterial protein toxins expressed by plasmid genes and released against co-located bacterial competitors.

METHODS: Three Shiga toxin-producing E. coli (STEC), whose genomes were sequenced previously, were analyzed using a combination of antibiotic induction, MALDI-TOF-TOF mass spectrometry, top-down proteomic analysis, and small plasmid sequencing. Protein biomarkers were identified using in-house software that matches protein mass and fragment ions of backbone cleavage by the aspartic acid effect. Predicted in silico protein structures assisted in the interpretation of protein ion fragmentation.

RESULTS: In addition to proteomic identification of phage-encoded Shiga toxin, we were able to identify plasmid-encoded immunity proteins for colicin D and E3. The genes for these plasmid-encoded proteins were not found in the previous genomic sequencing. However, resequencing of these strains for small plasmids revealed the genes to be present on 7-8 kb sized plasmids. Upstream of the colicin/immunity genes was an inverted repeat of the SOS/LexA box that represses gene expression until antibiotic challenge.

CONCLUSIONS: Our top-down proteomic method demonstrates that it is possible to screen putative pathogenic bacteria (whose genomes have been sequenced in full, in part or not at all) for the presence of phage- and plasmid-encoded toxin and colicin genes under SOS control. Small plasmid sequencing confirmed the presence of colicin/immunity genes (and their regulatory control) suggested from induction and top-down proteomic analysis.},
}

*Colicins/genetics/chemistry
*Proteomics/methods
*Plasmids/genetics
*Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
*Anti-Bacterial Agents/pharmacology
*SOS Response, Genetics
Escherichia coli Proteins/genetics
Shiga-Toxigenic Escherichia coli/genetics
Sequence Analysis, DNA