@article {pmid40706155,
year = {2025},
author = {Wang, YC and He, LY and Wu, HY and Qiao, LK and Huang, Z and Bai, H and Gao, FZ and Shi, YJ and Zhao, JL and Liu, YS and Ying, GG},
title = {High-risk plasmid-borne resistance genes from swine farm environments infiltrate deep soil and interact with the human gut microbiome via horizontal transfer.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139281},
doi = {10.1016/j.jhazmat.2025.139281},
pmid = {40706155},
issn = {1873-3336},
abstract = {Swine farms serve as critical reservoirs of antibiotic resistance genes (ARGs), yet the frequency of horizontal gene transfer (HGT) remains poorly understood. In this study, we explored the gene exchange within the "swine farm-human-pig" network and assessed its risks. We identified 16,612 plasmid contigs from 107 field samples, revealing a significant presence of previously uncharacterized plasmid types. Notably, 52.88 % of acquired ARGs were located on plasmids, with 71.22 % containing at least one mobile genetic element (MGE). We quantified HGTs at the microbial community level among the human gut, pig gut, and swine farm environments. Among 4687 metagenome-assembled genomes (MAGs), 3008 were involved in 11,250 HGTs. HGT linkages were most frequently identified between microbial genomes from the swine farm and the human gut microbiome. ARGs were involved in 91 HGT events, with 645 events linked to MGEs and 16 related to virulence factors, suggesting potential cross-species transmission of clinical pathogens. The detection of 32 Rank I ARGs and the identification of increased resistome risks underscore the extensive dispersion of livestock-related contaminants into more distant environmental compartments. This study elucidates the complexities of gene exchange networks in swine farm environments, underscoring the urgent need for strategies to mitigate risks associated with the antibiotic resistome.},
}

@article {pmid40704322,
year = {2025},
author = {Nazir, A and Nazir, A and Zuhair, V and Aman, S and Sadiq, SUR and Hasan, AH and Tariq, M and Rehman, LU and Mustapha, MJ and Bulimbe, DB},
title = {The Global Challenge of Antimicrobial Resistance: Mechanisms, Case Studies, and Mitigation Approaches.},
journal = {Health science reports},
volume = {8},
number = {7},
pages = {e71077},
pmid = {40704322},
issn = {2398-8835},
abstract = {BACKGROUND AND AIMS: Antimicrobial resistance (AMR) is projected to cause 10 million deaths annually by 2050 if left unaddressed, posing a severe threat to global health and modern medicine. This review analyzes the molecular and ecological mechanisms underlying antibiotic resistance and evaluates global efforts aimed at containment to identify actionable strategies to mitigate AMR's escalating impact.

METHODS: A systematic literature review was performed using databases including PubMed, ScienceDirect, Scopus, Google Scholar, and Web of Science, focusing on peer-reviewed studies from 2000 to 2024. Search terms included "antibiotic resistance," "resistance mechanisms," "horizontal gene transfer," and "AMR epidemiology." A total of 152 articles were selected based on predefined inclusion criteria relevant to resistance mechanisms, epidemiological data, clinical outcomes, and public health interventions.

RESULTS: Findings underscore three dominant resistance pathways: target site modification, enzymatic degradation (e.g., β-lactamases), and horizontal gene transfer via plasmids and transposons. Notably, resistance to last-resort antibiotics (e.g., colistin, carbapenems) is rising in pathogens such as Klebsiella pneumoniae and Acinetobacter baumannii, with treatment failure rates exceeding 50% in some regions. Surveillance gaps and unregulated antibiotic use, especially in LMICs, further accelerate resistance spread. Only a limited number of new antibiotic classes have been approved since 2010, underscoring the innovation gap.

CONCLUSION: AMR is a quantifiable, escalating crisis that undermines decades of progress in infectious disease control. Tackling it requires coordinated action: strengthening antimicrobial stewardship, incentivizing antibiotic R&D, integrating environmental and clinical surveillance under One Health frameworks, and implementing global policy reforms. Without prompt action, AMR could surpass cancer in annual mortality by mid-century.},
}

@article {pmid40701356,
year = {2025},
author = {Hu, L and Ye, Y and Li, Y and Tan, X and Liu, X and Zhang, T and Wang, J and Du, Z and Ye, M},
title = {Bacteria-algae synergy in carbon sequestration: Molecular mechanisms, ecological dynamics, and biotechnological innovations.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {108655},
doi = {10.1016/j.biotechadv.2025.108655},
pmid = {40701356},
issn = {1873-1899},
abstract = {Rising atmospheric CO2 levels require innovative strategies to increase carbon sequestration. Bacteria-algae interactions, as pivotal yet underexplored drivers of marine and freshwater carbon sinks, involve multiple mechanisms that amplify CO2 fixation and long-term storage. This review systematically describes the synergistic effects of bacteria-algae consortia spanning both microalgae (e.g., Chlorella vulgaris and Phaeodactylum tricornutum) and macroalgae (e.g., Macrocystis and Laminaria) on carbon sequestration. These effects include (1) molecular-level regulation (e.g., signal transduction via N-acyl-homoserine lactones (AHLs), and horizontal gene transfer), (2) ecological facilitation of recalcitrant dissolved organic carbon (RDOC) formation, and (3) biotechnological applications in wastewater treatment and bioenergy production. We highlight that microbial crosstalk increases algal photosynthesis by 20-40 % and contributes to 18.9 % of kelp-derived RDOC storage. Furthermore, engineered systems integrating algal-bacterial symbiosis achieve greater than 80 % nutrient removal and a 22-35 % increase in CO2 fixation efficiency (compared with axenic algal systems), demonstrating their dual role in climate mitigation and a circular economy. This review is the first to integrate molecular mechanisms (e.g., quorum sensing), ecological carbon transformation processes (e.g., the formation of RDOC), and applications in synthetic biology (e.g., CRISPR-engineered consortia) into a unified framework. Moreover, the novel strategy "microbial interaction network optimization" for enhancing carbon sinks is proposed. However, scalability challenges persist, including light limitations in photobioreactors and the ecological risks of synthetic consortia. By bridging microbial ecology with synthetic biology, this work provides a roadmap for harnessing bacteria-algae synergy to achieve carbon neutrality.},
}

@article {pmid40700401,
year = {2025},
author = {Grooters, SV and Mollenkopf, DF and Wittum, TE},
title = {The genetic context of blaIMP varies among bacterial families from One Health sources.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0327200},
doi = {10.1371/journal.pone.0327200},
pmid = {40700401},
issn = {1932-6203},
mesh = {DNA Transposable Elements/genetics ; *beta-Lactamases/genetics ; Plasmids/genetics ; Integrons/genetics ; *Bacteria/genetics/isolation & purification/drug effects ; Humans ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; Shewanella/genetics ; },
abstract = {The blaIMP resistance gene encodes a metallo-beta-lactamase in bacteria, which confers reduced susceptibility or resistance to all the beta-lactams, including carbapenems which are critical for treating life-threatening infections. The dissemination of blaIMP among various taxonomic families shows the diversity and range of horizontal gene transfer. Using short-read whole genome sequencing and bioinformatic tools, we determined the genetic motifs surrounding blaIMP present in 32 bacterial isolates recovered from environmental sources and agriculture facilities. blaIMP can be located extra-chromosomally on plasmids or within incomplete and complete Tn7 chromosomal structures. We identified a complete Tn7 transposon harboring the blaIMP-27 gene cassette within a class 2 integron located in chromosomal contigs of Shewanella spp. and Providencia spp. Acinetobacter spp. isolates were observed with truncated and incomplete Tn7 transposons, while conserving the class 2 integron and resistance gene cassettes. Additionally, IncQ1 plasmids carried by Proteus spp., Escherichia coli, and other Enterobacteriaceae spp. harbored class 2 integrons with blaIMP-64 and sat2 resistance gene cassettes. In an Acidovorax sp. isolate, blaIMP-27 and sat2 gene cassettes were found associated with an insertion sequence, ISL3 transposase, in an RP4 plasmid. The conserved structure of Tn7 in Shewanella spp. and Providencia spp. is consistent with these species being potential reservoirs from which other bacterial species have acquired partial Tn7 motifs, and the blaIMP-27 gene cassette. These data contribute to a broader understanding of the dissemination and temporality of blaIMP alleles and their mobile genetic elements.},
}

DNA Transposable Elements/genetics
*beta-Lactamases/genetics
Plasmids/genetics
Integrons/genetics
*Bacteria/genetics/isolation & purification/drug effects
Humans
Gene Transfer, Horizontal
Anti-Bacterial Agents/pharmacology
Shewanella/genetics

@article {pmid40699345,
year = {2025},
author = {Schöllkopf, AI and Ehrenreich, A and Liebl, W},
title = {SMC-like Wadjet system prevents plasmid transfer into Clostridium cellulovorans.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {170},
pmid = {40699345},
issn = {1432-0614},
support = {161B0930//German Federal Ministry of Education and Research/ ; 161B0930//German Federal Ministry of Education and Research/ ; 161B0930//German Federal Ministry of Education and Research/ ; },
mesh = {*Plasmids/genetics ; *Conjugation, Genetic ; *Gene Transfer, Horizontal ; *Clostridium cellulovorans/genetics ; *Chromosomes, Bacterial/genetics ; },
abstract = {This study demonstrates the impact of a Structure Maintenance of Chromosome (SMC)-like Wadjet system on the horizontal gene transfer of plasmids by conjugation to a recipient that naturally containing such a system for the first time. A Clostridium cellulovorans mutant with dramatically improved efficiency to receive plasmid DNA by conjugation was isolated and sequenced. Three spontaneous chromosomal deletions included a type II restriction-modification system, a putative CRISPR system, and a cluster of ORFs named jetABCD encoding a putative Wadjet system. Since nearly nothing is known about the role of naturally occurring Wadjet systems in their native host bacteria, markerless chromosomal deletion of jetABCD in the C. cellulovorans wildtype strain 743B was achieved and the effect on conjugative plasmid uptake was studied. The transconjugation frequency of the jetABCD mutant was increased by about five orders of magnitude compared to wildtype C. cellulovorans recipient cells. Bioinformatic analysis of genome sequences of the Bacillota phylum revealed near-complete mutually exclusive possession of either plasmids < 40 kb or jetABCD genes, indicating high efficiency of Wadjet systems in small plasmid prevention in bacteria. Importantly, the implications of this study go beyond the case of C. cellulovorans. Our study demonstrates that the eradication of Wadjet systems can dramatically improve the uptake of recombinant plasmids and thereby enhance genetic engineering of bacterial strains of interest for biotechnological applications. KEY POINTS: • Native Wadjet system inhibits plasmid transfer by conjugation in C. cellulovorans • Deleting jetABCD increased plasmid uptake by about five orders of magnitude • Possession of Wadjet systems efficiently block plasmid maintenance in Bacillota.},
}

*Plasmids/genetics
*Conjugation, Genetic
*Gene Transfer, Horizontal
*Clostridium cellulovorans/genetics
*Chromosomes, Bacterial/genetics

@article {pmid40698896,
year = {2025},
author = {Van Agtmaal, JL and Verheul, M and Vonken, L and Helsen, K and Vargas Guerrero, MG and Van Hoogstraten, SWG and Hurck, BJ and Pilla, G and Trinh, I and De Bruijn, GJ and Calum, HP and De Boer, MGJ and Pijls, BG and Arts, JJC},
title = {Antimicrobial resistance in orthopedics: microbial insights, clinical impact, and the necessity of a multidisciplinary approach-a review.},
journal = {Acta orthopaedica},
volume = {96},
number = {},
pages = {555-568},
doi = {10.2340/17453674.2025.43477},
pmid = {40698896},
issn = {1745-3682},
mesh = {Humans ; *Prosthesis-Related Infections/microbiology/drug therapy/prevention & control ; *Drug Resistance, Bacterial ; *Anti-Bacterial Agents/therapeutic use ; Antimicrobial Stewardship ; *Orthopedic Procedures ; Orthopedics ; },
abstract = {Antimicrobial resistance (AMR) is rising globally and is a threat and challenge for orthopedic surgery, particularly in managing prosthetic joint infections (PJIs). This review first explores several AMR mechanisms from a microbiological point of view, including selective pressure, horizontal gene transfer, and further dissemination. Second, the variation in the rise of AMR across countries is highlighted, including its impact on PJI. While countries with the highest AMR rates are expected to experience the most significant burden, no country will be immune to the increasing prevalence of PJI. Third, this review stresses that multidimensional strategies are needed to combat AMR's challenges in orthopedic surgery. These include raising awareness across all sectors, including healthcare professionals, the public, healthcare policymakers, and even politicians; advancing diagnostic technologies for early infection detection and classification of resistant or susceptible strains; promoting antibiotic stewardship; and developing new material technologies to prevent or cure PJI. This review highlights the urgent need for a coordinated response from clinicians, researchers, and policymakers to avoid AMR-related complications in PJI cases.},
}

Humans
*Prosthesis-Related Infections/microbiology/drug therapy/prevention & control
*Drug Resistance, Bacterial
*Anti-Bacterial Agents/therapeutic use
Antimicrobial Stewardship
*Orthopedic Procedures
Orthopedics

@article {pmid40698825,
year = {2025},
author = {Fässler, N and de Arriba, M and Biggel, M and Jelocnik, M and Borel, N and Marti, H},
title = {Development of shuttle vector-based transformation systems for veterinary and zoonotic chlamydiae.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0164125},
doi = {10.1128/spectrum.01641-25},
pmid = {40698825},
issn = {2165-0497},
abstract = {In veterinary medicine, the obligate intracellular bacteria Chlamydia (C.) abortus, Chlamydia caviae, and Chlamydia pecorum are known to cause ovine enzootic abortion, conjunctivitis in guinea pigs, and ocular/urogenital disease in koalas, respectively. Studying the biology of these bacteria has been challenging due to a dearth of genetic tools. This study aimed to establish stable transformation systems for C. abortus, C. pecorum, and C. caviae by introducing shuttle vectors carrying green fluorescent proteins. With the aim to select the most suitable green fluorescent protein for the tracking of chlamydiae in vitro, we further compared the fluorescence intensity of GFP to that of mNeonGreen. Transformed shuttle vectors comprised the native plasmid of the chlamydial species of interest, an Escherichia coli origin of replication (ori), a beta-lactamase (bla) or spectinomycin (aadA) resistance gene, and GFP or mNeonGreen for heterologous fluorescence expression. We compared the success of a C. suis-tailored transformation protocol (Protocol A) to that of an alternative protocol for C. psittaci and C. trachomatis (Protocol B), both of which employ calcium chloride for competence induction. Stable transformants were obtained for C. pecorum and C. caviae using protocols A and B, respectively, and we found that the fluorescence intensity of heterologously expressed GFP is higher than that of mNeonGreen. In contrast, pre-incubation with trypsin-EDTA prior to the application of calcium chloride was needed to obtain transformants of C. abortus. In summary, we established protocols for stable calcium chloride-mediated transformation for C. pecorum and C. abortus and expanded upon the genetic toolbox of C. caviae.IMPORTANCEChlamydiae are a diverse group of bacteria impacting human and animal health. Many of the veterinary species, such as Chlamydia abortus, Chlamydia caviae, and Chlamydia pecorum, which cause reproductive disorders and/or conjunctivitis, are zoonotic pathogens leading to a potentially life-threatening disease in humans. Our understanding of these species has been hampered due to a lack of genetic tools. In this study, we developed calcium chloride-mediated transformation protocols for each of these species: chlamydiae are mixed with shuttle vectors containing the complete species-specific plasmid sequence, an Escherichia coli origin of replication, and an antibiotic resistance gene for selection. We could further show that certain chlamydial species become more susceptible to genetic modification if they are pre-treated with trypsin-EDTA prior to the addition of calcium chloride and the vector of interest. Overall, we demonstrate that species-specific protocol refinement is indispensable to render chlamydiae competent for genetic transformation.},
}

@article {pmid40698728,
year = {2025},
author = {Qi, W and Tang, X and Huang, Y and Ma, S and Wang, J and Gao, B and Pang, J and Du, J and Wang, P and Zhan, S and Ni, BJ and Xu, S},
title = {Electron Transfer Expressway from Peroxydisulfate to O2 Mediated by Diatomic Sites Accelerating [1]O2 Production for Disinfection.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c01975},
pmid = {40698728},
issn = {1520-5851},
abstract = {Current studies on high-density single-atom catalysts (SACs) with the coexistence of single atomic and diatomic sites have ignored the underlying contribution of diatomic sites for persulfate-based disinfection technology. Herein, high-density atomic Ni anchored on N-doped carbon (Ni1-NC) containing abundant Ni diatomic (Ni2-N6) sites, was fabricated, exhibiting superior peroxydisulfate (PDS) activation to generate singlet oxygen ([1]O2) for disinfection compared with other M1-NC, due to the fact that Ni1-NC possessed the highest negative crystal orbital Hamilton population value. A dynamic promotion effect toward disinfection, relying on the level of external O2 was discovered. This promotion effect was achieved through the cooperation of PDS and O2 which was mediated by Ni2-N6 sites bridging electron transfer from PDS to O2, thereby suppressing the energy barriers of rate-determining steps. Disinfection with decreased horizontal gene transfer was achieved by disrupting coenzyme Q, inhibiting adenosine triphosphate synthesis, and degrading extracellular polymeric substances via [1]O2. A continuous flow system based on a Ni1-NC@sponge fixed reaction bed displayed persistent disinfection for 336 h under aeration. This work presents a transboundary integrated PDS disinfection strategy combining physical aeration and chemical oxidation through tailoring diatomic sites in SACs.},
}

@article {pmid40696136,
year = {2025},
author = {Tobin, LA and Lam, MMC and Hamidian, M},
title = {Pan-genus analysis and typing of antimicrobial resistance plasmids in Acinetobacter.},
journal = {npj antimicrobials and resistance},
volume = {3},
number = {1},
pages = {65},
pmid = {40696136},
issn = {2731-8745},
support = {APP2009163//National Health and Medical Research Council Investigator Grant/ ; },
abstract = {Plasmids play a central role in horizontal gene transfer and bacterial adaptation, especially in the context of antimicrobial resistance (AMR) among opportunistic pathogens. Some members of the genus Acinetobacter are known for their role in hospital-acquired infections, harboring plasmids that facilitate rapid adaptation to selective pressures. However, the extent of plasmid diversity and evolutionary dynamics within Acinetobacter has not been fully elucidated. In this study, we analysed 1846 complete and non-redundant Acinetobacter plasmid sequences, identifying 166 novel Replicase (Rep) protein types and providing a significant update to the Acinetobacter Plasmid Typing (APT) scheme, which now comprises 257 Rep types. A detailed phylogenetic analysis of the prevailing R3-type Rep sequences reveals two distinct evolutionary clades (A and B) and several additional subclades. This phylogenetic structure suggests evolutionary pressures within all clades, potentially influenced by host species distribution and environmental factors. Analysis of these plasmids highlights diverse plasmid types involved in dissemination of AMR within the genus in different niches, underscoring both clinical and natural environments as reservoirs of Acinetobacter plasmids. Our findings provide a refined framework for tracking Acinetobacter plasmids, advancing our understanding of plasmid-mediated AMR spread and informing strategies to combat the spread of AMR in this critical genus.},
}

@article {pmid40694848,
year = {2025},
author = {Garcillán-Barcia, MP and de la Cruz, F and Rocha, EPC},
title = {The extended mobility of plasmids.},
journal = {Nucleic acids research},
volume = {53},
number = {14},
pages = {},
doi = {10.1093/nar/gkaf652},
pmid = {40694848},
issn = {1362-4962},
support = {PIA/ANR-16-CONV-0005//Institut Pasteur/ ; ANR-10-LABX-62-IBEID//Laboratoire d'Excellence IBEID Integrative Biology of Emerging Infectious Diseases/ ; MCIN/AEI/10.13039/501100011033 PID2020-117923GB-I00//Spanish Ministry of Science and Innovation/ ; },
mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Bacteria/genetics ; Humans ; Conjugation, Genetic ; Interspersed Repetitive Sequences ; Bacteriophages/genetics ; },
abstract = {Plasmids play key roles in the spreading of many traits, ranging from antibiotic resistance to varied secondary metabolism, from virulence to mutualistic interactions, and from defense to antidefense. Our understanding of plasmid mobility has progressed extensively in the last few decades. Conjugative plasmids are still often the textbook image of plasmids, yet they are now known to represent a minority. Many plasmids are mobilized by other mobile genetic elements, some are mobilized as phages, and others use atypical mechanisms of transfer. This review focuses on recent advances in our understanding of plasmid mobility, from the molecular mechanisms allowing transfer and evolutionary changes of plasmids to the ecological determinants of their spread. In this emerging, extended view of plasmid mobility, interactions between mobile genetic elements, whether involving exploitation, competition, or elimination, affect plasmid transfer and stability. Likewise, interactions between multiple cells and their plasmids shape the latter patterns of transfer through transfer-mediated bacterial predation, interference, or eavesdropping in cell communication, and by deploying defense and antidefense activity. All these processes are relevant for microbiome intervention strategies, from plasmid containment in clinical settings to harnessing plasmids in ecological or industrial interventions.},
}

*Plasmids/genetics
*Gene Transfer, Horizontal
*Bacteria/genetics
Humans
Conjugation, Genetic
Interspersed Repetitive Sequences
Bacteriophages/genetics

@article {pmid40694305,
year = {2025},
author = {Marcharla, E and Vishnuprasadh, A and Gnanasekaran, L and Vinayagam, S and Sundaram, T and Ganesan, S},
title = {The Role of Functional Feed in Modulating Fish Gut Microbiome to Enhance Resistance Against Aquaculture Pathogens.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40694305},
issn = {1867-1314},
abstract = {The gut microbiome, comprising of diverse microbial species, plays a critical role in the immunological responses and physiological functions of fish. Functional feed components such as probiotics, prebiotics, immunostimulants (e.g. β-glucans), and bioactive compounds (e.g. phenolic compounds and terpenes) enhance disease resistance and overall health. This review highlights the diversity and composition of the fish gut microbiome and its significant role in immune modulation. It examines the ability of functional feed components, microbiome-associated metabolites, including antimicrobial peptides, bile acids, and short-chain fatty acids (SCFAs), to influence the fish immune system. Also, it focuses on the role of extracellular vesicles and quorum-sensing molecules in modulating gut health. Furthermore, high-throughput metabolomics techniques, such as gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance (NMR) spectroscopy, are utilised to analyse gut microbiome metabolites and optimise functional feeds. These characterisation techniques effectively detect the metabolites released in the microbiota for better feed utilisation. Functional feeds enhance growth performance by helping the fish to maintain stable gut microbiota, thus reducing the dependency on antibiotics. This review clearly establishes the transformative potential of different functional feeds for enhancing and promoting sustainable aquaculture practices. However, challenges such as horizontal gene transfer and long-term ecological impacts of microbiome alterations persist. Also, economic feasibility, regulations, and biosafety considerations may affect the widespread use of these functional feeds. Future studies should focus on refining feed formulations, understanding host-microbiome interactions, and leveraging advanced omics technologies to ensure ecological and economic sustainability in aquaculture systems.},
}

@article {pmid40693147,
year = {2025},
author = {Mageto, LM and Aboge, GO and Mekuria, ZH and Gathura, P and Juma, J and Mugo, M and Kebenei, CK and Imoli, D and Ongadi, BA and Kering, K and Mbae, CK and Kariuki, S},
title = {Genomic characterization of Vibrio cholerae isolated from clinical and environmental sources during the 2022-2023 cholera outbreak in Kenya.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1603736},
pmid = {40693147},
issn = {1664-302X},
abstract = {BACKGROUND: Cholera remains a public health challenge in Kenya. To better understand its dynamics, we analyzed Vibrio cholerae genomes from clinical and environmental samples collected during the 2022-2023 outbreak. These strains were compared with historical genomes from Kenya, Uganda, Tanzania, and Haiti to inform strategies for cholera prevention, control, and elimination in Kenya.

METHODS: Clinical (stool) and environmental (wastewater, drinking water, and household effluent) samples were collected from Nairobi county. Samples were analyzed for V. cholerae using culture and real time PCR. The environmental (n = 17) and clinical (n = 70) isolates were then subjected to phenotypic antimicrobial susceptibility testing using the Kirby-Bauer disk diffusion method. Whole genome sequencing was employed to characterize the genome, detect antimicrobial resistance genes, virulence factors, and mobile genetic elements. Phylogenetic analysis was performed to assess the genetic relationship and diversity of isolates from 2022 to 2023 outbreak, comparing them with isolates from historical outbreaks.

RESULTS: Clinical isolates carried key virulence genes (ctxA, ctxB7, zot, and hlyA) and were 100% resistant to multiple antibiotics, including ampicillin, cefotaxime, ceftriaxone, and cefpodoxime, but remained susceptible to gentamicin and chloramphenicol. In contrast, environmental isolates lacked ctxB gene but harbored toxR, als, and hlyA, showing variable antibiotic resistance (59% to ampicillin, 41% to trimethoprim-sulfamethoxazole, and 47% to nalidixic acid). All clinical isolates from 2022 to 2023 outbreak harbored IncA/C2 plasmids and several antimicrobial resistance genes including bla PER-7. Phylogenetic analysis revealed high genetic diversity in environmental strains, clustering outside the 7th pandemic El Tor lineage, while clinical isolates were highly clonal. Genomes from 2022 to 2023 outbreak were closely related to Kenyan cholera outbreak genomes from 2016 (15 single nucleotide polymorphisms, T13 lineage).

CONCLUSION: The 2022-2023 outbreak likely resulted from re-emergence of previously circulating strains rather than a new introduction. While the role of environmental reservoirs as a source of human infection remains unclear in our study, environmental isolates possess virulent and antimicrobial resistance genes that may spread via horizontal gene transfer. This highlights the need for continuous genomic surveillance to monitor V. cholerae evolution, track transmission patterns, and mitigate the spread of antimicrobial resistance.},
}

@article {pmid40693145,
year = {2025},
author = {Yao, Z and Yang, Y and Gong, Y and Shi, S and Ge, Y and Zeng, W and Zhao, D and Cao, J and Zhou, T and Shen, M},
title = {The ecological security risks of bronopol: a focus on antibiotic resistance gene dissemination.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1595833},
pmid = {40693145},
issn = {1664-302X},
abstract = {Disinfectants are commonly utilized by humans to combat microorganisms. However, residual disinfectants may promote environmental antimicrobial resistance by facilitating horizontal gene transfer (HGT) of antibiotic resistance genes. Bronopol is a routinely used disinfectant that persists in the environment, and previous studies have concentrated on its ecotoxicity rather than its implications on the propagation of resistance genes. This study aimed to establish an in vitro conjugation model to investigate whether bronopol promotes the transfer of antibiotic resistance genes (ARGs) via plasmid conjugation. Using Escherichia coli DH5α and DC8855 as donors harboring RP4-7 and bla NDM-4-positive IncFII(K) plasmids, respectively, and J53 as the recipient strain, we found that sub-inhibitory concentrations of bronopol (2 μg/L and 20 μg/L) significantly increased the conjugative transfer frequency (CTF) of both plasmids. Mechanistic analysis revealed that bronopol enhanced bacterial membrane permeability, as demonstrated by propidium iodide (PI) staining, 1-N-phenylnaphthylamine (NPN) fluorescent probes, transmission electron microscopy (TEM), and upregulation of the outer membrane protein gene ompC. Additionally, bronopol treatment upregulated RP4 plasmid-encoded genes involved in DNA transfer/replication (trfAp) and the global regulator of HGT (kilA/kilB). These findings highlight a previously unrecognized role of bronopol in facilitating the dissemination of antibiotic resistance genes, particularly those of clinical significance.},
}

@article {pmid40689446,
year = {2025},
author = {Gong, C and Liu, Y and Hu, Y and Luo, C and Zhang, Y and Guo, Z},
title = {The plant-derived Bt11S gene in whitefly: a key player in reproduction and RNAi-based pest management.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70067},
pmid = {40689446},
issn = {1526-4998},
support = {2021YFD1400600//National Key R & D Program of China/ ; 32221004//National Natural Science Foundation of China/ ; GZB20240839//Postdoctoral Fellowship Program of CPSF/ ; 2024M753572//China Postdoctoral Science Foundation/ ; CARS-23//Earmarked Fund for CARS/ ; //Beijing Key Laboratory for Pest Control and Sustainable Cultivation of Vegetables/ ; JCKJ2025-CG-01//Agricultural Science and Technology Innovation Program/ ; },
abstract = {BACKGROUND: Horizontal gene transfer (HGT), an understudied evolutionary phenomenon, influences host adaptation and reproduction in insects while providing novel targets for pest control. The whitefly Bemisia tabaci Mediterranean (MED) is a globally invasive pest known for its rapid reproduction and adaptability, which make it an ideal model for investigating HGT functions. In this study, we explored the role of the plant-derived Bt11S (11S globulin seed storage protein) in B. tabaci MED reproduction and assessed its potential for biocontrol applications.

RESULTS: Our results suggested that Bt11S was horizontally transferred from plants to whitefly, and the exact transfer location was determined on scaffold 1. Expression profiling analysis revealed significant Bt11S expression in B. tabaci adults, with widespread distribution across various organs. RNA interference (RNAi)-mediated silencing of Bt11S led to a marked reduction in whitefly fecundity, accompanied by depletion of the 11S protein and amino acids, underscoring the essential role of this gene in nutrient allocation for reproduction. Long-term suppression of the gene via virus-induced gene silencing (VIGS) consistently impaired whitefly fecundity, demonstrating its potential for pest control.

CONCLUSION: Our findings establish Bt11S, a plant-derived gene, as a multifunctional protein involved in B. tabaci reproductive fitness that is associated with amino acids and feeding. This discovery provides insight into eukaryotic HGT and positions Bt11S as a promising target for RNAi-based pest control strategies. By selectively targeting pest-specific HTGs, this approach provides an environmentally sustainable solution for managing B. tabaci infestations while minimizing impacts on nontarget organisms. © 2025 Society of Chemical Industry.},
}

@article {pmid40687859,
year = {2025},
author = {Yu, H and Li, J and Wang, Y and Zhang, T and Mehmood, T and Habimana, O},
title = {Dysbiosis and genomic plasticity in the oily scalp microbiome: a multi-omics analysis of dandruff pathogenesis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1595030},
pmid = {40687859},
issn = {1664-302X},
abstract = {INTRODUCTION: Dandruff, affecting ~50% of the global population, is a prevalent scalp condition linked to microbial dysbiosis and inflammation, significantly impacting quality of life.

METHODS: This study employed an integrative omics approach, utilizing 16S rRNA and ITS1 amplicon sequencing alongside shotgun metagenomics, to analyze the scalp microbiome of 65 individuals with varying scalp conditions (healthy oily, healthy non-oily, and dandruff oily).

RESULTS: Distinct microbial profiles were identified, with an increased abundance of pathogenic genera such as Staphylococcus in the dandruff oily (DO) group, contrasted with the presence of Cutibacterium in healthy cohorts.

DISCUSSION: Functional profiling revealed elevated DNA repair mechanisms in the DO group, indicative of stress stemming from pathogen overgrowth, while healthy non-oily samples demonstrated enhanced functions for scalp homeostasis. Notably, the increase in genomic plasticity in the DO group, characterized by antimicrobial resistance genes and mobile elements, underscores the complex interplay of microbial dynamics in dandruff pathology, advocating for microbiome-targeted therapies.},
}

@article {pmid40684596,
year = {2025},
author = {Mendonça, RS and de Souza, AJ and Leal, RMP and Osti, JF and Oliveira, RL and Regitano, JB},
title = {Industrial composting of sewage sludge mitigates antimicrobial resistance risks and preserves bacterial dynamics in tropical soils.},
journal = {Journal of environmental management},
volume = {391},
number = {},
pages = {126656},
doi = {10.1016/j.jenvman.2025.126656},
pmid = {40684596},
issn = {1095-8630},
abstract = {Industrial-scale thermophilic composting of sewage sludge (SS) offers a promising strategy to reduce antimicrobial resistance risks in agricultural soils, although the impacts of its application on soils remain unclear. This study evaluated the impact of SS compost, produced thermophilically with and without lime, on antibiotic resistance genes (ARGs) related to fluoroquinolones, sulfonamides, and tetracyclines, mobile genetic elements (MGEs), and bacterial communities in tropical clay and sandy loam soils over 100 days, using high-throughput qPCR and 16S rRNA gene sequencing. Actinobacteriota followed by Pseudomonadota, Chloroflexota, Acidobacteriota, and Bacteroidota dominated both soils, representing 80-96 % of total community. Fresh SS reduced microbial complexity and transiently enhanced ARGs (mainly sulfonamides) as well as MGEs (transposon and integrons), and enriched potential ARG hosts. Non-limed compost (NLC) initially disrupted bacterial community richness, diversity, and structure, reducing Pseudomonadota and Acidobacteriota abundances by 15 % and 5 %, respectively, while increasing Actinobacteriota by 19 % in average at both soils. Industrial composting effectively reduced ARGs, especially sulfonamide-related genes, with transposons and integrons playing central roles in early dissemination. Lime addition did not enhance ARG reduction but improved compost stability and briefly increased microbial diversity. Genera such as Atopobium, Candidatus Competibacter, Clostridium sensu stricto, Coxiella, Kocuria, Lysinibacillus, Micrococcus, Nocardiopsis, Paeniclostridium, and Terrisporobacter were identified as potential ARG carriers. These findings support industrial composting as a viable strategy to mitigate AMR risks while preserving microbial integrity in tropical agroecosystems. However, long-term studies are still needed to assess ARG persistence, horizontal gene transfer, and environmental transmission routes, mainly under tropical field conditions.},
}

@article {pmid40682888,
year = {2025},
author = {Wang, J and Zhou, Y and Li, X and Song, T and Ma, R and Yang, Y and Yin, J and Jiang, T and Li, G and Chang, J and Yuan, J},
title = {The hot air circulation ventilation composting system removes antibiotic resistance genes through competitive inhibition by core bacteria.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139239},
doi = {10.1016/j.jhazmat.2025.139239},
pmid = {40682888},
issn = {1873-3336},
abstract = {Livestock manure is a significant reservoir of antibiotic resistance genes (ARGs). Aerobic composting technology can produce mature compost while effectively removing ARGs. In this study, we developed an energy-saving and emission-reducing hot air circulating ventilated composting technology (HACV), which had no adverse effects on the composting process or compost maturity. The HACV composting altered bacterial communities, primarily driven by heterogeneous selection among deterministic factors (65 %). Specifically, it increased the complexity of bacterial networks and promoted the colonization of high-temperature-tolerant bacteria, such as Erysipelothrix, Oceanobacillus and unclassified_f_Bacillaceae. Topological analysis revealed that core bacteria primarily functioned as connectors in composting, serving as important ARGs hosts and facilitating their spread in conventional composting. Among these, a core pathogenic bacterium (Corynebacterium) carried and transmitted ARGs with higher risks. In contrast, although the number of core bacteria (Bacillus, Oceanobacillus, Caldicoprobacter, Saccharomonospora, and Lactobacillus) increased during HACV composting, these bacteria were not potential hosts of the target ARGs. This contributed to the removal of aadE by 80.49 %. Consequently, compared to conventional composting, HACV composting was more effective at controlling risky ARGs, particularly aac(6')-Ib-cr and sul1. Furthermore, the ARGs removal mechanism primarily involved inhibiting horizontal gene transfer (HGT) in HACV composting, attributed to competition between core bacteria and ARGs hosts. In summary, HACV composting effectively promotes ARGs removal and reduces the risk of bacterial resistance. ENVIRONMENTAL IMPLICATION: In this study, we developed an energy-saving and emission-reducing hot air circulation ventilation composting technology (HACV), which effectively removes antibiotic resistance genes (ARGs). The HACV system maintained composting efficiency and maturity while driving bacterial community succession through deterministic processes (heterogeneous selection). HACV composting increased the colonization of core bacteria in the microbial network. Acting as connectors, the core bacteria are not hosts of ARGs in the HACV system, inhibiting horizontal gene transfer (HGT) and remove ARGs through competition with host bacteria.},
}

@article {pmid40682884,
year = {2025},
author = {Liu, Y and Gu, J and Feng, K and Zhang, Y and Zhong, Z and Liu, S and Xing, D},
title = {Reassessing systemic blind spots in modern water disinfection paradigms.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139271},
doi = {10.1016/j.jhazmat.2025.139271},
pmid = {40682884},
issn = {1873-3336},
abstract = {Disinfection plays a crucial role in ensuring healthcare and the safety of drinking water and sewage reuse. However, our current understanding of the factors influencing disinfection remains incomplete. This review offers a comprehensive examination of the often-neglected aspects in disinfection, such as micro- and nanoplastics (MNPs), bacterial states, quorum sensing, and horizontal gene transfer. A meta-analysis was conducted to evaluate the exposure risk and impacts associated with MNPs in water disinfection systems. Our findings indicate that within a specific concentration range of 5 μg·L[-1] to 11.43 g·L[-1], higher concentrations of MNPs hinder the bacterial inactivation rate and significantly increase the frequency of horizontal gene transfer following disinfection. Furthermore, MNPs also promote the formation of disinfection by-products (DBPs), with larger size of MNPs having a stronger effect. Among the various types of MNPs, studies predominantly focus on the response of polyethylene, and polyethylene terephthalate caused distinct promotion of DBPs. Our review also highlights existing knowledge gaps and challenges in the disinfection processes and facilitates the assessment of the risk of these influence factors, thereby supporting the development of advanced disinfection technologies. Additionally, it suggests prospective research directions in the field of water disinfection, aiming at improving disinfection processes.},
}

@article {pmid40681522,
year = {2025},
author = {Xiang, X and Li, Y and Ye, J and Li, B and He, G and Zhu, M and Zhang, J and Zhang, B and Miao, M and Yang, Y},
title = {Chinese soy-based microbiome and associated microbial risks: a metagenomic investigation.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {136},
pmid = {40681522},
issn = {2055-5008},
support = {Z191100008619006//Beijing Municipal Science and Technology Commission/ ; CASNHP-MJN2023-04//the Chinese Association for Student Nutrition & Health Promotion-Mead Johnson Nutritionals (China) Joint Fund/ ; 21JZD039//Major Research Project on Philosophy and Social Sciences of the Ministry of Education/ ; 2021YFC2600501//National Key R&D Program Project of the Ministry of Science and Technology/ ; },
mesh = {Humans ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; *Bacteria/genetics/classification/isolation & purification ; *Glycine max/microbiology ; China ; Gene Transfer, Horizontal ; Food Microbiology ; *Fermented Foods/microbiology ; *Soy Foods/microbiology ; Fermentation ; *Microbiota ; East Asian People ; },
abstract = {Fermented foods are a longstanding part of the Chinese diet and have been recognized for promoting gut microbial diversity. However, their microbial composition remains poorly defined, raising concerns about potential exposure to pathogens and antibiotic resistance genes (ARGs). Using shotgun metagenomics, we examined microbiota of 93 representative samples spanning three major categories of traditional Chinese fermented soybean products. We identified distinct microbial and functional profiles across food types, with antagonism between beneficial taxa (Bacillales and Lactobacillales) and harmful Enterobacterales. Comparative analysis with public Chinese gut microbiomes revealed species- and strain-sharing between fermented foods and human gut microbiota, identifying certain products as sources of clinically relevant pathogens, including Klebsiella pneumoniae and Klebsiella quasipneumoniae. Horizontal gene transfer analysis highlighted potential transfer of ARGs (e.g., efflux pump genes) from food microbes to gut microbiota. Our findings underscore the need to integrate microbial surveillance into traditional fermentation to balance health benefits with food safety.},
}

Humans
*Metagenomics/methods
*Gastrointestinal Microbiome
*Bacteria/genetics/classification/isolation & purification
*Glycine max/microbiology
China
Gene Transfer, Horizontal
Food Microbiology
*Fermented Foods/microbiology
*Soy Foods/microbiology
Fermentation
*Microbiota
East Asian People

@article {pmid40680908,
year = {2025},
author = {Yaikhan, T and Yingkajorn, M and Duangsi-Ngoen, W and Thant, EP and Chaichana, N and Suwannasin, S and Singkhamanan, K and Churi, S and Surachat, K},
title = {Genomic characterization of a clinical Enterocloster aldenensis strain: First report in Thailand.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105800},
doi = {10.1016/j.meegid.2025.105800},
pmid = {40680908},
issn = {1567-7257},
abstract = {This study presents the first comprehensive genome analysis of Enterocloster aldenensis in Thailand, an organism typically found in the gut but occasionally acting as an opportunistic pathogen. A scrotal tissue sample from a patient with suspected Fournier's gangrene was initially collected for Bacteroides surveillance in Southern Thailand, E. aldenensis PSUA25 was identified to Bacteroides thetaiotaomicron by Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS) and later reclassified as E. aldenensis following whole-genome sequencing. Species confirmation via Average Nucleotide Identity analysis showed 97 % identity with the representative strain. Phylogenetic analysis using all available E. aldenensis genomes placed strain PSU25A in clade 3, closely related to AM40-2 AC-an isolate from human feces in China (NCBI BioSample: SAMN11413088) selected for comparative analysis based on high genomic similarity. Comparative analysis revealed shared antimicrobial resistance genes, including poxtA, vanYG, vanWI, and vanTG. Unique to PSU25A were two mobile genetic elements: a conjugative transposon (Tn6009 with tetM) and a phage-associated region, suggesting horizontal gene transfer. This study emphasizes the need for accurate microbial identification, as misidentification can impact treatment decisions. Understanding the genomic traits of E. aldenensis from specific regions provides valuable insights into its pathogenic potential.},
}

@article {pmid40679857,
year = {2025},
author = {Katsande, P and Davies, AR and Chisnall, T and Vhoko-Tapesana, K and Willcocks, S and Majuru, CS and Mubau, T and Stabler, RA and Card, RM},
title = {Dissemination of extended-spectrum beta-lactamase-producing Escherichia coli in poultry in Zimbabwe.},
journal = {Microbial genomics},
volume = {11},
number = {7},
pages = {},
doi = {10.1099/mgen.0.001454},
pmid = {40679857},
issn = {2057-5858},
mesh = {*Escherichia coli/genetics/isolation & purification/drug effects/enzymology/classification ; *beta-Lactamases/genetics/metabolism ; Animals ; Zimbabwe/epidemiology ; *Poultry/microbiology ; *Escherichia coli Infections/veterinary/microbiology/epidemiology ; Whole Genome Sequencing ; *Poultry Diseases/microbiology/epidemiology ; Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Plasmids/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Multilocus Sequence Typing ; Gene Transfer, Horizontal ; },
abstract = {Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli are resistant to the critically important third- and fourth-generation cephalosporin antibiotics and present a risk to animal and human health. In Zimbabwe, there is an evidence gap concerning the prevalence and diversity of ESBL-producing E. coli in poultry. In this study, we screened for ESBL-E. coli at farms (n=50) and markets (n=10) using MacConkey agar supplemented with 4 µg ml[-1] ceftriaxone. ESBL-E. coli were detected at every market and at 21 farms, giving a farm-level prevalence of 42%. Seventy isolates were obtained and tested for antimicrobial susceptibility, whilst 69 of these were further analysed by whole-genome sequencing. A total of eight distinct bla CTX-M variants were identified, and 69 out of 70 isolates were multidrug-resistant. Genomic analysis revealed evidence for clonal expansion of an ESBL-producing clone and horizontal gene transfer via plasmids being responsible for the dissemination of ESBL-E. coli. Geographic Information System mapping was used to visualize the distribution of the ESBL-producing clones. For example, ST1141 isolates were clonal, having a highly conserved core genome, and harboured bla CTX-M-15 and 11 additional antimicrobial resistance genes on a ~338 kbp IncHI2 plasmid which was not present in other isolates. This clone was present at nine farms. In contrast, a conserved ~93 kbp IncFII plasmid harbouring bla CTX-M-55 was present in isolates from three different multilocus sequence types obtained from six farms. This study provides insight into the burden and distribution of ESBL-E. coli at poultry farms in Zimbabwe and provides molecular genetic evidence for clonal expansion and plasmid transfer as being important mechanisms for the dissemination of ESBL-E. coli in this setting. This study underscores the importance of adopting measures, such as prudent antimicrobial use and farm biosecurity, that can limit the development and dissemination of ESBL-producing E. coli.},
}

*Escherichia coli/genetics/isolation & purification/drug effects/enzymology/classification
*beta-Lactamases/genetics/metabolism
Animals
Zimbabwe/epidemiology
*Poultry/microbiology
*Escherichia coli Infections/veterinary/microbiology/epidemiology
Whole Genome Sequencing
*Poultry Diseases/microbiology/epidemiology
Anti-Bacterial Agents/pharmacology
Microbial Sensitivity Tests
Plasmids/genetics
Drug Resistance, Multiple, Bacterial/genetics
Multilocus Sequence Typing
Gene Transfer, Horizontal

@article {pmid40677084,
year = {2025},
author = {Hu, L and Li, M and Liu, YF and Zheng, H and Wei, ZH and Wang, XY and Hua, J and Mou, MJ and Luo, XX and Li, FM},
title = {[Occurrence Characteristics and Consumption Risk of Antibiotic Resistance Genes in Organic Vegetables].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {7},
pages = {4723-4732},
doi = {10.13227/j.hjkx.202406155},
pmid = {40677084},
issn = {0250-3301},
mesh = {*Vegetables/microbiology ; *Organic Agriculture ; *Drug Resistance, Microbial/genetics ; Soil Microbiology ; Raphanus/microbiology ; Coriandrum/microbiology ; Genes, Bacterial ; Bacteria/genetics ; *Food Contamination/analysis ; },
abstract = {Agricultural soil has become an important reservoir and transmission source of antibiotic resistance genes （ARGs） because of the extensive application of organic fertilizers such as livestock and poultry manure in organic agriculture production. This greatly increases the risk of foodborne transmission of ARGs in organic agricultural products. However， the extent of ARGs contamination in different types of organic vegetables and its driving factors remain unclear. Therefore， two organic and traditional farming species： green radish （Raphanus sativus L.） and coriander （Coriandrum sativum L.） species were selected as representatives to compare and analyze the abundance of ARGs and mobile gene elements （MGEs） and microbial community structure of the vegetable surface bacteria and endophytic bacteria using real-time PCR and 16S rRNA sequencing technology. Compared to conventional farming practices， organic farming significantly increased the abundance of ARGs among both epiphytic and endophytic bacteria on vegetables. The enrichment levels reached up to 78.9 times and 1.99 times， respectively. Furthermore， compared with that in coriander， green radishes exhibited a higher accumulation of ARGs. Similarly， the relative abundance of MGEs in endophytic bacteria of organically grown vegetables was significantly higher than those of the conventionally grown vegetables. Additionally， the abundance of MGEs positively correlated with the abundance of ARGs （P<0.05）， indicating that the organic farming practices increased the abundance of ARGs in the microbiomes of the vegetables by promoting horizontal gene transfer. Furthermore， network analysis showed that the interactions between ARGs and bacteria were more complex under organic farming practices， enriching 30 bacterial genera as potential hosts. Among them， 14 bacterial genera （e.g.， Microbacterium， Aeromicrobium， and Glutamicibacter） were significantly associated with high-risk ARGs （aadA， tetM， and floR）. These findings demonstrated that organic farming practices can increase the risk of human intake of ARGs by introducing potential ARG host bacteria and enriching MGEs， and root vegetables are more significantly affected by organic farming practices compared to leafy vegetables. This study provides a theoretical basis for assessing the health risks of ARGs contamination in edible vegetables under organic agricultural ecosystems.},
}

*Vegetables/microbiology
*Organic Agriculture
*Drug Resistance, Microbial/genetics
Soil Microbiology
Raphanus/microbiology
Coriandrum/microbiology
Genes, Bacterial
Bacteria/genetics
*Food Contamination/analysis

@article {pmid40674104,
year = {2025},
author = {Cox-Fermandois, A and Berríos-Pastén, C and Serrano, C and Arros, P and Poblete-Castro, I and Marcoleta, A},
title = {Large-scale analysis of polyhydroxyalkanoate synthases in Pseudomonas: highly diverse enzymes with potential for a novel class and dissemination by horizontal gene transfer.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf179},
pmid = {40674104},
issn = {1365-2672},
abstract = {AIMS: To investigate the diversity, phylogenetic distribution, and structural features of polyhydroxyalkanoate (PHA) synthases (PhaCs), key enzymes for producing bioplastics, in different well-known and poorly-studied species of Pseudomonas. As Antarctic Pseudomonas spp. with unique PhaCs and PHA synthesis capabilities have been reported, we aimed to explore the PhaC dotation and classes in strains from this and other environments and the dissemination potential of the phaC genes.

METHODS AND RESULTS: We compared 859 genomes from 186 Pseudomonas species, including 33 from Antarctica. PhaC gene identification, multiple alignments, phylogenetic inference, and 3D structure prediction were applied to compare and classify the PhaCs. Most isolates encoded two class II PhaCs, some showing additional class II and class I enzymes, especially from Antarctica, outstanding P. frigusceleri MPC6 harboring five PhaCs, one from a potential novel class. Different PhaC subclasses were proposed based on this diversity. Despite substantive sequence variation, all the PhaCs showed a highly conserved 3D structure. Also, several phaC genes were inside putative genomic islands, phages, and plasmids, supporting their acquisition by multiple horizontal transfer routes.

CONCLUSIONS: To our knowledge, this is the first report investigating the PhaCs present across the Pseudomonas genus, unveiling a remarkable diversity of these enzymes and their common dissemination in mobile elements, likely contributing to the host cell fitness. Our findings underline the potential of Pseudomonads from Antarctica and other environments and their PhaCs for producing PHAs with varying monomer compositions and properties. Future research is essential to elucidate the enzymatic properties of this underexplored PhaC diversity.},
}

@article {pmid40673658,
year = {2025},
author = {Li, B and Baniasadi, HR and Phillips, MA and Michael, AJ},
title = {The Pseudomonas aeruginosa Type VI secretion system toxin Tse8 evolved from a novel N-carbamoylputrescine amidohydrolase.},
journal = {The Biochemical journal},
volume = {},
number = {},
pages = {},
doi = {10.1042/BCJ20253210},
pmid = {40673658},
issn = {1470-8728},
abstract = {The polyamine putrescine is synthesized primarily from L-arginine via agmatine in bacteria. There are currently three known routes from agmatine to putrescine, including direct conversion by agmatinase. The other two routes use agmatine deiminase to produce N-carbamoylputrescine from agmatine, then one of two nonhomologous enzymes, putrescine transcarbamylase or N-carbamoylputrescine amidohydrolase (NCPAH) convert N-carbamoylputrescine to putrescine. Here, we functionally identify enzymes from phylogenetically distant bacteria, the gamma-proteobacterium Shewanella oneidensis, and the actinomycetota species Microterricola gilva, that are novel alternative, nonhomologous, noncanonical NCPAHs that we term AguY, which have emerged by convergent evolution. Kinetic analysis indicates that the AguY enzymes are as efficient as the canonical NCPAH from Pseudomonas aeruginosa, in converting N-carbamoylputrescine to putrescine. Genomic evidence suggests that the AguY enzymes may participate in putrescine biosynthetic or agmatine catabolic pathways, and are occasionally encoded in genomes that also encode agmatinase. We show that the Type VI secretion system toxin Tse8 from Pseudomonas aeruginosa has evolved from AguY. It is formally possible that AguY evolved directly or indirectly from the ancient glutamine amidohydrolase GatA, a component of the transamidosome, an RNA/protein complex required for production of glutamine-charged tRNA. Our study provides a further example of the prevalence of convergent evolution and horizontal gene transfer in polyamine biosynthesis, suggesting pervasive selective pressure to evolve polyamine metabolism in bacteria.},
}

@article {pmid40673602,
year = {2025},
author = {Bohunická, M and Johansen, JR and Pietrasiak, N and Jusko, BM and Mesfin, M and Becerra-Absalón, I},
title = {Kalymmatonema gen. nov. (Scytonemataceae, Cyanobacteria): A desert soil crust genus previously identified as Scytonema hyalinum, with description of seven species new to science.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70058},
pmid = {40673602},
issn = {1529-8817},
support = {PAPIIT Project IN206821//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; 89340//California Institute for Biodiversity/ ; DACA88-95-C-0015//U.S. Army Construction Engineering Research Laboratory/ ; N62473-21-2-0002//U.S. Navy/ ; DEB-0842702//U.S. National Science Foundation, Division of Environmental Biology/ ; DEB-9870201//U.S. National Science Foundation, Division of Environmental Biology/ ; GAČR 22-06374S//Grantová Agentura České Republiky/ ; },
abstract = {Numerous cyanobacterial strains previously identified as Scytonema hyalinum were determined to be phylogenetically distant from the type species of Scytonema, S. hofmannii. Morphological and molecular evidence suggests this distinct clade necessitates placement in a new genus, and we have described Kalymmatonema gen. nov. herein. Kalymmatonema has been demonstrated to exhibit five ribosomal operons, all of which differed in both sequence and secondary structure of conserved helical domains in the 16S-23S internal transcribed spacer rRNA region. Four of these operon copies were highly similar in 16S and 23S rRNA gene sequences, whereas the divergent fifth copy is thought to represent a whole-operon horizontal gene transfer event. Through in-depth analysis, we were able to recognize seven species new to science, the type species K. desertorum sp. nov., K. arcangelii comb. nov., K. chimaera sp. nov., K. ethiopiense sp. nov., K. gypsitolerans sp. nov., K. mateoae sp. nov., and K. oahuense sp. nov. We also created the new combination, K. hyalinum comb. nov., in order to include the original Scytonema hyalinum in this new genus based upon the common morphological feature of a mucilaginous apical cap on the trichomes. Kalymmatonema displays a complex evolution of its ribosomal operons, with evidence not only of horizontal gene transfer but also of internal rearrangements and mobile genetic elements that have transposed the tRNA-containing region of the ITS rRNA region among the four similar operons. Additional investigation of the evolutionary history of this interesting genus will likely lead to a better understanding of the processes shaping ribosomal evolution in cyanobacteria.},
}

@article {pmid40671960,
year = {2025},
author = {},
title = {Widespread remote introgression in the grass genomes.},
journal = {ArXiv},
volume = {},
number = {},
pages = {},
pmid = {40671960},
issn = {2331-8422},
abstract = {Genetic transfers are pervasive across both prokaryotes and eukaryotes, encompassing canonical genomic introgression between species or genera and horizontal gene transfer (HGT) across kingdoms. However, DNA transfer between phylogenetically distant species, here defined as remote introgression (RI), has remained poorly explored in evolutionary genomics. In this study, we present RIFinder, a novel phylogeny-based method for RI event detection, and apply it to a comprehensive dataset of 122 grass genomes. Our analysis identifies 622 RI events originating from 543 distinct homologous genes, revealing distinct characteristics among grass subfamilies. Specifically, the subfamily Pooideae exhibits the highest number of introgressed genes while Bambusoideae contains the lowest. Comparisons among accepted genes, their donor copies and native homologs demonstrate that introgressed genes undergo post-transfer localized adaptation, with significant functional enrichment in stress-response pathways. Notably, we identify a large Triticeae-derived segment in a Chloridoideae species Cleistogenes songorica, which is potentially associated with its exceptional drought tolerance. Furthermore, we provide compelling evidence that RI has contributed to the origin and diversification of biosynthetic gene clusters of gramine, a defensive alkaloid chemical, across grass species. Collectively, our study establishes a robust method for RI detection and highlights its critical role in adaptive evolution.},
}

@article {pmid40669567,
year = {2025},
author = {Chen, X and Smagghe, G and Chen, YM and Zang, LS},
title = {Laterally acquired chitinase genes in venom facilitate parasitism in egg parasitoid wasps.},
journal = {Insect biochemistry and molecular biology},
volume = {},
number = {},
pages = {104362},
doi = {10.1016/j.ibmb.2025.104362},
pmid = {40669567},
issn = {1879-0240},
abstract = {Parasitoid wasps (Hymenoptera) play a crucial role in ecosystems and agroforestry pest management as biological control agents. These wasps utilize venom proteins to suppress host immunity and regulate physiology, facilitating offspring development. Although venom functions have been studied in some parasitoids, their roles in egg parasitoids remain poorly understood. In this study, we employed genomic and transcriptomic sequencing to identify venom proteins in Anastatus japonicus and Anastatus fulloi, two egg parasitoids used in biological control. We discovered a significant expansion of GH19 chitinase in their genomes, with phylogenetic analysis indicating acquisition via lateral gene transfer (LGT) from microsporidian. Functional characterization revealed that four highly expressed GH19 chitinases, Aj13071 / Aj13072 in A. japonicus and Af23628 / Af23629 in A. fulloi are essential for host egg penetration; silencing these genes increased penetration time and resulted in smaller or incomplete holes. Additionally, silencing Aj13071 and Aj13072 in A. japonicus impaired female fecundity, while Af23628 and Af23629 in A. fulloi affected venom reservoir development and egg load, respectively. These findings underscore the critical roles of GH19 chitinases in host penetration and reproduction, offering new insights into the molecular mechanisms driving parasitism in egg parasitoids. This study advances our understanding of venom evolution and supports the development of targeted biological control strategies.},
}

@article {pmid40669229,
year = {2025},
author = {Liu, S and Zhang, Y and Cui, Y and Du, W and Li, Y and Xiong, Z and Wang, J and Wu, Z and Yuan, J and Liu, W},
title = {Close interactions between prokaryotes and plasmids or viruses highlight a pivotal role of horizontal gene transfer in shaping antibiotic/metal(loid) resistome and their prokaryotic supercarriers in untreated hospital sewage.},
journal = {Water research},
volume = {286},
number = {},
pages = {124178},
doi = {10.1016/j.watres.2025.124178},
pmid = {40669229},
issn = {1879-2448},
abstract = {Unveiling horizontal gene transfer (HGT) of antibiotic (ARGs) and metal(loid) resistance genes (MRGs) in hospital sewage is critical for surveilling antimicrobial resistance (AMR) mobility that poses huge threats to public health. Using metagenomic shotgun sequencing, we provided an integrate insight into AMR characters and the relevant HGT in untreated sewage from one of the world's largest comprehensive hospitals from Oct 2022 to Aug 2023. We uncovered higher richness and diversity of ARGs or MRGs than mobile genetic elements (MGEs), while MGEs exhibited the highest abundance, suggesting great HGT potentials. Higher number of ARG, MRG, and MGE subtypes and abundances of putative human pathogens were found in autumn-winter than in spring-summer. ARG- and MGE-carrying prokaryotes outcompeted non-carriers in abundances, and multi-ARG and MGE carriers outcompeted single ones. Resistome supercarriers occupying 25 % of prokaryotic abundance harbored higher functional diversity and more metabolic capacity than other prokaryotes, which could be related to more predicted HGT events. Notably, 30 %, 22 %, and 40 % of prokaryote-carrying ARGs, MRGs, and MGEs were associated with HGTs. Diversity variation of plasmids as a critical contributor to HGT was positively correlated with those of prokaryotes and ARGs or MRGs. Plasmids carrying high-risk ARGs (e.g., multidrug and tetracycline types) showed higher abundances than prokaryotes and viruses. Most bacterial taxa may undergo high levels of active viral replication (phylum-specific virus/host abundance ratios >12). Hundreds of virulent viruses could lyse abundant ARG or MRG supercarriers and hosts of multidrug, multi-metals, and As resistome, whilst one temperate virus infecting multiple Azonexus supercarriers may contribute the HGT of Hg resistome. We found the dominance of stochasticity in assembling of ARGs/MGEs rather than prokaryotes or viruses, which was likely owed to functional redundancy led by HGT. Overall, this study sheds lights on a pivotal role of HGT in driving microbial community and functionality, and provides a guidance for the optimization of the treatment strategies particularly on MGEs.},
}

@article {pmid40664747,
year = {2025},
author = {He, P and Peng, J and Wei, L and Wu, Y and Zhang, L and Zhou, Q and Song, S and Quintana, M and Wu, Z and Wu, J},
title = {Decoupling Pharmaceutical Contamination and Antibiotic Resistance Risks in Mid-Yangtze Drinking Water Systems: The Pivotal Role of Nutrient-Driven Horizontal Gene Transfer.},
journal = {Environmental management},
volume = {},
number = {},
pages = {},
pmid = {40664747},
issn = {1432-1009},
support = {No. HKY-2021-KY17-1//Wuhan Science and Technology Center of Ecology and Environment/ ; No. 2022-LHYJ-02-0506-01//the Yangtze River joint research phase II project/ ; },
abstract = {The Yangtze River, a critical drinking water source for over 500 million people, faces escalating contamination from pharmaceuticals and antibiotic resistance genes (ARGs). This study systematically investigated 11 water sources and 39 tap water sites in the Mid-Yangtze River, quantifying 10 pharmaceuticals and 384 ARGs via ultra-trace analysis (UPLC-MS/MS) and HT-qPCR. Pharmaceuticals occurred at low total concentrations (1.45-6.41 ng/L), with tap water levels reduced by 1-2 orders of magnitude post-treatment. Notably, we observed decoupling between pharmaceutical exposure and ARGs proliferation-while pharmaceuticals posed minimal human health risks (RQh <10[-4]) and moderate ecological risks (MRQe = 0.84), environmental factors (nitrogen, phosphorus, organic matter) explained 51.2% of ARGs variation, far exceeding pharmaceutical contributions (2.9%). Dissolved organic carbon, nitrate nitrogen, and total phosphorus emerged as primary environmental drivers of ARGs/MGEs proliferation, with mobile genetic elements (MGEs, e.g., tnpA-2, intI1) serving as central hubs for horizontal transfer. Network analysis revealed anti-inflammatories (ibuprofen/naproxen) unexpectedly co-occurred with resistance determinants despite their low selective pressure. This decoupling mechanism demonstrates that nutrient-driven gene transfer supersedes pharmaceutical selection in sustaining ARGs persistence, even under low exposure conditions. The findings necessitate paradigm shifts in risk management: controlling nutrient loads and targeting MGEs may prove more effective than solely regulating pharmaceuticals for mitigating antimicrobial resistance in drinking water systems.},
}

@article {pmid40663383,
year = {2025},
author = {Tao, S and Fang, Y and Zheng, L and Zhang, H and Xu, Y and Liang, W},
title = {Mechanistic study of the immune defense function of the CRISPR1-Cas system in Enterococcus faecalis.},
journal = {Virulence},
volume = {16},
number = {1},
pages = {2530665},
pmid = {40663383},
issn = {2150-5608},
mesh = {*Enterococcus faecalis/genetics/immunology/drug effects ; *CRISPR-Cas Systems ; Plasmids/genetics ; Gene Transfer, Horizontal ; Mutation ; Drug Resistance, Bacterial/genetics ; Transformation, Bacterial ; },
abstract = {Enterococci are Gram-positive cocci that are considered to be one of the causative agents of hospital-acquired infections. CRISPR-Cas is an adaptive immune system with targeted defense functions against foreign invading nucleic acids and plays an important role in antibiotic resistance. In this study, we aimed to investigate II-A CRISPR-Cas-mediated immunity and the molecular mechanism underlying the horizontal transfer of drug resistance genes in Enterococcus faecalis. The mutant strains were constructed by the homologous recombination strategy. The interference of plasmid transformation by the Enterococcus faecalis CRISPR1/Cas system was confirmed through plasmid transformation efficiency. The different mutation positions in the protospacer sequence S1 and PAM region recombinant plasmids were constructed through enzyme digestion and sequencing verification to assess the impact of the CRISPR-encoded immunity. In the wild-type strain, the transformation efficiency of plasmids pAT28-S1-S9 containing protospacers and PAM sites decreased (p < 0.05). Single-base mutations at positions 25 and 28 of the protospacer region eliminated the ability of the wild-type strain to prevent plasmid transformation containing the protospacer and PAM sites (p > 0.05), whereas a single mismatch at protospacer positions 2,10,18,23 did not affect the ability of CRISPR-Cas system-positive strains to interfere with plasmid transformation (p < 0.05). There was no significant difference between the wild-type strain and the mutant strain in the transformation efficiency of the pS1-pΔPAM plasmid without PAM and plasmids containing single mutations (p > 0.05). In conclusion, the CRISPR-Cas system can block the transformation of matching protospacer sequences, and mutations near or within the protospacer adjacent motif (PAM) allow the plasmid to escape CRISPR-encoded immunity.},
}

*Enterococcus faecalis/genetics/immunology/drug effects
*CRISPR-Cas Systems
Plasmids/genetics
Gene Transfer, Horizontal
Mutation
Drug Resistance, Bacterial/genetics
Transformation, Bacterial

@article {pmid40662585,
year = {2025},
author = {Márquez-Friedrichs, F and Nolly, MB and Ferreyra, A and Zuloaga, L and Dominguez, S and Secotaro, A and Rathour, VS and Damiani, MT and Contreras, L and Sánchez, DG},
title = {Shifts in bla genes and Class 1 integron prevalence in beta-lactamase-producing bacteria before and after the COVID-19 pandemic in Mendoza, Argentina.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0277124},
doi = {10.1128/spectrum.02771-24},
pmid = {40662585},
issn = {2165-0497},
abstract = {This study analyzes the molecular epidemiology of bla genes and Class 1 integron in broad-spectrum beta-lactamase (BSBL) and extended-spectrum beta-lactamase (ESBL) producing strains of bacteria isolated from clinical samples of hospitalized and ambulatory patients before and after the COVID-19 pandemic. Isolates obtained in two periods were compared: the first corresponding to the years November 2019-March 2020, and the second to the years November 2021-April 2022. We evaluate changes in resistance patterns of antibiotics associated with pressures on the healthcare system and social lockdowns. A total of 156 isolates were analyzed: 78 from the first period (61 hospitalized, 17 ambulatory) and 78 from the second period (47 hospitalized, 31 ambulatory). Escherichia coli and Klebsiella pneumoniae were the predominant bacterial species, representing 85% of the isolates in both periods. The frequency of ambulatory ESBL-producing isolates increased significantly, from 22% (17/78) to 40% (31/78; P < 0.01) in the second period. The prevalence of blaSHV increased from 24% (19/78) to 72% (56/78; P < 0.01) in the second period, while the blaCTX-M-2 group, absent in the first period, was detected in 43% (34/78) of isolates from the second period. Strains from the second period exhibited greater genetic complexity, with an increased prevalence of combinations involving three or more bla genes, including isolates carrying up to five of such genes. Class 1 integron showed a strong correlation with resistance to ciprofloxacin and trimethoprim-sulfamethoxazole. The gene blaOXA-1, previously associated with resistance to beta-lactamase inhibitors, did not show a clear pattern in the second period.IMPORTANCEAntimicrobial resistance associated with the production of extended-spectrum beta-lactamase (ESBL) represents a critical global health challenge, particularly due to the limited development of new antibiotics. This is the first report from Argentina's central-west region examining the prevalence of beta-lactamase-encoding genes, providing a framework for future research. Our findings reveal a significant increase in bacteria with the ESBL phenotype, particularly among ambulatory populations post-pandemic, suggesting a concerning spread of multidrug-resistant bacteria outside hospital environments. This could compromise empirical antibiotic treatments for ambulatory patients, increasing the risk of severe complications. Our results highlight the urgent need for ongoing surveillance to detect virulent strains before clonal spread or horizontal gene transfer occurs in the community. They also emphasize the importance of strategies to ensure the prudent use of antimicrobials and mitigate the increasing prevalence of resistance genes, which threatens the effectiveness of current therapeutic options.},
}

@article {pmid40661335,
year = {2025},
author = {Fernández Ríos, D and Benítez Candia, N and Quintana, SA and Goberna, MF and Nara Pereira, E and Arrúa, AA and Castro Alegría, A},
title = {Naturally transgenic plants and the need to rethink regulatory triggers in biotechnology.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {13},
number = {},
pages = {1600610},
pmid = {40661335},
issn = {2296-4185},
}

@article {pmid40661007,
year = {2025},
author = {Li, YL and Zhang, JY and Fu, YB and Sun, MQ and Miao, BB and Gong, XY and Han, X and Xing, H and Gao, PF and Li, JC and Tang, YT and Fan, XY and Ge, YL and Zhou, HJ and Li, J and Dong, AY},
title = {[Genetic diversity analysis of oxacillinase in 241 clinical isolates of Pseudomonas aeruginosa].},
journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]},
volume = {59},
number = {7},
pages = {1004-1012},
doi = {10.3760/cma.j.cn112150-20240920-00756},
pmid = {40661007},
issn = {0253-9624},
support = {81861138053//National Natural Science Foundation of China/ ; },
mesh = {*Pseudomonas aeruginosa/genetics/isolation & purification/enzymology ; *beta-Lactamases/genetics ; *Genetic Variation ; Humans ; Drug Resistance, Bacterial ; Microbial Sensitivity Tests ; Gene Transfer, Horizontal ; },
abstract = {Objective: To analyze the carriage status, subtype distribution and flanking gene sequence characteristics of oxacillinases (OXA enzyme) in 241 clinical strains of Pseudomonas aeruginosa, and assess their roles in the drug resistance of Pseudomonas aeruginosa and ability to horizontally transfer across species. Methods: Clinical P. aeruginosa isolates were collected from four hospitals in Sanya, Tangshan, Zhangjiakou, and Beijing. The prevalence of oxacillinases and their flanking gene sequences was analyzed by whole-genome sequencing (NGS) and bioinformatic approaches. Results: A total of 241 isolates of P. aeruginosa were gathered, and 35 blaOXA subtypes were identified through screening of 252 blaOXA genes. These genes were classified into three subfamilies: blaOXA-50-like (241, 95.6%), blaOXA-1-like (9, 3.6%) and blaOXA-10-like (2, 0.8%). Among these, 11 subtypes (11, 31.4%) were novel blaOXA subtypes. Nine of these belonged to the blaOXA-50-like subfamily and were designated as blaOXA-1244, blaOXA-1245, blaOXA-1246, blaOXA-1250, blaOXA-1252, blaOXA-1253, blaOXA-1254, blaOXA-1255, and blaOXA-1256. The remaining two belonged to the blaOXA-10-like subfamily and were named blaOXA-1247 and blaOXA-1248. Compared to the amino acid sequence of OXA-10, the newly identified subtype OXA-1247 exhibited a mutation at position 117, where a valine was replaced by a leucine. This change was thought to improve the enzyme's ability to hydrolyze carbapenems. In the analysis of the flanking sequences of the blaOXA genes, Class I integrons were identified in four bacterial strains. The variable regions of these integrons carried three distinct patterns of resistance gene cassettes: aac(6')-Ib-blaOXA-1247-ant(3'')-Ia, aac(6')-Ib-blaOXA-1248 and aac(6')-Ib-blaIMP-45-blaOXA-1-catB3. Among these, the strain BJ2326 carried a class I integron that was connected to the downstream ISCR1 element to form a composite class I integron structure, additionally carrying the resistance gene blaPER-1. Out of the 223 non-wild-type P. aeruginosa strains, 127 strains exhibited non-wild-type profiles to the four beta-lactam antibiotics MEM, CAZ, FEP, and TZP, with the combination of MEM+CAZ+FEP being the most prevalent, representing 57.0% of the total. Conclusions: The blaOXA genes in 241 clinical P. aeruginosa strains showed diversity. Some blaOXA genes had a co-transfer risk with the metallo-β-lactamase resistance gene blaIMP-45. Among the 11 newly discovered blaOXA subtypes, the new subtype OXA-1247 may have carbapenemase activity and potential for horizontal transfer.},
}

*Pseudomonas aeruginosa/genetics/isolation & purification/enzymology
*beta-Lactamases/genetics
*Genetic Variation
Humans
Drug Resistance, Bacterial
Microbial Sensitivity Tests
Gene Transfer, Horizontal

@article {pmid40657958,
year = {2025},
author = {Li, H and Li, GF and Zhou, Y and Pan, XF and Yang, XR and Cai, C and Su, JQ},
title = {Growth Stage-Dependent Variations of Antibiotic Resistance and Potential Pathogens in Earthworm Gut: Potential Risk to Soil Health.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c03332},
pmid = {40657958},
issn = {1520-5851},
abstract = {Under the "One Health" framework, microbial resistance and pathogenicity across environments and animals pose significant health threats and have become a global issue. Although antibiotic resistance genes (ARGs) in earthworm guts and their influence on soil ARGs have been studied, how earthworm life stages affect ARGs and potential pathogens in the gut and soil remains unclear. Here, we assessed intestinal ARGs and virulence factor genes (VFGs) during earthworm development (egg, juvenile, and adult) and their influence on soil ARGs and potential pathogens. Our results showed that ARGs and potential pathogens were widespread and varied within earthworm guts at different growth stages. Earthworm guts harbored significantly (p < 0.05) fewer high-risk ARGs than soil, indicating potential roles of earthworms in soil ARG mitigation. Conversely, potential pathogens were significantly (p < 0.05) higher in guts than in soil. We further found that earthworms across life stages increased soil potential pathogens and reinforced ARG-mobile genetic element (MGE)-pathogen linkages in the soil ecosystem. ARG spread in earthworm guts relied more on vertical transmission than horizontal gene transfer (HGT). These results suggest that earthworms harbor abundant and diverse ARGs and potential pathogens, influencing soil microbiota and resistomes, which reveal earthworm-associated risks to soil ecosystem health.},
}

@article {pmid40657948,
year = {2025},
author = {Urquhart, AS and Forsythe, A and Vogan, AA},
title = {Are Fungal Disease Outbreaks Instigated by Starship Transposons?.},
journal = {Molecular plant pathology},
volume = {26},
number = {7},
pages = {e70124},
pmid = {40657948},
issn = {1364-3703},
mesh = {*DNA Transposable Elements/genetics ; *Plant Diseases/microbiology/genetics ; *Disease Outbreaks ; Genes, Fungal ; *Fungi/genetics/pathogenicity ; },
abstract = {New outbreaks of fungal diseases are an ongoing threat to global agriculture. One known mechanism generating novel diseases is the horizontal transfer of genes between fungal species. Yet we have little understanding of how such transfers are mediated. Here, we raise the possibility that Starships, a recently discovered superfamily of giant transposable elements, might be responsible. To support this hypothesis, we discuss three potential cases where Starships may have mediated disease outbreaks. These are ToxA in wheat pathogens, genes underlying Glomerella leaf spot on apple trees, and the defoliating gene cluster of Verticillium dahliae on cotton. In the Verticillium example, we provide strong evidence for a Starship-mediated mechanism: disease-promoting genes reside in closely related Starships across distantly related species. We aim to spark interest in Starships' roles in fungal pathogens and how this knowledge could inform disease management strategies.},
}

*DNA Transposable Elements/genetics
*Plant Diseases/microbiology/genetics
*Disease Outbreaks
Genes, Fungal
*Fungi/genetics/pathogenicity

@article {pmid40655388,
year = {2025},
author = {Jhalora, V and Bist, R},
title = {A Comprehensive Review of Molecular Mechanisms Leading to the Emergence of Multidrug Resistance in Bacteria.},
journal = {Indian journal of microbiology},
volume = {65},
number = {2},
pages = {844-865},
pmid = {40655388},
issn = {0046-8991},
abstract = {UNLABELLED: Multidrug resistance (MDR) in bacteria poses a serious global health threat, compromising the effectiveness of antibiotics. MDR causes approximately 700,000 deaths annually, with MDR tuberculosis alone claiming 230,000 lives. While bacteria inherently possess intrinsic resistance, acquired resistance stands out as the primary culprit in MDR development. Acquired resistance mechanisms mediated by the bacterial cell wall, nucleic acids, and proteins play a pivotal role in the genesis of MDR. Bacteria can modify their cell wall structure, produce resistant enzymes, exhibit mutations in antibiotic-targeted genes, and acquire resistant genes through horizontal gene transfer. Bacteria can produce proteins that act as enzymes, chemically modifying or directly degrading the antibiotic molecules, leading to the loss of their functionality. Apart from these mechanisms, biofilms also play a pivotal role in MDR expansion. Despite the development of several antibiotics since the discovery of penicillin, continuous structural and molecular modifications in bacteria render these antibiotics ineffective against MDR. The most recent approaches such as clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (CRISPR-Cas), nanotechnology, a combination of CRISPR-Cas, and nanoparticles, show promise in treating MDR. Thus, this review delves deep into the molecular mechanisms of MDR, emphasizing the limitations of current antibiotics due to bacterial evolution and highlighting current strategies in the fight against MDR bacteria. This will drive comprehensive research to uncover additional resistance mechanisms and develop innovative strategies to combat resistant bacteria effectively.

SUPPLEMENTARY INFORMATION: The online version supplementary material available at 10.1007/s12088-024-01384-6.},
}

@article {pmid40654884,
year = {2025},
author = {Wirbel, J and Hickey, AS and Chang, D and Enright, NJ and Dvorak, M and Chanin, RB and Schmidtke, DT and Bhatt, AS},
title = {Discovering Broader Host Ranges and an IS-bound Prophage Class Through Long-Read Metagenomics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.09.652943},
pmid = {40654884},
issn = {2692-8205},
abstract = {Gut bacteriophages profoundly impact microbial ecology and human health, yet they are greatly understudied. Using deep, long-read bulk metagenomic sequencing, a technique that overcomes fundamental limitations of short-read approaches, we tracked prophage integration dynamics in 12 longitudinal stool samples from six healthy individuals, spanning a two-year timescale. While most prophages remain stably integrated into their host over two years, we discover that ∼5% of phages are dynamically gained or lost from persistent bacterial hosts. Within the same sample, we find evidence of population heterogeneity in which identical bacterial hosts with and without a given integrated prophage coexist simultaneously. Furthermore, we demonstrate that phage induction, when detected, occurs predominantly at low levels (1-3x coverage compared to the host region). Interestingly, we identify multiple instances of integration of the same phage into bacteria of different taxonomic families, challenging the dogma that phage are specific to a host of a given species or strain. Lastly, we describe a new class of phages, which we name "IScream phages". These phages co-opt bacterial IS30 transposases to mediate their integration, representing a previously unrecognized form of phage domestication of selfish bacterial elements. Taken together, these findings illuminate fundamental aspects of phage-bacterial dynamics in the human gut microbiome and expand our understanding of the evolutionary mechanisms that drive horizontal gene transfer and microbial genome plasticity in this ecosystem.},
}

@article {pmid40654663,
year = {2025},
author = {Banks, EJ and Bardy, P and Tran, NT and Nguyen, PM and Maqbool, A and Le, TBK},
title = {A bacterial CARD-NLR immune system controls the release of gene transfer agents.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.08.652646},
pmid = {40654663},
issn = {2692-8205},
abstract = {Bacteria have evolved a wide array of immune systems to detect and defend against external threats including mobile genetic elements (MGEs) such as bacteriophages, plasmids, and transposons. MGEs are often selfish, exploiting their bacterial hosts to propagate, however they can also provide adaptive advantages through horizontal gene transfer. Gene transfer agents (GTAs), which are non-infectious domesticated prophages, represent a unique class of beneficial MGEs that facilitate bacterial gene transfer. Despite their domestication, GTAs retain phage-like features, including the requirement for host cell lysis to release particles, that may inadvertently trigger host immunity. How GTAs might avoid, subvert, or possibly adopt host immune systems to complete their life stages is poorly understood. Here, we identify a tripartite system, LypABC, that is essential for GTA-mediated cell lysis in Caulobacter crescentus. LypABC resembles caspase recruitment domain-nucleotide-binding leucine-rich repeat (CARD-NLR) anti-phage defence systems that mediate abortive infection wherein infected cells die to prevent phage proliferation, thereby protecting the overall bacterial population. LypABC-deficient cells produce host DNA-packed GTA particles and eventually die but cannot lyse to release GTA particles. Moreover, overproduction of LypABC is highly toxic to both GTA-producing and non-producing cells, highlighting the need for strict regulation. We find that such regulation is achieved transcriptionally by a repressor, RogB, which binds the promoters of lypABC and of essential GTA activator genes, thus coupling GTA activation and host cell lysis. While traditionally considered antagonistic towards MGEs, our findings here suggest that immunity components are versatile and can be adapted to support MGEs.},
}

@article {pmid40652256,
year = {2025},
author = {Tang, Y and Zhan, P and Wu, Y and Zhang, T and Yin, D and Gao, Y and Yu, Y and Qiu, S and Zhao, J and Zhang, X and Ma, Z and Chen, Y and Zhao, L and Mao, S and Huang, J and Chen, WH and Liu, J},
title = {Landscape of mobile genetic elements and their functional cargo across the gastrointestinal tract microbiomes in ruminants.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {162},
pmid = {40652256},
issn = {2049-2618},
mesh = {Animals ; *Ruminants/microbiology ; *Gastrointestinal Microbiome/genetics ; *Interspersed Repetitive Sequences ; Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Plasmids/genetics ; Gene Transfer, Horizontal ; *Gastrointestinal Tract/microbiology ; Metagenome ; },
abstract = {BACKGROUND: Mobile genetic elements (MGEs) drive horizontal gene transfer and microbial evolution, spreading adaptive genes across microbial communities. While extensively studied in other ecosystems, the role of MGEs in shaping ruminant gastrointestinal microbiomes-especially their impact on diversity, adaptation, and dietary responsiveness-remains largely unexplored. This study systematically profiles MGE distribution and functionality across gastrointestinal regions in multiple ruminant species to advance our understanding of microbial adaptation.

RESULTS: Across 2458 metagenomic samples from eight ruminant species, we identified 4,764,110 MGEs-a ~ 216-fold increase over existing MGE databases. These elements included integrative and conjugative elements, integrons, insertion sequences, phages, and plasmids, with mobilization patterns largely confined to closely related microbial lineages. The distribution of MGEs varied by GIT regions, often reflecting nutritional gradients. In a validation cohort, GH1-carrying plasmids enriched in carbohydrate-active enzymes were found to predominate in the stomach, showing notable responsiveness to forage-based diets. All annotated MGEs have been compiled into a publicly accessible database, rumMGE (https://rummge.liulab-njau.com), to support further research.

CONCLUSIONS: This study substantially expands the catalog of known MGEs in ruminants, revealing their diverse roles in microbial evolution and functional adaptation to dietary changes. The findings provide a valuable resource for advancing research on microbial functionality and offer insights with potential applications for enhancing ruminant health and productivity, through strategies aimed at modulating the microbiome in agricultural contexts. Video Abstract.},
}

Animals
*Ruminants/microbiology
*Gastrointestinal Microbiome/genetics
*Interspersed Repetitive Sequences
Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
Plasmids/genetics
Gene Transfer, Horizontal
*Gastrointestinal Tract/microbiology
Metagenome

@article {pmid40652164,
year = {2025},
author = {Lv, T and Bi, X and Zheng, L and Zhao, Y and Zhou, Y and Wu, T and Shen, P and Zhu, D and Chen, S and Chen, Y},
title = {Mobile genetic elements mediating antimicrobial resistance drive the evolutionary process of Clostridioides difficile ST37/RT017.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {659},
pmid = {40652164},
issn = {1471-2164},
support = {2020YFE0204300//the National Key Research and Development Program of China/ ; 82073609//National Nature Science Foundation of China/ ; },
abstract = {BACKGROUND: Clostridioides difficile (C. difficile) ST37/RT017 is one of the most prevalent genotypes, exhibiting resistance to multiple antimicrobial agents and widespread dissemination, particularly in East Asia. However, its evolutionary history and genetic adaptation remains limited. Here, we aimed to systematically assess the genetic diversity, key evolutionary events, and potential driving forces of C. difficile ST37/RT017.

RESULTS: To explored dynamic trends in the genomic characterization, diversity and changes, both phylogenetic and Bayesian evolutionary analyses revealed that the C. difficile ST37/RT017 strains were clustered into three variant lineages as a directed bus-like topology, from VL I, to VL II, and VL III. An incremental increase in the median number of resistance genes was observed, with one in VL I, five in VL II, and six in VL III. Distinguishing features included variations in resistance genes or fluoroquinolone resistance mutation, such as erm(B), tet(M), aac(6’)-Ie-aph(2’’)-Ia, ant(6)-Ia and gyrA (T82I). Further analysis of evolutionary mechanisms revealed that Tn916, carrying tet(M), was present in 87.9% (160/182) of VL III and 92.6% (163/176) of VL II, but only 4.1% (5/122) of VL I. The Tn6194-like element, carrying erm(B), was found in 25.3% (46/182) of VL II and 84.7% (149/176) of VL III, with none detected in VL I. Furthermore, other functional genes, especially srtB, were notable in C. difficile ST37/RT017, which gradually acquired resistance genes from VL I to VL II and VL III.

CONCLUSIONS: The systematically analysis in this study suggests that the acquisition of antibiotic resistance genes was the primary driver of adaptive evolution in C. difficile ST37/RT017. Horizontal gene transfer, particularly through mobile genetic elements is a key genetic mechanism in the adaptive evolution of C. difficile ST37/RT017. Based on these genetic profiles, the active establishment and optimization of a rational system for antibiotic use will be crucial to prevent the emergence of a C. difficile ST37/RT017 variant.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-025-11822-4.},
}

@article {pmid40651546,
year = {2025},
author = {Tang, J and Hu, Z and Zhang, X and Mou, Q and Du, L and Daroch, M},
title = {Evolutionary insights from the pangenome and pigment profiles of Parasynechococcus.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108408},
doi = {10.1016/j.ympev.2025.108408},
pmid = {40651546},
issn = {1095-9513},
abstract = {Parasynechococcus is one of the two essential alongside Prochlorococcus photosynthetic cyanobacteria that contribute primary productivity in the ocean. Despite its global importance its specie delimitation remains controversial. Herein, a pangenome analysis of 39 high-quality genomes was conducted to delineate Parasynechococcus species. Core-gene phylogram revealed the classification of these genomes into 18 well-defined putative genospecies, which was corroborated by ANI index and GTDB classification. Moreover, numerous interspecies and intraspecies HGT events were detected, some of which may be responsible for the inconsistencies between core-gene and pan-gene phylograms. Besides, the profiling of phycobilisome rod region in Parasynechococcus genomes unraveled intriguing diversity of their genomic organization, pigment type and genomic cluster variants. The diversification process was hypothesized to be mediated by the putative mobile elements located in these regions. Moreover, phylogeny incongruence between the genes within phycobilisome rod region and the core genome indicate distinct evolutionary history, which could be ascribed to lateral gene transfer. Conclusively, the results provide insights into the diversity and evolution of Parasynechococcus from the perspective of pangenome and pigment type, facilitating the evolutionary research and exploration of this important taxon.},
}

@article {pmid40651383,
year = {2025},
author = {Javaid, A and Tabassum, N and Karthikeyan, A and Kim, YM and Jung, WK and Khan, F},
title = {Beta-lactamases in lactic acid bacteria: Dual role in antimicrobial resistance spread and environmental detoxification of antibiotic residues.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139220},
doi = {10.1016/j.jhazmat.2025.139220},
pmid = {40651383},
issn = {1873-3336},
abstract = {Lactic acid bacteria (LAB) are widely used in food production and as probiotics. However, their potential role in the spreading of antimicrobial resistance (AMR) remains underexplored. A major AMR mechanism is the production of beta-lactamases, which is well-documented in most pathogenic bacteria; the diversity and functionality of these enzymes in LAB are less understood. Here, we explored the genomic diversity of beta-lactamase genes in LAB in a broad range of publicly available LAB genomes. Our findings revealed the presence of two distinct types of beta-lactamase genes in LAB: ampC-type beta-lactamases (class C), likely developed within LAB lineages, and blaTEM-type (class A), potentially acquired via HGT. Phylogenetic and structural analysis revealed similarities between LAB-derived ampC genes and clinically relevant class C beta-lactamases, while blaTEM-type genes were identified to be often flanked by mobility-related genetic elements, indicating a potential for horizontal gene transfer (HGT). Molecular docking studies further showed that LAB beta-lactamases may hydrolyze a broad spectrum of beta-lactam antibiotics, particularly aminopenicillins and cephalosporins. These findings will contribute to the broader field of AMR research, highlighting the importance of monitoring beta-lactamase production by LAB and its implications for food safety, bioremediation of beta-lactam antibiotic residues in wastewater and agro-industrial effluents.},
}

@article {pmid40651382,
year = {2025},
author = {Wang, H and Zeng, H and Zhang, J and Zhou, Q},
title = {Single-chamber differs from dual-chamber bioelectrochemical systems in wastewater treatment and methane recovery under combined exposure to microplastics and antibiotics.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139175},
doi = {10.1016/j.jhazmat.2025.139175},
pmid = {40651382},
issn = {1873-3336},
abstract = {The coexistence of microplastics (MPs) and antibiotics in wastewater poses important threats to microbial ecosystems and methane recovery during anaerobic digestion (AD). This study systematically compares the methanogenic performance and microbial response of single- and dual-chamber bioelectrochemical systems (BES) (0.8 V) exposed to a mixture of MPs (10 mg/L) and antibiotics (1 mg/L). Results demonstrated that single-chamber BES significantly enhanced methanogenesis, achieving a 21.19 % increase in methane production compared to conventional AD, while dual-chamber BES exhibited limited activity due to ammonia inhibition and acetate accumulation. Meanwhile, pollutant exposure dramatically altered the functional enzyme activities and microbial community structure. Metagenomic analysis revealed that methane was primarily produced via the acetoclastic pathway mediated by Methanothrix, with electrical stimulation promoting direct interspecies electron transfer. Pollutant exposure drastically altered microbial communities, reducing Euryarchaeota and enriching fermentative bacteria (e.g., Proteiniphilum). Notably, antibiotic resistance genes (ARGs) increased across all systems, with electrode carriers amplifying ARGs proliferation. However, single-chamber BES showed superior resistance to horizontal gene transfer of ARGs. Key metabolic pathways (e.g., glycolysis, TCA cycle) were markedly inhibited, highlighting the cascading effects of pollutants on microbial energetics. These findings highlight the potential of single-chamber BES for treating co-contaminated wastewater, providing critical insights for optimizing BES configurations.},
}

@article {pmid40650971,
year = {2025},
author = {Ma, J and Jiang, X and Bi, H and Li, J and Ma, X and Chi, X and Tang, Y and Liu, Z and Li, H},
title = {Horizontal acquisition of the Type I restriction-modification system enhances bacterial pathogenicity by mediating methylation of transcription factor-encoding genes.},
journal = {Nucleic acids research},
volume = {53},
number = {13},
pages = {},
doi = {10.1093/nar/gkaf659},
pmid = {40650971},
issn = {1362-4962},
support = {32460244//National Natural Science Foundation of China/ ; 225MS009//Hainan Provincial Natural Science Foundation/ ; 322RC589//Hainan Provincial Natural Science Foundation/ ; ZDYF2024XDNY164//Hainan Province Science and Technology Special Fund/ ; 22206152//National Natural Science Foundation of China/ ; },
mesh = {*DNA Methylation ; Animals ; *Transcription Factors/genetics/metabolism ; Mice ; *Gene Transfer, Horizontal ; Gene Expression Regulation, Bacterial ; Phylogeny ; Flagella/genetics ; Genome, Bacterial ; Bacterial Proteins/genetics/metabolism ; *DNA Restriction-Modification Enzymes/genetics ; *Bacteria/genetics/pathogenicity ; Evolution, Molecular ; },
abstract = {The Type I restriction-modification (RM) system, encoded by the hsdR, hsdM, and hsdS genes, plays a crucial role in shaping the prokaryotic DNA methylation landscape. Although known for defending against foreign DNA, key aspects of its evolutionary trajectory and functional implications after stable inheritance remain poorly understood. In this study, we identified four primary types of Type I RM systems across 4273 prokaryotic genomes based on gene arrangement. Among these, the 5'-hsdR, hsdM, hsdS-3' (RMS) configuration emerged as the most evolutionarily advanced form. Phylogenetic reconstruction revealed that RMS was formed through gene duplication, horizontal gene transfer, and gene loss, and it now stably exists in bacteria. Functional characterization demonstrated that RMS deletion in bacteria led to the absence of flagella and a significant reduction in their ability to colonize and infect mice. Integrated multi-omics analysis uncovered a potential regulatory cascade where RMS modulates the expression of transcription factors via DNA methylation, which in turn regulate downstream flagellar and chemotaxis genes, thereby influencing bacterial pathogenicity. These findings establish a complete evolutionary-functional paradigm, elucidating how (evolutionary trajectory) and why (functional constraints) RMS has been stably inherited in bacterial genomes, and revealing the molecular mechanism through which RMS orchestrates bacterial pathogenicity.},
}

*DNA Methylation
Animals
*Transcription Factors/genetics/metabolism
Mice
*Gene Transfer, Horizontal
Gene Expression Regulation, Bacterial
Phylogeny
Flagella/genetics
Genome, Bacterial
Bacterial Proteins/genetics/metabolism
*DNA Restriction-Modification Enzymes/genetics
*Bacteria/genetics/pathogenicity
Evolution, Molecular

@article {pmid40650002,
year = {2025},
author = {Msweli, SM and Padayachee, T and Khumalo, T and Nelson, DR and Lamb, DC and Syed, K},
title = {Structure-Function Analysis of the Steroid-Hydroxylating Cytochrome P450 109 (CYP109) Enzyme Family.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
doi = {10.3390/ijms26136219},
pmid = {40650002},
issn = {1422-0067},
support = {PMDS230527110616 and MND210504599108//National Research Foundation (NRF), South Africa/ ; RA22102865602//National Research Foundation (NRF), South Africa/ ; },
mesh = {*Cytochrome P-450 Enzyme System/chemistry/metabolism/genetics ; Hydroxylation ; *Steroids/metabolism/chemistry ; Phylogeny ; Structure-Activity Relationship ; Humans ; Catalytic Domain ; Bacteria/enzymology ; Models, Molecular ; },
abstract = {Steroids are found in bacteria and eukaryotes, and genes potentially encoding steroid metabolic enzymes have also been identified in giant viruses. For decades, hydroxylated steroids have been utilized in medicine to treat various human diseases. The hydroxylation of steroids can be achieved using microbial enzymes, especially cytochrome P450 monooxygenases (CYPs/P450s) and is well documented. Understanding the structural determinants that govern the regio- and stereoselectivity of steroid hydroxylation by P450s is essential in order to fully exploit their potential. Herein, we present a comprehensive analysis of the steroid-hydroxylating CYP109 family across the domains of life and delineate the structural determinants that govern steroid hydroxylation. Data mining, annotation, and phylogenetic analysis revealed that CYP109 family members are highly populated in bacteria, and indeed, these members passed from bacteria to archaea by horizontal gene transfer, leading to the evolution of P450s in archaea. Analysis of twelve CYP109 crystal structures revealed large, flexible, and dynamic active site cavities that can accommodate multiple ligands. The correct positioning and orientation of the steroid in the active site cavity and the nature of the C17 substituent on the steroid molecule influence catalysis. In an analogous fashion to the CYP107 family, the amino acid residues within the CYP109 binding pocket involve hydrophilic and hydrophobic interactions, influencing substrate orientations and anchoring and determining the site of hydroxylation and catalytic activity. A handful of amino acids, such as Val84, Val292, and Ser387 in CYP109B4, have been found to play a role in determining the catalytic regiospecificity, and a single amino acid, such as Arg74 in CYP109A2, has been found to be essential for the enzymatic activity. This work serves as a reference for the precise understanding of CYP109 structure-function relationships and for P450 enzymes in general. The findings will guide the genetic engineering of CYP109 enzymes to produce valuable steroid molecules of medicinal and biotechnological importance.},
}

*Cytochrome P-450 Enzyme System/chemistry/metabolism/genetics
Hydroxylation
*Steroids/metabolism/chemistry
Phylogeny
Structure-Activity Relationship
Humans
Catalytic Domain
Bacteria/enzymology
Models, Molecular

@article {pmid40649886,
year = {2025},
author = {Chang, TY and Lin, LC and Kao, CY and Lu, JJ},
title = {Study of lug Operon, SCCmec Elements, Antimicrobial Resistance, MGEs, and STs of Staphylococcus lugdunensis Clinical Isolates Through Whole-Genome Sequencing.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
doi = {10.3390/ijms26136106},
pmid = {40649886},
issn = {1422-0067},
support = {TCRD-TPE-NSTC-113-18 and TCRD-TPE-114-04(1/3)//Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation/ ; NSTC 113-2320-B-303-006//National Science and Technology Council, Taiwan/ ; },
mesh = {*Staphylococcus lugdunensis/genetics/drug effects/isolation & purification ; Whole Genome Sequencing ; *Operon ; Humans ; *Staphylococcal Infections/microbiology ; Multilocus Sequence Typing ; Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Interspersed Repetitive Sequences ; Phylogeny ; Microbial Sensitivity Tests ; *Bacterial Proteins/genetics ; CRISPR-Cas Systems ; },
abstract = {Staphylococcus lugdunensis is a coagulase-negative staphylococcus known for its significant pathogenic potential, often causing severe infections such as endocarditis and bacteremia, with virulence comparable to S. aureus. Despite general susceptibility to most antibiotics, the emergence of oxacillin-resistant strains is increasingly concerning. This study conducted whole-genome sequencing on 20 S. lugdunensis isolates from Chang Gung Memorial Hospital to explore their genetic diversity, antimicrobial resistance mechanisms, and mobile genetic elements. The lugdunin biosynthetic operon, essential for antimicrobial peptide production, was present in multilocus sequence typing (MLST) types 1, 3, and 6 but absent in STs 4, 27, and 29. Additionally, IS256 insertion elements, ranging from 7 to 17 copies, were identified in four strains and linked to multidrug resistance. CRISPR-Cas systems varied across STs, with type III-A predominant in ST1 and ST6 and type IIC in ST4, ST27, and ST29; notably, ST3 lacked CRISPR systems, correlating with a higher diversity of SCCmec elements and an increased potential for horizontal gene transfer. Phage analysis revealed stable phage-host associations in ST1, ST6, and ST29, whereas ST4 displayed a varied prophage profile. Phenotypic resistance profiles generally aligned with genomic predictions, although discrepancies were observed for aminoglycosides and clindamycin. These findings highlight the complex genetic landscape and evolutionary dynamics of S. lugdunensis, emphasizing the need for genomic surveillance to inform clinical management and prevent the spread of resistant strains.},
}

*Staphylococcus lugdunensis/genetics/drug effects/isolation & purification
Whole Genome Sequencing
*Operon
Humans
*Staphylococcal Infections/microbiology
Multilocus Sequence Typing
Genome, Bacterial
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
Drug Resistance, Multiple, Bacterial/genetics
Interspersed Repetitive Sequences
Phylogeny
Microbial Sensitivity Tests
*Bacterial Proteins/genetics
CRISPR-Cas Systems

@article {pmid40648052,
year = {2025},
author = {Ciniglia, C and Pollio, A and Pozzuoli, E and Licata, M and Nappi, N and Davis, SJ and Iovinella, M},
title = {Mosaic Evolution of Membrane Transporters in Galdieriales.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {13},
pages = {},
doi = {10.3390/plants14132043},
pmid = {40648052},
issn = {2223-7747},
support = {IF\R2\2320049//Biological Sciences Research Council (BBSRC) White Rose Doctoral Training Partnership, the UKRI National Productivity Investment Fund (NPIF) through the BBSRC, and the Royal Society/ ; D.R. 509 del 13/06/2022//University of Campania L. Vanvitelli, Caserta 848 (Progetto MIREA)/ ; },
abstract = {Membrane transporters are vital for solute movement and localisation across cellular compartments, particularly in extremophilic organisms such as Galdieriales. These red algae thrive in geothermal and metal-rich environments, where adaptive transporter systems contribute to their metabolic flexibility. While inventories of transporter genes in the species Galdieria sulphuraria have previously been compiled, their phylogenetic origins remain incompletely resolved. Here, we conduct a comparative phylogenetic analysis of three transporter families-Major Facilitator Superfamily (MFS). Amino acid-Polyamine-Organocation (APC) and the natural resistance-associated macrophage protein (Nramp)-selected from overexpressed transcripts in G. sulphuraria strain SAG 107.79. Using sequences from six Galdieriales species and orthologs from diverse taxa, we reconstructed maximum likelihood trees to assess conservation and potential horizontal gene transfer (HGT). The MFS subfamilies revealed contrasting patterns: sugar porters (SPs) exhibited polyphyly and fungal affinity, suggesting multiple HGT events, while phosphate:H[+] symporters (PHSs) formed a coherent monophyletic group. APC sequences were exclusive in G. sulphuraria and extremophilic prokaryotes, indicating a likely prokaryotic origin. In contrast, Nramp transporters were broadly conserved across eukaryotes and prokaryotes, showing no signs of recent HGT. Together, these findings highlight the mosaic evolutionary history of membrane transporters in Galdieriales, shaped by a combination of vertical inheritance and taxon-specific gene acquisition events, and provide new insight into the genomic strategies underpinning environmental resilience in red algae.},
}

@article {pmid40647009,
year = {2025},
author = {Trząskowska, M and Naammo, EE and Salman, M and Afolabi, A and Wong, CWY and Kołożyn-Krajewska, D},
title = {Risk Profile of Bacteriophages in the Food Chain.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {13},
pages = {},
doi = {10.3390/foods14132257},
pmid = {40647009},
issn = {2304-8158},
abstract = {Phages are considered effective biocontrol agents for improving food safety due to their specific interaction with pathogens. It is essential to recognise that zero risk does not exist, and as biological agents, phages must be continuously evaluated for potential adverse effects on human health in both food and clinical contexts. This is the first bacteriophage risk profile performed according to the methodology recommended by FAO/WHO and EFSA. Key safety concerns regarding phage use in the food sector include the risk of horizontal gene transfer, especially regarding antibiotic resistance genes among bacteria. While such occurrences are contextually dependent and rare, they warrant further scrutiny. Moreover, improper phage application during food processing could lead to the emergence of resistant bacterial strains, compromising the long-term efficacy of phage interventions. Currently, there is limited evidence indicating any health risks linked to phage consumption or pathogenic behaviour (e.g., possible association between bacteriophages and Parkinson's disease). Despite numerous studies affirming the safety and efficacy of phages in the food chain, continuous monitoring remains crucial. In particular, the responses of susceptible populations to phage exposure should be carefully examined.},
}

@article {pmid40643763,
year = {2025},
author = {Naqvi, SAH and Abbas, A and Hasnain, A and Bilal, Z and Hakim, F and Shabbir, M and Amin, A and Iqbal, MU},
title = {Advancing fungal phylogenetics: integrating modern sequencing, dark taxa discovery, and machine learning.},
journal = {Archives of microbiology},
volume = {207},
number = {9},
pages = {192},
pmid = {40643763},
issn = {1432-072X},
mesh = {*Fungi/genetics/classification/isolation & purification ; *Machine Learning ; *Phylogeny ; High-Throughput Nucleotide Sequencing/methods ; Mycoses/microbiology/diagnosis ; Humans ; Genome, Fungal ; DNA, Fungal/genetics ; },
abstract = {The study of fungal genetics has undergone transformative advancements in recent decades, profoundly reshaping our understanding of fungal diversity, evolution, and pathogenesis. This review synthesizes cutting-edge molecular techniques revolutionizing fungal diagnostics, with a focus on DNA fingerprinting, next-generation sequencing (NGS), and third-generation sequencing (TGS), alongside their applications in species identification, phylogenetic reconstruction, and disease management. We critically evaluated the utility of molecular markers such as the Internal Transcribed Spacer (ITS), Large Subunit (LSU), and protein-coding genes (e.g., RPB1, RPB2, TEF1-α), which have emerged as indispensable tools for resolving taxonomic ambiguities and cryptic species complexes. While ITS remains the gold standard for fungal barcoding due to its high interspecific variability, multi-locus strategies integrating loci like β-tubulin and CaM enhance resolution in challenging genera such as Aspergillus, Fusarium, and Penicillium. The review underscores the limitations of traditional morphology-based taxonomy, particularly its inability to address cryptic speciation or non-reproductive fungal phases. Advances in NGS platforms (e.g., Illumina, PacBio, Oxford Nanopore) have overcome these barriers, enabling high-throughput genomic analyses that reveal unprecedented fungal diversity in environmental and clinical samples. TGS technologies, with their long-read capabilities (> 10 kb), now facilitate the assembly of complex genomes, identification of structural variants, and exploration of horizontal gene transfer events, offering new insights into fungal adaptation and pathogenicity. Despite these breakthroughs, challenges persist in resolving intragenomic variation, reconciling gene tree discordance, and standardizing workflows for large-scale fungal population studies. The integration of multi-omics approaches (transcriptomics, proteomics, metabolomics) and machine learning algorithms promises to address these gaps, enabling predictive modeling of antifungal resistance and host-pathogen interactions. Collaborative efforts among mycologists, clinicians, and bioinformaticians are critical to harmonizing data sharing, refining diagnostic pipelines, and translating genomic insights into precision therapies. Fungal-related diseases pose escalating threats to global agriculture, healthcare, and ecosystem stability. Climate change further exacerbates pathogen spread and antifungal resistance, necessitating innovative management strategies. Emerging tools such as CRISPR-based diagnostics, portable sequencers (MinION), and synthetic biology platforms hold promise for real-time pathogen surveillance and engineered biocontrol solutions. By bridging genomic innovation with interdisciplinary collaboration, this review charts a roadmap for advancing fungal diagnostics, enhancing taxonomic clarity, and mitigating the socio-economic impacts of fungal diseases in an era of rapid environmental change.},
}

*Fungi/genetics/classification/isolation & purification
*Machine Learning
*Phylogeny
High-Throughput Nucleotide Sequencing/methods
Mycoses/microbiology/diagnosis
Humans
Genome, Fungal
DNA, Fungal/genetics

@article {pmid40643650,
year = {2025},
author = {Khan, MS and Neyaz, A and Shukla, LK and Saleem, M and Ahmad, I},
title = {Epidemiological and molecular characterisation of carbapenemase-producing Pseudomonas aeruginosa from a tertiary care hospital, India.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {},
number = {},
pages = {},
pmid = {40643650},
issn = {1432-1912},
support = {Grant No. R.G.P.2/152/46//The Deanship of Research and Graduate Studies, King Khalid University, Abha, Saudi Arabia/ ; },
abstract = {This study investigates the epidemiological and molecular characteristics of carbapenemase-producing Pseudomonas aeruginosa among 382 clinical isolates. Carbapenemase production was significantly associated with male gender (χ[2] = 4.97; p = 0.025; Cramer's V = 0.114) and with higher prevalence in casualty (χ[2] = 6.89; p = 0.009; Cramer's V = 0.134). A notably greater proportion of carbapenemase-producing isolates were recovered from pus specimens (χ[2] = 5.50; p = 0.019; Cramer's V = 0.120), suggesting specific tissue tropism. Antibacterial susceptibility profiling revealed high resistance to β-lactams (e.g. cefepime (40.2%), ceftazidime (42.4%)) and fluoroquinolones (ciprofloxacin (36.5%), levofloxacin (38.9%)), while colistin (84.4%) and amikacin (83.1%) retained high efficacy. Among carbapenem-resistant strains (n = 258), multidrug resistance (MDR) was most prevalent (55.4%), followed by extensively drug-resistant (XDR, 35.7%) and pan-drug-resistant (PDR, 8.9%) phenotypes. Molecular analysis of 164 resistant isolates identified blaNDM-1 as the dominant gene (32.9%), followed by blaOXA-48 (17.1%) and blaVIM (9.1%). Co-expression patterns were frequent, with dual and triple gene combinations suggesting horizontal gene transfer and clonal dissemination. Gene distribution showed male predominance and high prevalence in ICU, Surgery, and TB & Chest departments, indicating critical hotspots for MDR containment. Specimen-wise, blaNDM-1 was prominent in pus, wound swabs, and blood, while blaOXA-48 and blaVIM were enriched in sputum, pleural fluid, and BAL. The triple gene combination was most prevalent in BAL and urine samples. These findings highlight a high burden of carbapenem resistance, driven by blaNDM-1 and its combinations, with significant clinical and infection control implications. Robust antibacterial stewardship and targeted surveillance in high-risk departments are imperative to curb the spread of these highly resistant pathogens.},
}

@article {pmid40642983,
year = {2025},
author = {Kałuski, Ł and Stefańczyk, E and Głowacka-Rutkowska, A and Gawor, J and Empel, J and Orczykowska-Kotyna, M and Szczypkowska, A and Żuchniewicz, K and Gromadka, R and Łobocka, M},
title = {Characterization of a novel Phietavirus genus bacteriophage and its potential for efficient transfer of modified shuttle plasmids to Staphylococcus aureus strains of different clonal complexes.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0333224},
doi = {10.1128/spectrum.03332-24},
pmid = {40642983},
issn = {2165-0497},
abstract = {UNLABELLED: Staphylococcus aureus is a significant human pathogen responsible for various nosocomial and community-acquired infections, leading to considerable morbidity and mortality worldwide. Temperate bacteriophages contribute to its virulence and facilitate the dissemination of pathogenicity traits. We isolated a novel siphovirus of the Phietavirus genus, ASZ22RN, derived from a prophage of an S. aureus clonal complex 7 strain and capable of propagating in the prophage-free laboratory strain RN4220. ASZ22RN either productively infected or lysed from without all 47 tested S. aureus clinical strains across 12 clonal complexes (CCs), demonstrating its ability to puncture their cell envelopes. When ASZ22RN was propagated in RN4220 cells harboring an S. aureus-Escherichia coli plasmid replicating via theta mode, it transduced the plasmid to plasmid-free RN4220 with low frequency. The transduction frequency increased by nearly five orders of magnitude when the plasmid contained a fragment of ASZ22RN DNA (terS). Most terS+ plasmid-transducing particles carried plasmid concatamers, while some carried plasmid-phage DNA hybrids, as demonstrated by DNA sequencing. Strains from all tested CCs served as recipients for transduction, regardless of the presence of type I restriction-modification enzymes targeting plasmid/phage DNA, or prophages with lysis-lysogeny switch regions conferring superinfection immunity to ASZ22RN. Our results indicate that intracellular phage defense systems do not prevent phage-mediated plasmid transfer and demonstrate a simple method for introducing plasmids constructed in E. coli into clinical S. aureus isolates. Moreover, the presence of the ASZ22RN lysis-lysogeny switch region in 21% of tested ASZ22RN-resistant strains highlights superinfection exclusion as a dominant mechanism of resistance to siphoviruses in staphylococci.

IMPORTANCE: This study highlights the capacity of a newly isolated staphylococcal Phietavirus, ASZ22RN, to transfer a low-copy-number shuttle Staphylococcus aureus-Escherichia coli plasmid to various S. aureus strains representing major clonal complexes from among clinical isolates. By increasing the plasmid transduction efficiency in an ASZ22RN-specific manner, we show that the primary factor determining a given strain's ability to be a recipient in transduction is the capacity of transducing phage to puncture the cell envelopes of this strain. This can be determined not only based on productive phage infection but also lysis from without. Major intracellular mechanisms protecting S. aureus from productive phage infection do not impede the transduction-mediated acquisition of plasmids. Moreover, the lack of phage DNA in most of the plasmid-transducing virions indicates the lack of phage contamination in most transductants. Our results offer a promising approach for developing efficient pipelines to introduce plasmids constructed in E. coli to clinical S. aureus isolates.},
}

@article {pmid40638953,
year = {2025},
author = {Ge, P and Rashid, FM and Dame, RT},
title = {The role of nucleoid-associated proteins in mediating responses to environmental changes.},
journal = {Current opinion in microbiology},
volume = {87},
number = {},
pages = {102628},
doi = {10.1016/j.mib.2025.102628},
pmid = {40638953},
issn = {1879-0364},
abstract = {Bacteria face diverse environmental challenges, such as changes in temperature, pH, and osmolarity, and exposure to antibiotics, which necessitate adaptive responses for survival. The chromosome-structuring nucleoid-associated proteins (NAPs) are key to these responses owing to their role in global gene regulation. In this review, we summarize the functional interplay between environmental challenges and NAPs, and the adaptive responses mediated by NAPs. Specifically, physicochemical environmental factors modify the transcription level of NAP genes and affect protein activity, which facilitates bacterial adaptation via a short-term strategy. Additionally, NAPs regulate horizontally transferred genes, such as those involved in antibiotic resistance and virulence, by affecting their expression and integration into the host genome. Via this long-term strategy, NAPs contribute to both stress resilience and the evolution of bacterial traits, ensuring survival under environmental stress while facilitating genetic diversity through horizontal gene transfer.},
}

@article {pmid40638393,
year = {2025},
author = {Zhang, S and Li, X and Li, Z and Zhang, Y and Wang, Y and Xu, L},
title = {Horizontal gene transfer-mediated enhancement of gut antifungal defense facilitates host plant adaptation in an invasive pest.},
journal = {Cell reports},
volume = {44},
number = {7},
pages = {115970},
doi = {10.1016/j.celrep.2025.115970},
pmid = {40638393},
issn = {2211-1247},
abstract = {Invasive pests exploit adaptive mechanisms including horizontal gene transfer (HGT) to overcome environmental challenges. Here, we show that the invasive fall webworm Hyphantria cunea acquires a chitinase gene (HcuChiA) via HGT, facilitating adaptation to the novel host Metasequoia glyptostroboides. Comparative transcriptomics across five host plants and an artificial diet identified HcuChiA as uniquely upregulated on M. glyptostroboides. Single-cell transcriptomics and spatiotemporal profiling confirmed gut-specific expression, and phylogenetic analysis traced HcuChiA to a bacterial donor. RNAi knockdown of HcuChiA increased the larval mortality on M. glyptostroboides, while recombinant HcuChiA displayed chitinase activity and broad-spectrum antifungal effects against entomopathogens. Elimination of gut fungi abolished the RNAi-induced mortality increase, demonstrating HcuChiA's role in gut antifungal immunity. These findings reveal that HGT-derived enzymes enhance host expansion in invasive pests by strengthening immune defenses, offering insights into multi-host adaptation and the evolutionary significance of HGT.},
}

@article {pmid40638214,
year = {2025},
author = {Paintsil, EK and Adu-Asiamah, CK and Boahen, KG and Akenten, CW and Kwarteng, A and Berg, S and Obiri-Danso, K and May, J and Dekker, D and Ofori, LA},
title = {Genomic insights into the diversity, antimicrobial resistance and zoonotic potential of Campylobacter fetus across diverse hosts and geographies.},
journal = {Microbial genomics},
volume = {11},
number = {7},
pages = {},
pmid = {40638214},
issn = {2057-5858},
mesh = {Animals ; *Campylobacter fetus/genetics/drug effects/classification/isolation & purification/pathogenicity ; Humans ; Cattle ; *Campylobacter Infections/microbiology/veterinary ; Sheep ; Genome, Bacterial ; Genetic Variation ; *Zoonoses/microbiology ; Phylogeny ; Genomics ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Reptiles/microbiology ; },
abstract = {Introduction. Campylobacter fetus causes reproductive diseases in livestock and can lead to zoonotic infections such as bacteraemia, particularly in immunocompromised individuals. Despite its significance, its genomic characteristics remain poorly understood. This study analysed 114 publicly available C. fetus genomes to provide global insights into genetic diversity, antimicrobial resistance (AMR) and zoonotic risk.Results. A total of 32 distinct sequence types (STs) were identified across 111 of the 114 C. fetus genomes, spanning 6 continents and diverse hosts (cattle, humans, sheep and reptiles). The majority of strains from cattle (75.6%, n/N=34/45) were assigned to ST-4, which was the most prevalent overall (n=45), while human-associated genomes exhibited the highest diversity with 16 STs. C. fetus subsp. venerealis (Cfv) and its biovar intermedius (Cfvi) genomes clustered closely, forming distinct branches at the biovar level; however, six Cfv genomes were located within Cfvi clades, suggesting a shared ancestry. C. fetus subsp. testudinum (Cft), primarily isolated from humans (60.0%, n/N=18/30), exhibited a more diverse genetic profile, with 20 STs. Cfv from North America and Cfvi from South America formed distinct geographic clusters, while C. fetus subsp. fetus genomes showed no clear geographic patterns, indicating global spread. Pangenomic analysis revealed substantial variation in gene presence/absence in Cft. Five AMR genes were detected, with tet(O) (n=3) being the most common. A total of 220 plasmid contigs were identified across 47 genomes, predominantly in Cfvi (66.8%, n/N=147/220) and Cfv (29.1%, n/N=64/220). Horizontal gene transfer analysis identified 140 genomic islands across 41 genomes, and virulence factor analysis revealed cheY as the sole conserved virulence gene across 35 genomes.Conclusion. These findings provide critical insights into the genomic diversity, zoonotic potential and global distribution of C. fetus, emphasizing the need for integrated genomic and epidemiological strategies to assess its impact on human and animal health.},
}

Animals
*Campylobacter fetus/genetics/drug effects/classification/isolation & purification/pathogenicity
Humans
Cattle
*Campylobacter Infections/microbiology/veterinary
Sheep
Genome, Bacterial
Genetic Variation
*Zoonoses/microbiology
Phylogeny
Genomics
*Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
Reptiles/microbiology

@article {pmid40637797,
year = {2025},
author = {Giani, NM and Lim, SJ and Anderson, LC and Paterson, AT and Engel, AS and Campbell, BJ},
title = {Variation in accessory and horizontal gene transfer-associated genes drives lucinid endosymbiont diversity.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf074},
pmid = {40637797},
issn = {1574-6941},
abstract = {Lucinid bivalves harbor environmentally acquired endosymbionts within the class Gammaproteobacteria and genus Candidatus Thiodiazotropha. Despite recent studies focused on lucinid endosymbiont genomic and functional diversity, processes influencing species diversity have been understudied. From the analysis of 333 metagenome-assembled genomes (MAGs) from 40 host species across eight waterbodies and 77 distinct locations, 272 were high quality MAGs of Ca. Thiodiazotropha endosymbionts that represented 11 genomospecies. Of those, two new genomospecies from lucinids collected from The Bahamas and Florida (USA) were identified, Ca. Thiodiazotropha fisheri and Ca. Thiodiazotropha grosi. Metabolic specialization was evident, such as potential adaptations to diverse carbon sources based on detection of C1 metabolic genes in eight genomospecies. Genes associated with defense, symbiosis/pathogenesis, and horizontal gene transfer (HGT) were also distinct across genomospecies. For instance, Ca. T. taylori exhibited lower abundances of HGT-associated genes compared to other genomospecies, particularly Ca. T. endolucinida, Ca. T. lotti, and Ca. T. weberae. HGT-associated genes were linked to previously unreported retron-type reverse transcriptases, dsDNA phages, and phage resistance. Collectively, the pangenome highlights how lucinid endosymbiont diversity has been shaped by geographic and host-specific interactions linked to gene loss and HGT through time.},
}

@article {pmid40633655,
year = {2025},
author = {Parab, AS and Ghose, M and Manohar, CS},
title = {Antibiotic-resistant bacteria in marine productive zones of the eastern Arabian Sea: Implications for human and environmental health.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {383},
number = {},
pages = {126793},
doi = {10.1016/j.envpol.2025.126793},
pmid = {40633655},
issn = {1873-6424},
abstract = {The increasing threat of antibiotic resistance is a major global concern affecting human and environmental health. Marine environments, though underexplored, are emerging as significant reservoirs for antibiotic resistance genes (ARGs). This study provides genome-resolved shotgun metagenomic insights into the seasonal and spatial dynamics of ARGs in the chlorophyll maximum zones of the eastern Arabian Sea, focusing on bacterial communities from coastal (30 m) and offshore (600 m) depths. Using a shotgun metagenomic approach, 31 potential ARGs were identified across both non-monsoon and monsoon seasons, with higher abundance observed in offshore stations during the non-monsoon season. Multidrug resistance genes such as blaEFM-1, catB2 and mexK, conferring resistance to carbapenems, chloramphenicol and multiple antibiotics, were prevalent in taxa like Staphylococcus sp., Qipengyuania sp. and Alcanivorax sp. Clinically relevant taxa, including Pseudomonas sp. and Staphylococcus sp., harbored ARGs, which may raise concerns regarding potential seafood-mediated ARG transmission. The significant enrichment and co-localization of mobile genetic elements (MGEs) with ARGs suggest enhanced horizontal gene transfer among native marine bacteria in the offshore environments. However, the limited distribution of ARGs and the absence of associated MGEs during the monsoon season may result from dilution caused by freshwater influx. Comparative functional analysis revealed stress-related functional enrichment in ARG-carrying metagenomic assembled genomes, suggesting environmental stress may enhance the spread of ARGs within offshore microbial communities. These findings challenge the coastal-centric view of marine antibiotic resistance by identifying offshore waters as underrecognized ARG reservoirs. Establishing a genomic baseline for One Health ARG surveillance, this study underscores the urgent need to integrate offshore regions into global monitoring frameworks to protect marine ecosystems and safeguard public health.},
}

@article {pmid40628208,
year = {2025},
author = {Wu, Y and Tan, D and Wang, D and Ogendi, GM and Balcazar, JL and Zhu, D and Sun, M and Hu, F},
title = {Bacteriophage facilitated transmission of multidrug efflux pump regulatory genes in Pseudomonas aeruginosa.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {139151},
doi = {10.1016/j.jhazmat.2025.139151},
pmid = {40628208},
issn = {1873-3336},
abstract = {The emergence of multidrug-resistant Pseudomonas aeruginosa strains, primarily driven by efflux pumps that expel antibiotics, poses a serious global health threat. Phages, particularly members of the class Caudoviricetes (94.7 %), play a significant role in the horizontal transfer of genetic material among bacterial hosts, potentially contributing to the acquisition and spread of antibiotic resistance genes. In this study, analysis of 6712 P. aeruginosa genomes from the JGI-IMG/VR virus database revealed that all P. aeruginosa RefSeq genome assemblies (GCF accessions) contained efflux pump genes (MexAB-oprM, MexCD-oprJ, and MexEF-oprN) as well as their associated regulatory genes (mexT, mexR, and nfxB). Notably, these genes can be transmitted through phage-mediated horizontal gene transfer, as evidenced by their detection in viral sequences. Among phages harboring these genes, 43.9 % were identified as lysogenic. These phages were predominantly associated with aquatic (33.2 %), human (19.0 %), and terrestrial (16.4 %) environments worldwide, highlighting the potential risks of environmental contamination. Experimental validation using PA1 and PAO1 strains confirmed the role of phages in facilitating horizontal gene transfer. These findings highlight the urgent need to implement surveillance and mitigation measures targeting phage-associated antibiotic resistance dissemination, with direct implications for both public health and environmental safety.},
}

@article {pmid40626882,
year = {2025},
author = {Bello-López, E and Kawabata, A and Cantero, J and Mendoza, S and Pertile, E and Perez-Osegura, A and Cevallos, MA and Peralta, H and Aguilar-Vera, A and Castillo-Ramirez, S},
title = {Genomic epidemiology reveals antibiotic resistance transfer and polyclonal dissemination of Acinetobacter baumannii in a Paraguayan hospital.},
journal = {Antimicrobial agents and chemotherapy},
volume = {},
number = {},
pages = {e0007725},
doi = {10.1128/aac.00077-25},
pmid = {40626882},
issn = {1098-6596},
abstract = {Acinetobacter baumannii is a major nosocomial pathogen worldwide and, specifically, in Latin America. Genomic epidemiology has been instrumental in determining the transmission dynamics of A. baumannii in many countries of the world, yet some Latin American countries have conducted no genomic epidemiology studies. Here, we conduct the first genomic epidemiology study about this pathogen in Paraguay. We sequenced 43 isolates from a big tertiary hospital in Paraguay collected from different wards in 2021 and 2022. Our genomic epidemiology analyses, including almost 200 genomes and considering the main international clones (ICs), show that IC1, IC2, IC4, IC5, and IC7 were found in the hospital. We found novel genetic variation (three novel sequence types as per the Oxford MLST scheme and one as per the Pasteur scheme) within IC7. Antibiotic susceptibility tests show that all but one of the Paraguayan isolates were resistant to carbapenems. Notably, 98% were classified as multidrug-resistant. We detected plasmids in almost all the Paraguayan isolates. Furthermore, we detected cases of recent horizontal transfer of important antibiotic resistance genes between different ICs. On a general note, our findings highlight polyclonal spreading across different hospital wards and horizontal transfer of clinically relevant antibiotic resistance genes among the different clones. On a more local note, this is the first genomic epidemiology study of A. baumannii in Paraguay and will be a reference point for future studies in the country and the region.},
}

@article {pmid40623962,
year = {2025},
author = {Monte, DFM and de Lima Rocha, AD and Lemos, MLP and de Lima, LA and Cabrera, JM and da Silva, NJ and Huang, X and Chen, Z and Brown, EW and Allard, MW and Bell, RL and Toro, M and Meng, J and de Oliveira, CJB},
title = {High Prevalence of Plasmid-Mediated Quinolone Resistance in Salmonella enterica Serovars Isolated From Surface Water.},
journal = {Environmental microbiology},
volume = {27},
number = {7},
pages = {e70140},
doi = {10.1111/1462-2920.70140},
pmid = {40623962},
issn = {1462-2920},
support = {U01FDU001418//U.S. Department of Health and Human Services/ ; Finance Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)/ ; 420755/2023-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 3136678/2020-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 88887.898770/2023-00//Fundação de Apoio à Pesquisa do Estado da Paraíba (FAPESQ)/ ; //Financiadora de Estudo e Projetos (FINEP)/ ; },
mesh = {*Quinolones/pharmacology ; *Salmonella enterica/genetics/drug effects/isolation & purification/classification ; *Plasmids/genetics ; *Anti-Bacterial Agents/pharmacology ; Phylogeny ; Brazil ; *Drug Resistance, Bacterial/genetics ; Serogroup ; Multilocus Sequence Typing ; Microbial Sensitivity Tests ; Whole Genome Sequencing ; *Fresh Water/microbiology ; Prevalence ; },
abstract = {Considering the increasing reports of Salmonella enterica strains resistant to quinolones, antimicrobials frequently employed as therapeutic agents globally, our goal was to investigate the occurrence of plasmid-mediated quinolone resistance (PMQR) determinants in S. enterica recovered from natural surface waters in Paraíba state, Brazil. Water samples (n = 230) were collected monthly in triplicate using modified Moore swabs from 29 sampling sites belonging to 10 large dams. After conventional microbial isolation, representative isolates (n = 938) were submitted to whole genome sequencing, assembly and annotation. Antimicrobial resistance genes (ARGs) were identified, and core genome multilocus sequence typing (cgMLST) was used to infer phylogenetic relationships. Among recovered S. enterica, 130 (13.9%) isolates harboured PMQR determinants; 124 (95.4%) harboured qnrB19, while 6 (4.6%) harboured qnrS1. Multiple other ARGs associated with resistance to aminoglycosides, β-lactams, sulphonamides, tetracyclines and fosfomycin were identified. The diversity of ARGs and plasmids suggests a highly complex resistance landscape. Phylogenetic analysis revealed clustering by serovar and sequence type but not by resistance profile or geographic origin. The absence of association between phylogeny and ARGs highlights the potential role of horizontal gene transfer in disseminating resistance genes in water. Our findings reinforce the importance of antimicrobial resistance surveillance in surface waters.},
}

*Quinolones/pharmacology
*Salmonella enterica/genetics/drug effects/isolation & purification/classification
*Plasmids/genetics
*Anti-Bacterial Agents/pharmacology
Phylogeny
Brazil
*Drug Resistance, Bacterial/genetics
Serogroup
Multilocus Sequence Typing
Microbial Sensitivity Tests
Whole Genome Sequencing
*Fresh Water/microbiology
Prevalence

@article {pmid40623055,
year = {2025},
author = {Frazão, N and Seixas, E and Mischler, M and Moura-de-Sousa, J and Barreto, HC and Gordo, I},
title = {Clonal interference and genomic repair during strain coexistence in the gut.},
journal = {PLoS genetics},
volume = {21},
number = {7},
pages = {e1011777},
doi = {10.1371/journal.pgen.1011777},
pmid = {40623055},
issn = {1553-7404},
abstract = {Humans and other mammals are colonized by multiple strains of Escherichia coli, but the tempo and mode of evolution of different coexisting strains, between whom horizontal gene transfer (HGT) can occur, is poorly understood. Here, we follow in real time the evolution of two phylogenetic distinct strains of E. coli that co-colonize the mouse gut with different population sizes. We find qualitative differences in evolutionary dynamics between strains within the same host. In the strain with larger population size intense clonal interference occurs and polymorphism at a neutral marker locus is maintained, while in the strain with lower population size complete selective sweeps and loss of neutral marker polymorphism occurs. Strain coexistence is also accompanied by rich dynamics of HGT from one strain to the other. Strikingly, a rare HGT event could restore a previously lost genomic region in the recipient strain. Furthermore, we detect for the first time a case of phage piracy in the gut, where a putative phage satellite, lacking essential genes for their own replication, was likely mobilized by a helper phage to transfer between bacterial hosts. Our results show that HGT is a key mechanism underlying genetic exchanges and adaptive genomic repair in the mammalian gut.},
}

@article {pmid40622509,
year = {2025},
author = {Can, A and Baysal, Ö},
title = {A Chitinase Gene Belonging to Serratia marcescens GBS19 Reveals Horizontal Gene Transfer within Bacterial Strains Besides its Biocontrol Potential Against Myzus persicae.},
journal = {Biochemical genetics},
volume = {},
number = {},
pages = {},
pmid = {40622509},
issn = {1573-4927},
abstract = {Microorganisms produce diverse enzymes with applications in biological control and pest management. Chitinase enzymes degrade chitin, a structural component of insect exoskeletons and fungal cell walls, offering sustainable and environmentally friendly solutions for agricultural pest and pathogen management. This study focused on the chiA gene from our original strain belonging to Serratia marcescens identified using multi locus sequencing and ribosomal DNA analysis, amplified via PCR, cloned into expression vectors, and expressed as a recombinant protein. The chiA enzyme was purified using His-tag affinity chromatography and showed optimal activity at 40 °C and pH 5. The purified chiA enzyme exhibited strong insecticidal activity against Myzus persicae, with an lethal dose50 of 15.8 ppm. The comparative genomic analysis using MUMMER4 and MAUVE, identified horizontal gene transfer (HGT) events and genomic rearrangements within reference strain and our strain GBS19. The recombinant chiA enzyme exhibited 98.4% similarity with reference chiA sequences, highlighting its evolutionary conservation. Molecular docking studies confirmed a binding affinity of - 5.74 kcal/mol between the enzyme and chitin monomers, supported by interaction studies with modeled chitin layer. In addition, we have also predicted the most variable mutations required for enzyme stability and enzymatic activity enhancement in cloned amino acid sequence using protein AI tool, which will also guide us further studies linked to site-directed mutagenesis. This study demonstrates the potential of S. marcescens chitinase as an effective biocontrol agent against Myzus persicae. It underscores the importance of recombinant DNA technology in sustainable agriculture and sheds light on the evolutionary adaptation of chitinase genes through HGT and mutational events.},
}

@article {pmid40621911,
year = {2025},
author = {Yu, J and Gao, J-W and Cao, K and He, D-Y and Xu, L and Fu, G-Y and Sun, C},
title = {Characterization of two novel species of the genus Flagellimonas reveals the key role of vertical inheritance in the evolution of alginate utilization loci.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0091725},
doi = {10.1128/spectrum.00917-25},
pmid = {40621911},
issn = {2165-0497},
abstract = {Flavobacteriaceae is the major participant in the degradation of algal polysaccharides. With diverse polysaccharide utilization loci (PULs) and specific carbohydrate-active enzymes (CAZymes), Flavobacteriaceae strains appear to have different abilities in algal polysaccharide degradation and therefore change their roles in the bacterial community. Here, we identified two novel isolates as two novel species of genus Flagellimonas with the names Flagellimonas alginolytica sp. nov. and Flagellimonas cixiensis sp. nov. Furthermore, the comprehensive genomic comparison of 41 Flagellimonas genomes revealed that Flagellimonas strains were diverse in the CAZymes and PUL profiles and exhibited a preference for polysaccharides derived from brown algae. The evolutionary analysis of alginate utilization loci (AUL) in this genus illuminated that the function genes in AULs, that is, PL7 and PL17, were more reliant on the stable inheritance from ancestors associated with gene duplication and loss rather than horizontal gene transfer (HGT) from outside, and the AUL structures exhibited a trend of simplification which resulted in the incidental decrease in alginate degradation ability. This study highlights the important role of vertical inheritance in the evolution of AULs and proves that the discrepancy in AUL structure can arouse phenotypic differences, providing a new perspective on the evolution of AUL and the niche adaptation mechanism of Flavobacteriaceae strains.IMPORTANCEFlavobacteriaceae play an important role in the marine carbon cycle with their noteworthy ability in algal polysaccharides degradation, which is primarily reliant on diverse polysaccharide utilization loci (PULs). Our study highlights the crucial role of vertical inheritance in the evolution of alginate utilization loci (AUL) in Flagellimonas strains and reveals the AUL structural simplification found in Flagellimonas strains that will lead to the reduction of alginate degradation ability. These insights advance understanding of niche adaptation strategy and related evolutionary mechanisms of Flavobacteriaceae strains.},
}

@article {pmid40619778,
year = {2025},
author = {Bhide, AJ},
title = {Redefining the nitroplast: Recent insights into the endosymbiontto- organelle transition.},
journal = {Journal of biosciences},
volume = {50},
number = {},
pages = {},
pmid = {40619778},
issn = {0973-7138},
mesh = {*Symbiosis/genetics ; Gene Transfer, Horizontal ; Photosynthesis/genetics ; *Plastids/genetics ; Cyanobacteria/genetics ; Rhodophyta/genetics ; Mitochondria/genetics ; Chlorophyta/genetics ; Alphaproteobacteria/genetics ; Biological Evolution ; Evolution, Molecular ; Dinoflagellida/genetics ; },
abstract = {One of the most remarkable events in cellular evolution is the endosymbiosis of α-proteobacteria with a single archaean host cell, a rare evolutionary process, which eventually led to the transformation of symbionts into fully functional mitochondrial organelles in eukaryotes. Evolutionary events related to plants occurred almost 1.6 billion years ago, when eukaryotic heterotrophs acquired a β-cyanobacterium (containing 1B RUBISCO) in what is termed as primary endosymbiosis. Further, this composite cell lineage evolved into three photosynthetic lineages: green algae (plants), red algae and the glaucophytes. Thereafter, a secondary, and tertiary endosymbiosis event occurred giving rise to distinct kinds of green and red-derived photosynthetic plastids, which can be observed in a few haptophytes and dinoflagellates respectively. Eventually, these endosymbionts acquired characteristic cellular properties such as two/multiple envelope membranes and reduction of their genomes through either loss or concerted endosymbiotic gene transfer (EGT) into the nucleus, which ultimately led to the decline of more than three quarters of coding capacity and complete loss of several metabolic pathways. This loss, however, is partly compensated by import of nuclearencoded proteins as well as proteins acquired by horizontal gene transfer (HGT). For most proteins, specific transport mechanisms from nucleus/cytoplasm to organelle exist. The proteins are typically translated as a preprotein with specific signal sequences targeted to the organelle membrane. These membranes harbour receptors, in some cases soluble receptors, for recognition of these signal sequences. Proteins are then internalised using a set of translocation machineries (Gould et al. 2006).},
}

*Symbiosis/genetics
Gene Transfer, Horizontal
Photosynthesis/genetics
*Plastids/genetics
Cyanobacteria/genetics
Rhodophyta/genetics
Mitochondria/genetics
Chlorophyta/genetics
Alphaproteobacteria/genetics
Biological Evolution
Evolution, Molecular
Dinoflagellida/genetics

@article {pmid40614847,
year = {2025},
author = {Wang, R and Chen, H and Liu, Y},
title = {Metagenomic insights into the characteristics and co-migration of antibiotic resistome and metal(loid) resistance genes in urban landfill soil and groundwater.},
journal = {Environmental research},
volume = {285},
number = {Pt 1},
pages = {122285},
doi = {10.1016/j.envres.2025.122285},
pmid = {40614847},
issn = {1096-0953},
abstract = {The heavy metals and antibiotic resistance genes (ARGs) in landfills showed a significant correlation; however, the relationship between metal(loid) resistance genes (MRGs) and ARGs in contaminated environments, as well as whether they co-migrate with human pathogenic bacteria (HPB), remains unclear. This study is the first to report the characteristics and co-migration of ARGs and MRGs in the soil and groundwater of aged urban landfill sites. Our findings indicated that quinolone, efflux, and macrolide-lincosamide-streptogramin represented the most abundant ARGs identified. Notably, ARG abundance was higher in groundwater compared to soil, with subtype diversity reflecting a similar trend; however, microbial diversity in soil was greater. Metagenome-assembled genomes data indicated a higher risk of antibiotic-resistant HPB in groundwater. It is imperative to focus on HPB that co-carry ARGs and MRGs alongside mobile genetic elements (MGEs), such as Ralstonia pickettii and Pseudomonas stutzeri. Genes conferring resistance to copper and mercury, as well as MGEs such as qacEdelta and intI1, played a critical role in promoting horizontal gene transfer of antibiotic resistance. MRG may promote ARG migration by affecting the permeability of the cell membrane. Procrustes analysis revealed a strong similarity (87 %) between heavy metals and MRG structures. Variance partitioning analyses demonstrated that both heavy metals and biological factors jointly governed landfill ARGs (96.2 %), exerting a more substantial influence in groundwater than in soil. This study serves as a reference for managing landfill, while emphasizing the importance of addressing the co-migration of MRGs and ARGs in pathogens when controlling the spread of risks.},
}

@article {pmid40612915,
year = {2025},
author = {Vasta, GR and Bianchet, MA},
title = {F-type lectins: Structural and functional aspects, and potential biomedical applications.},
journal = {BBA advances},
volume = {8},
number = {},
pages = {100166},
pmid = {40612915},
issn = {2667-1603},
abstract = {Among the multiple animal lectin families recognized to date, F-type lectins (FTLs), fucose-binding lectins characterized by an FTL domain (FTLD), constitute the most recent lectin family to be identified and structurally characterized. The structure of the FTL from the European eel Anguilla anguilla revealed a novel jellyroll lectin fold (the "F-type" fold) with unique fucose- and calcium-binding sequence motifs. The FTL lectin family comprises proteins that may exhibit single or multiple FTLD, in combination with structurally and functionally distinct domains, and can form oligomeric associations that display high-avidity multivalent binding. Differences in fine carbohydrate specificity among tandemly arrayed FTLDs present in any FTL polypeptide subunit, together with the expression of multiple FTL isoforms in a single individual supports a broad diversity in ligand recognition. Widely distributed in invertebrates, protochordates, ectothermic vertebrates, birds, and monotreme and marsupial mammals, the FTLD is also present in some bacterial proteins and viruses but absent in placental mammals. The taxonomically broad, and discontinuous distribution of the FTLD, suggests an extensive structural and functional diversification of this lectin family, including horizontal gene transfer in viruses and prokaryotic organisms, together with possible gene loss and/or cooption along the lineages leading to the mammals. FTLs' biological roles range from pathogen recognition in innate immunity to fertilization, cell adhesion and cell aggregation, and as bacterial virulence factors, among others. The specificity of FTLs for fucosylated moieties should provide ample opportunities for novel applications in glycan and cell separation, and innovative diagnostic, preventive, and therapeutic approaches in cancer and infectious disease.},
}

@article {pmid40479505,
year = {2025},
author = {Pianezza, R and Scarpa, A and Haider, A and Signor, S and Kofler, R},
title = {Spatiotemporal Tracking of Three Novel Transposable Element Invasions in Drosophila melanogaster over the Last 30 Years.},
journal = {Molecular biology and evolution},
volume = {42},
number = {7},
pages = {},
doi = {10.1093/molbev/msaf143},
pmid = {40479505},
issn = {1537-1719},
support = {NSF-EPSCoR-1826834 and NSF-EPSCoR-2032756//National Science Foundation/ ; P35093 and P34965//Austrian Science Fund (FWF)/ ; },
mesh = {Animals ; *DNA Transposable Elements ; *Drosophila melanogaster/genetics ; Gene Transfer, Horizontal ; Evolution, Molecular ; Genome, Insect ; },
abstract = {Transposable elements (TEs) are repetitive sequences capable of mobilizing within genomes, exerting a significant influence on evolution throughout the tree of life. Using a novel approach that does not require prior knowledge of the sequence of repeats, we identified three novel TE invasions in Drosophila melanogaster: McLE spread between 1990-2000, Souslik between 2009-2012, and Transib1 between 2013-2016. We recapitulate previous findings, revealing that a total of 11 TEs invaded D. melanogaster over the past two centuries. These 11 invasions increased the fly genome by ∼1 Mbp. Using data from over 1,400 arthropod genomes, we provide evidence that these TE invasions were triggered by horizontal transfers, with Drosophila simulans and species of the Drosophila willistoni group acting as putative donors. Through the analysis of ∼600 short-read datasets spanning diverse geographic regions, we reveal the rapidity of TE invasions: Transib1 swiftly multiplied from three isolated epicenters in 2014 to all investigated populations in just 2 years. Our findings suggest that anthropogenic activities, which facilitate the range and population expansions of D. melanogaster, could have accelerated the rate of horizontal transposon transfer as well as the spread of the TEs into the worldwide population. Given the significant impact of TEs on evolution and the potential involvement of humans in their dispersal, our research has crucial implications for both evolution and ecology.},
}

Animals
*DNA Transposable Elements
*Drosophila melanogaster/genetics
Gene Transfer, Horizontal
Evolution, Molecular
Genome, Insect

@article {pmid40612392,
year = {2025},
author = {Ma, Y and Lei, Z and Zhang, Y and Liu, Q and Zhang, F and Zu, H and Yang, X and Li, Z and Lu, B},
title = {Tracing the evolutionary trajectory of the IncP-2 plasmid co-harboring bla IMP-45 and bla VIM-1: an outbreak of Pseudomonas aeruginosa co-producing IMP-45 and VIM-1 carbapenemases in China.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1623241},
pmid = {40612392},
issn = {2235-2988},
mesh = {*beta-Lactamases/genetics/metabolism ; *Pseudomonas aeruginosa/genetics/drug effects/enzymology/isolation & purification ; *Plasmids/genetics ; Humans ; China/epidemiology ; *Pseudomonas Infections/epidemiology/microbiology ; *Bacterial Proteins/genetics/metabolism ; *Disease Outbreaks ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; Microbial Sensitivity Tests ; Molecular Docking Simulation ; Evolution, Molecular ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {BACKGROUND: Carbapenem-resistant Pseudomonas aeruginosa (CRPA) poses a significant global health risk, particularly for immunocompromised individuals. This study documents an outbreak of CRPA strains co-harboring bla VIM-1 and bla IMP-45 on IncP-2 plasmids in a Chinese tertiary hospital, resulting in poor outcomes for transplant patients.

METHODS: 17 ST313 VIM-1-IMP-45 CRPA strains were collected from transplant patients, and antibiotic susceptibility was tested via microbroth dilution. Whole genome sequencing (WGS) identified drug resistance and virulence mechanisms, analyzed ST313 P. aeruginosa phylogeny, and traced bla VIM-1 and bla IMP-45 origins. Conjugation experiments were conducted to assess the conjugative potential of the IncP-2 plasmid co-harboring bla VIM-1 and bla IMP-45. Structural and molecular docking studies explored the PBP3 (P527S) mutation's role in aztreonam resistance.

RESULTS: From February 2022 to July 2024, 17 ST313 VIM-1-IMP-45 CRPA strains from 10 transplant patients were identified. All strains were extensively drug-resistant but sensitive to colistin and cefiderocol. WGS showed bla IMP-45 and bla VIM-1 on an IncP-2 megaplasmid. Phylogenetic analysis indicated high homology with plasmids carrying bla IMP-45. Further analysis of the genetic environment showed that the IncP-2 plasmid co-harboring bla VIM-1 and bla IMP-45 was formed by the insertion of a Tn3-family transposon carrying bla VIM-1 into the IncP-2 plasmid carrying bla IMP-45. In addition aztreonam-resistant strains (14/15) had a PBP3 (P527S) mutation, with molecular docking studies suggesting reduced aztreonam binding.

CONCLUSIONS: This study reports a clonal outbreak of ST313 P. aeruginosa strains co-producing IMP-45 and VIM-1 carbapenemases in a tertiary hospital. The evolutionary path of the IncP-2 plasmid co-harboring bla IMP-45 and bla VIM-1 was elucidated.},
}

*beta-Lactamases/genetics/metabolism
*Pseudomonas aeruginosa/genetics/drug effects/enzymology/isolation & purification
*Plasmids/genetics
Humans
China/epidemiology
*Pseudomonas Infections/epidemiology/microbiology
*Bacterial Proteins/genetics/metabolism
*Disease Outbreaks
Phylogeny
Anti-Bacterial Agents/pharmacology
Whole Genome Sequencing
Microbial Sensitivity Tests
Molecular Docking Simulation
Evolution, Molecular
Drug Resistance, Multiple, Bacterial/genetics

@article {pmid40609725,
year = {2025},
author = {Chen, M and Song, L and Ye, C and Grossart, HP and Yang, Y and Li, S and Liao, H and Gong, Y and Che, R and Zhang, Q},
title = {Dynamic relationships of antibiotic resistomes and greenhouse gas-functioning microbes across diverse habitats.},
journal = {Environmental research},
volume = {284},
number = {},
pages = {122272},
doi = {10.1016/j.envres.2025.122272},
pmid = {40609725},
issn = {1096-0953},
abstract = {Reservoir ecosystems with diverse habitats form critical interfaces where antibiotic resistance genes (ARGs) and greenhouse gas (GHG) emissions converge. Despite their distribution and ecological implications of ARGs across diverse habitats remain greatly unknown. There is a critical gap in dissecting the interlinkages between antibiotic resistomes and GHG-functioning microbes. Thus, we aimed to investigate the relationship between antibiotic resistomes and GHG-functioning microbes in various habitats of the Three Gorges reservoir, encompassing water, sediment, and riparian top- and sub-soil. We provide a comprehensive assessment of ARG abundance and diversity across four habitats. Significant differences in ARG, with riparian zones exhibiting more than twice the ARG abundance of water. Horizontal gene transfer of ARGs was more frequent in water, suggesting a pivotal role in aquatic ARG dissemination. The GHG-functioning microbes displayed habitat-specific composition and diversity, with key genera like Neisseria and Azoarcus in riparian subsoil, contrasting with Streptomyces in other habitats. The dynamic relationship of antibiotic resistomes and GHG-functioning microbes ranges from synergistic to competitive in varied habitats, reflecting antibiotic resistomes can influence ecological function stability. This study emphasizes the importance of considering resistomes in the context of global change, advancing our understanding of environmental management and conservation strategies in these critical ecosystems.},
}

@article {pmid40607640,
year = {2025},
author = {Jia, X and Zhang, X and Chen, X and Fernie, AR and Wen, W},
title = {The horizontally transferred gene, CsMTAN, rewired purine traffic to build caffeine factories in tea leaves.},
journal = {Journal of integrative plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jipb.13957},
pmid = {40607640},
issn = {1744-7909},
support = {32161133017//National Natural Science Foundation of China/ ; 32494781//National Natural Science Foundation of China/ ; },
abstract = {Purine-related metabolites are central to primary metabolic pathways in plants and serve as precursors for purine alkaloid biosynthesis in caffeinated species such as tea plants (Camellia sinensis). In this study, metabolite profiling of two tissues (young and mature leaves) was performed across 183 genetically diverse tea accessions, identifying and quantifying 10 purine alkaloid-related metabolites. Metabolite genome-wide association studies revealed 17 significant loci associated with these metabolites, including both known loci such as caffeine synthase and 16 novel loci (P < 1.05 × 10[-5]). Through functional annotation and in vitro enzymatic assay, we characterized 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (CsMTAN) as the causal gene underlying natural variation in adenosine and adenine content. CsMTAN can catalyze the degradation of both 5'-methylthioadenosine and S-adenosylhomocysteine to release adenine. The T → A nucleotide substitution at SNP55151898, which leads to a phenylalanine → tyrosine substitution at residue 179 (F179Y), resulted in a significant alteration of enzyme activity in vitro, as evidenced by an approximately 50% reduction in adenine abundance (P < 0.05). Transient overexpression of CsMTAN-A and CsMTAN-T in Nicotiana benthamiana both significantly increased adenine content and dramatically decreased adenosine content, providing direct evidence for the functional involvement of CsMTAN in plant purine metabolism. CsMTAN-T overexpression resulted in significantly lower adenosine level than CsMTAN-A (P < 0.05). Phylogenetic analysis across 115 species and protein structural modeling revealed a distinct evolutionary divergence between plant MTAN evolution and species phylogeny, strongly suggesting the occurrence of horizontal gene transfer events in the evolutionary history of plant MTANs. This study thus furthered our understanding of the genetics and molecular mechanisms regulating purine metabolism and purine alkaloid biosynthesis in tea plants and provided novel targets for molecular breeding and synthetic biology applications.},
}

@article {pmid40607638,
year = {2025},
author = {Hou, J and Liu, M and Yang, K and Liu, B and Liu, H and Liu, J},
title = {Genetic variation for adaptive evolution in response to changed environments in plants.},
journal = {Journal of integrative plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jipb.13961},
pmid = {40607638},
issn = {1744-7909},
support = {No. 32030006//National Natural Science Foundation of China/ ; No. 32270302//National Natural Science Foundation of China/ ; 2024NSFSC0340//Natural Science Foundation of Sichuan Province/ ; },
abstract = {Plants adapt to their local environments through natural or artificial selection of optimal phenotypes. Recent advances in genomics and computational biology, which integrate phenotypic and multi-omics data, have facilitated the rapid identification of key genes and allelic variations that underlie these adaptive evolutionary processes. Understanding the underlying molecular mechanisms has significantly enhanced our knowledge of how plants respond to changed habitats, including various biotic and abiotic stresses. In this review, we highlight recent progress in elucidating the genetic basis of phenotypic variation in morphological traits and stress responses, as well as the emergence of new ecotypes, subspecies, and species during adaptive evolution across varied environments. This occurs through allelic divergences in both coding and non-coding regions in both model and non-model plants. Furthermore, the terrestrialization and early diversification of land plants involved the acquisition of additional genes, primarily through horizontal gene transfer and whole-genome duplication, which facilitated the development of complex molecular pathways to adapt to increasingly diverse environments. Finally, we discuss emerging trends and prospects for exploring and utilizing beneficial alleles for environmental adaptation, to guide crop breeding efforts in response to global climate change.},
}

@article {pmid40606176,
year = {2025},
author = {Du, H and Lu, C and Latif, MZ and Du, J and Liu, Y and Li, H and Ding, X},
title = {Thermophilic microbial agents promote the fermentation progression of spent mushroom compost and pig manure.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1575397},
pmid = {40606176},
issn = {1664-302X},
abstract = {Livestock and poultry manure, as a significant organic resource, had an enormous annual production but a utilization rate of less than 50%. Improperly managed manure had become the primary source of agricultural non-point pollution, posing severe challenges to the ecological environment. Achieving efficient resource utilization of livestock manure was a critical step in promoting green agricultural development. Existing research indicated that microbial activity significantly influences the transfer and dissemination of antibiotic resistance genes (ARGs) and the community dynamics of human pathogenic bacteria (HPB) during pig manure composting. However, the specific mechanisms remain unclear. This study innovatively introduced two thermophilic microbial agents (TMS1 and CTMS2) into a pig manure-spent mushroom compost (SMC) aerobic composting system to systematically investigate their regulatory effects on pollutant reduction. The results showed that persistent ARGs (ErmF, ErmQ, ErmX, blaR1, QnrA1, QnrA6, bla-F, QnrA2, QnrA5, Qnra4 and bla-VIM) primarily rely on vertical gene transfer (VGT) for dissemination, whereas easily removable ARGs (tetX, tetW, tetG, tetC, suI1 and suI2) were regulated by both horizontal gene transfer (HGT) and VGT. Notably, the co-addition of thermophilic microbial agents and SMC reduced persistent ARGs by lg0.45-3.73, significantly decreased the abundances of HPB such as Bacteroides and Treponema, and reduced the enrichment of related metabolic pathways, greatly improving compost quality. In stark contrast, the control group (with only SMC and no thermophilic microbial agents) exhibited ARG proliferation. Overall, the application of thermophilic microbial agents not only extended the high temperature phase of composting by over 30% and shortened the composting cycle by 50%, but more importantly, it achieved comprehensive improvement in compost quality by selectively enriching functional microbial communities such as Pseudomonas. This study provides a theoretical foundation and data support for the industrial application of CTMS2 in the safe production of organic fertilizers and the synergistic control of environmental risks.},
}

@article {pmid40606165,
year = {2025},
author = {Jers, C and Mišetić, H and Ravikumar, V and Garg, A and Franjević, D and Domazet-Lošo, T and Mijakovic, I},
title = {Gene age and genome organization in Escherichia coli and Bacillus subtilis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1512923},
pmid = {40606165},
issn = {1664-302X},
abstract = {Using genomic phylostratigraphy, we examined the organization of Escherichia coli and Bacillus subtilis genomes from the perspective of evolutionary age of their genes. Phylostratigraphy analysis classifies individual genes into age-related bins, called phylostrata. Based on this analysis, several common features emerged in the genomes of the two model bacteria. More recent genes tend to be shorter and are expressed less frequently, or only in specific conditions. In terms of genomic location, new genes are enriched in areas containing prophages, suggesting a link with horizontal gene transfer. Interestingly, while most bacterial transcription regulators belong to the oldest phylostrata, they regulate expression of both older and more recent genes alike. A large fraction of bacterial operons contains genes from different phylostrata. This suggests that newer genes are integrated in the existing framework for regulating gene expression, and that the establishment of new regulatory circuits typically do not accompany acquisition of new genes. One striking difference between E. coli and B. subtilis genomes was observed. About 87.0% of all E. coli genes belong to the evolutionary oldest physlostratum. In B. subtilis, this number is only 71.8%, indicating a more eventful evolutionary past in terms of acquisition of new genes, either by gene emergence or by horizontal transfer.},
}

@article {pmid40604389,
year = {2025},
author = {Yang, J and Wang, L and Liang, Q and Wang, Y and Yang, X and Wu, X and Pei, X},
title = {Microbiome, resistome, and potential transfer of antibiotic resistance genes in Chinese wet market under One Health sectors.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {406},
pmid = {40604389},
issn = {1471-2180},
support = {TB2024045//Special Funding for Postdoctoral Research Projects in Sichuan Province/ ; 2022ZDZX0017//Department of Science and Technology of Sichuan Province (Major Science and Technology Projects)/ ; 2022ZDZX0017//Department of Science and Technology of Sichuan Province (Major Science and Technology Projects)/ ; 2022ZDZX0017//Department of Science and Technology of Sichuan Province (Major Science and Technology Projects)/ ; },
abstract = {BACKGROUND: Antibiotic resistance has become a serious challenge to global public health. The spread of antibiotic resistance genes (ARGs) among humans, animals, and the environment has become a critical issue within the “One Health” framework. Chinese wet market with live poultry trade provides an interface for close interaction between humans and chickens, and is considered as potential source for disease dissemination. However, the understanding of ARGs in this kind of market, including their shared profiles, influencing factors, and potential horizontal transfer subtypes and directions, remains limited.

RESULTS: In this study, we explored the microbiome, resistome, and mobility of ARGs, and identified putative horizontal gene transfer (HGT) events in the Chinese wet market system by utilizing metagenomic assembly and binning. Consequently, a total of 1080 ARG subtypes were identified from 36 metagenomes, and 221 subtypes were shared among human feces, chicken feces, chicken carcasses, and the environment. The composition of ARGs was influenced by mobile genetic elements (MGEs) and bacterial communities. As for the host of ARGs, 89 ARG-carrying genomes (ACGs) were identified, with 18 of them carrying multiple ARGs and MGEs, indicating the potential mobility of ARGs. Notably, six ACGs were identified as opportunistic pathogens carrying multiple ARGs and MGEs, which were annotated as Escherichia coli, Acinetobacter johnsonii, Klebsiella variicola, Klebsiella pneumoniae, and Citrobacter freundii. In addition, 164 potential HGT events were identified based on ACGs, and ParS, vanB, ugd, and macB were annotated as potentially transferred ARG subtypes in humans and the wet market.

CONCLUSIONS: This study offers new insights into the potential for HGT of ARGs within a Chinese wet market setting, highlighting putative transmission patterns among humans, poultry, and the environment. To our knowledge, few studies have explored ARG transfer potential in this context using metagenome-assembled genomes, making this a valuable contribution to One Health surveillance.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04115-z.},
}

@article {pmid40602897,
year = {2025},
author = {Liang, S and Zhang, W and Semaha, P and Rocher, D and Liu, L and Gao, Y},
title = {Microelectrolysis facilitated the plasmid-mediated horizontal transfer of antibiotic resistance genes at the microbial community level.},
journal = {Journal of environmental sciences (China)},
volume = {157},
number = {},
pages = {470-477},
doi = {10.1016/j.jes.2025.01.029},
pmid = {40602897},
issn = {1001-0742},
mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents ; Wastewater/microbiology ; },
abstract = {The escalating global dissemination of plasmid-mediated antibiotic resistance poses a formidable threat to global health. Conjugation stands as a pivotal mechanism for horizontal gene transfer among bacterial populations, facilitating the spread of antibiotic resistance genes (ARGs). Microelectrolysis has garnered attention as an efficacious strategy for mitigating antibiotic concentrations in wastewater, yet its potential impact on ARG horizontal transfer remain largely unexplored. This comprehensive investigation unveils that microelectrolysis not only influences but significantly accelerates the conjugative transfer of ARG-harboring plasmids. Remarkably, this phenomenon is corroborated at the microbial community scale, underscoring its ecological relevance. Alarmingly, the study highlights the vulnerability of intestinal microorganisms to acquire antibiotic resistance under electrolytic stimulation, posing heightened risks to both animal and human health. Delving deeper, the study elucidates the underlying mechanisms responsible for this enhanced conjugative transfer. It reveals that microelectrolysis augments the abundance of mating-competent cells, triggers the generation of reactive oxygen species, inflicts modest membrane damage, and upregulates the expression of genes critical for conjugation. These findings collectively contribute to a more profound comprehension of the environmental dissemination dynamics and associated public health implications of ARGs in the context of wastewater treatment employing microelectrolytic technologies.},
}

*Plasmids/genetics
*Gene Transfer, Horizontal
*Drug Resistance, Microbial/genetics
Anti-Bacterial Agents
Wastewater/microbiology

@article {pmid40602895,
year = {2025},
author = {Li, S and Xi, Y and Wang, K and Wan, N and Liu, H and Ho, SH},
title = {Responses of antibiotic resistance genes and microbial community in the microalgae-bacteria system under sulfadiazine: Mechanisms and implications.},
journal = {Journal of environmental sciences (China)},
volume = {157},
number = {},
pages = {443-456},
doi = {10.1016/j.jes.2024.12.003},
pmid = {40602895},
issn = {1001-0742},
mesh = {*Microalgae/physiology ; *Sulfadiazine/toxicity ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/drug effects ; *Water Pollutants, Chemical/toxicity ; Waste Disposal, Fluid/methods ; *Microbiota/drug effects ; Anti-Bacterial Agents ; Genes, Bacterial ; Sewage/microbiology ; },
abstract = {Microalgae-bacteria system is an emerging alternative for sustainable wastewater treatment. Exploring the structure and diversity of microbial community in microalgae-bacteria system under sulfadiazine stress can contribute to the understanding of the sulfadiazine behavior in environments. Furthermore, as important carriers of antibiotic resistance genes (ARGs), microalgae can influence the profiles of ARGs either directly or indirectly through the secretion of metabolites. However, the effects of sulfadiazine on ARGs dissemination of microalgae-bacteria systems remain underreported. Herein, the impacts of sulfadiazine (1 mg/L) on the structural diversity and metabolic activity of microorganisms were examined in microalgae-bacteria systems. Results showed that microalgae-bacteria system could remove NH4[+]-N better (about 72.3 %) than activated sludge system, and hydrolysis was the first step in sulfadiazine degradation. A high level of intI1 (5.7 × 10[4] copies/mL) was detected in the initial media of the microalgae-bacteria system. Microalgae could hamper the rate of horizontal gene transfer activation. Compared with activated sludge system, the abundance of sul genes (sul1, sul2, sul3, and sulA) was significantly lowered after treating with microalgae-bacteria system. Additionally, the number of proteins and the sum of polysaccharides in the extracellular polymeric substances of the activated sludge system were lower than those of the microalgae-bacteria system. Microalgae can alter microbial communities. The genus Rozellomycota predominated all samples. Fungi with relatively high abundance increased in the microalgae-bacteria system, including Dipodascaceae, Rhodotorula, and Geotrichum. These results offer valuable insights into the application processes involving microalgae-bacteria system.},
}

*Microalgae/physiology
*Sulfadiazine/toxicity
*Drug Resistance, Microbial/genetics
*Bacteria/genetics/drug effects
*Water Pollutants, Chemical/toxicity
Waste Disposal, Fluid/methods
*Microbiota/drug effects
Anti-Bacterial Agents
Genes, Bacterial
Sewage/microbiology

@article {pmid40601807,
year = {2025},
author = {Wang, Y and Feng, Z and Wu, W and Zhan, Z and Huang, J and Guo, C and He, J},
title = {Emergence of highly virulent Aeromonas dhakensis in channel catfish aquaculture: Genomic insights into pathogenicity and antimicrobial resistance.},
journal = {Virulence},
volume = {16},
number = {1},
pages = {2525933},
doi = {10.1080/21505594.2025.2525933},
pmid = {40601807},
issn = {2150-5608},
mesh = {Animals ; *Fish Diseases/microbiology/pathology ; *Ictaluridae/microbiology ; *Gram-Negative Bacterial Infections/microbiology/veterinary/pathology ; Virulence ; *Aeromonas/pathogenicity/genetics/drug effects/isolation & purification ; Aquaculture ; Virulence Factors/genetics ; Genome, Bacterial ; Whole Genome Sequencing ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Genomics ; *Drug Resistance, Bacterial ; },
abstract = {Aeromonas dhakensis has emerged as a significant pathogen in aquaculture, causing severe disease outbreaks and resulting in substantial economic losses. However, its pathogenic mechanism and virulence factors remain largely unexplored. In this study, we isolated a highly virulent strain of A. dhakensis, CWH5, from a severe disease outbreak in farmed channel catfish (Ictalurus punctatus). Through comprehensive whole-genome analysis, we elucidated its pathogenicity and the genetic basis for its high virulence and multi-antimicrobial resistance in channel catfish. Experimental infections showed that CWH5 exhibited exceptional virulence, with an LD50 of (5.37 ± 0.31) ×10[5] CFU/fish and causing 100% mortality within 24 h at a concentration of 10[7] CFU/fish. Histopathological examinations revealed severe multi-organ damage, including extensive hepatocellular necrosis, gill epithelial destruction, and fin tissue deterioration. Whole-genome sequencing revealed a 4.92 Mb circular chromosome encoding sophisticated virulence mechanisms, such as complete Type III, IV, and VI secretion systems, and a vast arsenal of 60 antibiotic resistance genes across 15 drug classes. Comparative genomic analysis positioned CWH5 within the A. dhakensis clade, sharing the highest sequence similarity with A. dhakensis CIP 107,500[T]. The co-localization of virulence and resistance determinants within mobile genetic elements suggests the potential for horizontal gene transfer. Our work underscored the importance of A. dhakensis CWH5 as an emerging pathogen in channel catfish aquaculture, providing crucial insights into the molecular mechanisms of its exceptional virulence and implying significant implications for disease management and antimicrobial resistance surveillance in aquaculture settings.},
}

Animals
*Fish Diseases/microbiology/pathology
*Ictaluridae/microbiology
*Gram-Negative Bacterial Infections/microbiology/veterinary/pathology
Virulence
*Aeromonas/pathogenicity/genetics/drug effects/isolation & purification
Aquaculture
Virulence Factors/genetics
Genome, Bacterial
Whole Genome Sequencing
Anti-Bacterial Agents/pharmacology
Drug Resistance, Multiple, Bacterial/genetics
Genomics
*Drug Resistance, Bacterial

@article {pmid40600175,
year = {2025},
author = {Etesami, H},
title = {The dual nature of plant growth-promoting bacteria: Benefits, risks, and pathways to sustainable deployment.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100421},
pmid = {40600175},
issn = {2666-5174},
abstract = {Plant growth-promoting bacteria (PGPB) are pivotal in sustainable agriculture, enhancing crop productivity and reducing reliance on chemical inputs. However, their dual role as beneficial agents and potential stressors remains underexplored. This review examines the paradoxical adverse effects of PGPB, challenging the predominantly optimistic narrative surrounding their use. At the plant level, unintended consequences include hormonal imbalances (e.g., auxin-induced root inhibition), phytotoxic metabolite production (e.g., hydrogen cyanide), and trade-offs between growth and defense mechanisms. At the soil level, risks encompass disrupted microbial diversity, altered nutrient cycling, and horizontal gene transfer that may foster pathogenicity. These outcomes are driven by environmental factors (soil pH and moisture), host-specific interactions, and application practices. Mitigation strategies emphasize rigorous strain selection, optimized dosing, and integrated soil management to balance efficacy with ecological safety. Advances in multi-omics technologies and synthetic consortia design offer predictive insights into strain behavior, while long-term ecological assessments are critical to address legacy impacts. The review underscores the necessity of a nuanced, evidence-based approach to PGPB deployment, harmonizing agricultural benefits with environmental stewardship. By addressing knowledge gaps in microbial ecology and risk assessment, this work supports strategies prioritizing both agricultural resilience and soil biodiversity to ensure PGPB contribute sustainably to global food security.},
}

@article {pmid40600145,
year = {2025},
author = {Piispa, M and Vainio, A and Halkilahti, J and Lyytikäinen, O and Räisänen, K},
title = {Detecting plasmid-mediated dissemination of bla KPC-3 and bla OXA-48-like genes in Enterobacterales across Finnish healthcare organizations using hybrid genome assembly.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1567913},
pmid = {40600145},
issn = {1664-302X},
abstract = {The spread of carbapenemase-producing Enterobacterales (CPE) is a global concern. While the majority of the CPE outbreaks are due to clonal spread, recent findings highlight the transmission of carbapenemase gene-carrying plasmids across various bacterial species, exacerbated by extensive antibiotic use in hospitals. This study aimed to identify plasmid-mediated horizontal transfer of carbapenemase genes among Enterobacterales isolated from patient samples and hospital environment samples in three healthcare organizations in Finland. Using a hybrid assembly of short and long reads, we could complete the genome assembly and compare the plasmids harboring the bla KPC-3 and bla OXA-48-like genes. Our findings reveal indications of interspecies and intraspecies plasmid-mediated gene transfer of bla KPC-3 and bla OXA-48-like, emphasizing the role of horizontal gene transfer (HGT) in outbreaks. The study underscores the need for comprehensive infection control and surveillance beyond specific species to prevent the spread of antimicrobial resistance genes. These results suggest that expanding outbreak investigations to an interspecies level could be beneficial.},
}

@article {pmid40600140,
year = {2025},
author = {Shahed, K and Islam, SI and Sangsawad, P and Jung, WK and Permpoonpattana, P and Linh, NV},
title = {Benchmarking pangenome dynamics and horizontal gene transfer in Mycobacterium marinum evolution.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1537826},
pmid = {40600140},
issn = {1664-302X},
abstract = {Horizontal gene transfer (HGT) is a key driver of microbial evolution, promoting genetic diversity and contributing to the emergence of antibiotic resistance. This study explores the pangenome dynamics and HGT in Mycobacterium marinum (M. marinum), a close relative of Mycobacterium tuberculosis. Multiple pangenome datasets were analyzed to quantify gene gain, loss, and pangenome openness, utilizing Panstripe and a Generalized Linear Model (GLM) framework to assess gene presence/absence across strains. Additionally, a comparative benchmarking analysis of gene ontology (GO) annotations were conducted using eggNOG and InterProScan to evaluate their functional annotation accuracy. Our findings demonstrated significant differences in gene gain and loss rates, suggesting variations in annotation accuracy and the presence of mobile genetic elements (MGE). Single nucleotide polymorphisms (SNPs) were also identified, highlighting the genetic variability that may impact strain-specific traits such as pathogenicity and antibiotic resistance. Pangenome of M. marinum was characterized as highly open, with substantial variability in gene content, reflecting ongoing genetic exchange and adaptability. Functional annotation benchmarking demonstrated that eggNOG and InterProScan provided complementary insights, with each tool excelling in distinct strengths of gene function identification. Overall, these findings highlight the complex interplay between HGT, pangenome evolution, and antibiotic resistance in M. marinum, and the analytical framework presented here provides a robust approach for future studies aiming to inform therapeutic interventions and vaccine development.},
}

@article {pmid40600027,
year = {2025},
author = {Lewicka, AJ and Lyczakowski, JJ and Pardyak, L and Dubniewicz, K and Latowski, D and Arent, Z},
title = {Beyond serology: saccharide profiling enables identification of antigenically similar Leptospira and prompts re-evaluation of bacterial lipopolysaccharide evolution.},
journal = {Frontiers in molecular biosciences},
volume = {12},
number = {},
pages = {1581587},
pmid = {40600027},
issn = {2296-889X},
abstract = {Leptospirosis is a zoonotic infectious disease of growing importance in both human and veterinary medicine. Gram-negative spirochetes of Leptospira are traditionally classified into serovars based on their antigenic identity, which must be ascertained to design effective treatment procedures for humans and appropriate vaccination strategies in pets and livestock. Unfortunately, identifying Leptospira serovars is challenging and currently requires access to a wide panel of reference strains, animal-derived antisera, or monoclonal antibodies. Here, we describe a new method for the identification of Leptospira serovars that is based on monosaccharide composition analysis of the polysaccharide part of bacterial lipopolysaccharide (LPS) structures. Our approach requires no animal sacrifice and can be implemented in any laboratory equipped for chromatographic analysis. An LPS sugar fingerprint that is specific to each bacterial isolate that we studied can be generated. Importantly, sugar profiling of LPS enables distinguishing Leptospira serovars that are antigenically very similar. Using our new approach, we discover that the LPS structures of two cattle pathogens belonging to two different species: Leptospira interrogans and Leptospira borgpetersenii, and to one serovar: Hardjo, can be distinguished despite sharing major similarities. Through extensive phylogenetic analysis, we reveal which specific glycosyltransferases of the LPS biosynthesis rfb locus likely drove the emergence of these similarities and identify a single glycosyltransferase that might have contributed to the formation of saccharide differences in the LPS structure. Our findings have implications for future work on the evolution of bacterial polysaccharide synthesis and highlight the importance of preventing horizontal gene transfer between pathogenic bacteria.},
}

@article {pmid40597104,
year = {2025},
author = {Blais, C and Colp, MJ and Sarre, LA and de Mendoza, A and Archibald, JM},
title = {Epigenetic silencing and genome dynamics determine the fate of giant virus endogenizations in Acanthamoeba.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {171},
pmid = {40597104},
issn = {1741-7007},
support = {GBMF5782//Gordon and Betty Moore Foundation/ ; GBMF5782//Gordon and Betty Moore Foundation/ ; GBMF5782//Gordon and Betty Moore Foundation/ ; RGPIN-2019-05058//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2019-05058//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2019-05058//Natural Sciences and Engineering Research Council of Canada/ ; ERC-StG 950230/ERC_/European Research Council/International ; ERC-StG 950230/ERC_/European Research Council/International ; },
mesh = {*Acanthamoeba/virology/genetics ; *Giant Viruses/genetics/physiology ; *Epigenesis, Genetic ; *Gene Silencing ; *Virus Integration/genetics ; *Genome, Protozoan ; *Genome, Viral ; Gene Transfer, Horizontal ; },
abstract = {BACKGROUND: Endogenized giant viruses are emerging as major contributors to the genome evolution of microbial eukaryotes, with both degraded and fully functional latent viruses being found integrated in diverse lineages. The mechanisms that determine the fate of viral integrants are poorly understood, however. Acanthamoeba is a unicellular eukaryote known for undergoing lateral gene transfer (LGT) with viruses. Here we have leveraged chromosome-scale assemblies of two strains of Acanthamoeba, Neff and C3, to investigate the genomic mechanisms that mediate the fate of viral integrations in eukaryotic genomes.

RESULTS: Viral integrations in the C3 and Neff genomes are largely non-overlapping and disproportionately found in sub-telomeric regions. Multiple partial copies of these insertions are found throughout the Neff genome, but they are not expressed, do not obviously encode functions associated with their own mobility, and are colonized by host mobile elements. Viral regions are hypermethylated and highly condensed, suggesting that the expression of recently acquired viral DNA is suppressed in heterochromatic regions.

CONCLUSIONS: We propose a model for the trajectory of viral sequences in Acanthamoeba: (i) integration of DNA from giant viruses, (ii) epigenetic suppression of the viral DNAs, allowing them to persist in the genome, and (iii) deterioration of viral genomes by point mutation, mobile element colonization, and intra- and inter-chromosomal recombination. Viral integrations in Acanthamoeba spp. are transient and may not have long-lasting effects on the fitness of the amoeba. Our work highlights the importance of host genome dynamics and epigenetic silencing for understanding the evolution of endogenized viral elements.},
}

*Acanthamoeba/virology/genetics
*Giant Viruses/genetics/physiology
*Epigenesis, Genetic
*Gene Silencing
*Virus Integration/genetics
*Genome, Protozoan
*Genome, Viral
Gene Transfer, Horizontal

@article {pmid40596330,
year = {2025},
author = {Puangseree, J and Hein, ST and Prathan, R and Srisanga, S and Chuanchuen, R},
title = {Genomic insights into multidrug - resistant Salmonella enterica isolates from pet dogs and cats.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22104},
pmid = {40596330},
issn = {2045-2322},
support = {N42A660897//National Research Council of Thailand/ ; HEAF67310045//Thailand Science Research and Innovation Fund Chulalongkorn University (Fundamental Fund) Fiscal year 2567/ ; },
mesh = {Animals ; Dogs ; Cats ; *Salmonella enterica/genetics/drug effects/isolation & purification ; *Drug Resistance, Multiple, Bacterial/genetics ; *Pets/microbiology ; Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; Plasmids/genetics ; *Salmonella Infections, Animal/microbiology ; *Dog Diseases/microbiology ; Microbial Sensitivity Tests ; *Cat Diseases/microbiology ; Genomics ; Genome, Bacterial ; },
abstract = {Companion animals are recognized as potential reservoirs and transmitters of antimicrobial resistance (AMR) within the One Health framework. However, in-depth knowledge on AMR in pet animals remains limited. This study aimed to characterize Salmonella from companion dogs and cats using Whole Genome Sequencing (WGS). A total of 25 Salmonella obtained from clinically healthy household dogs and cats were serotyped and had their antimicrobial susceptibility tested. A discrepancy between the serovars identified by traditional slide agglutination tests and those determined by WGS analysis was observed. The isolates exhibited multidrug resistance (MDR) (n = 18) and harbored several resistance genes either chromosomally encoded or plasmid associated. Tn3 and IS26 were commonly found flanking AMR genes and class 1 integrons, while an unusual qacL-IS256-sul3 arrangement was also frequently observed. Similar AMR genes and insertion sequences were found among dogs and cats from different provinces, suggesting clonal spread and horizontal gene transfer of AMR. The similarity between plasmids (i.e., IncX1 and IncI1 plasmid) carrying AMR genes (e.g., aadA1, qacL, sul3, blaTEM-1B, qnrS1, dfrA, tetA) in Salmonella from pets in this study and those from other sources (e.g., humans, food producing animals and environment) in different countries was revealed, suggesting that pet dogs and cats may play a significant role in the global spread of AMR. The finding underscores the role of household pets as silent reservoirs of MDR Salmonella and the need for a One Health approach to tackle the issue. Public health campaigns promoting hygiene practices among pet owners should be encouraged. Pet animals should be incorporated into AMR monitoring and surveillance programs as a component of One Health framework.},
}

Animals
Dogs
Cats
*Salmonella enterica/genetics/drug effects/isolation & purification
*Drug Resistance, Multiple, Bacterial/genetics
*Pets/microbiology
Anti-Bacterial Agents/pharmacology
Whole Genome Sequencing
Plasmids/genetics
*Salmonella Infections, Animal/microbiology
*Dog Diseases/microbiology
Microbial Sensitivity Tests
*Cat Diseases/microbiology
Genomics
Genome, Bacterial

@article {pmid40595289,
year = {2025},
author = {Kador, SM and Islam, KT and Rubaiyat, RN and Bhuiyan, MIU and Chakrovarty, T and Rahman, MS and Islam, OK and Islam, MT},
title = {Abundance and transmission of antibiotic resistance and virulence genes through mobile genetic elements in integrated chicken and fish farming system.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20953},
pmid = {40595289},
issn = {2045-2322},
support = {22-FoBST 05//Research Cell, Jashore University of Science and Technology/ ; SRG-221252//Special Research Grant, Ministry of Science and Technology, Bangladesh/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Interspersed Repetitive Sequences/genetics ; Aquaculture ; Fishes ; *Virulence Factors/genetics ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/pathogenicity/drug effects ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Virulence/genetics ; Bangladesh ; },
abstract = {Integrated chicken and fish farming systems, common in Bangladesh, present significant public health risks due to the spread of antimicrobial resistance genes (ARGs) and virulence factors (VFGs) through mobile genetic elements (MGEs). This study employs metagenomic sequencing to explore the diversity and abundance of ARGs, VFGs, and MGEs in various environmental samples from these farming systems. A total of 384 ARGs were detected, with tetracycline resistance genes such as tetM and tetX being the most abundant, alongside macrolide-lincosamide-streptogramin and aminoglycoside resistance genes. Droppings harbored the highest proportion of ARGs (62.2%), whereas sediment served as a reservoir for multi-metal resistance genes. Virulence factors associated with immune modulation, such as pvdL and tssH, and biofilm formation genes like algC were particularly prevalent in sediment and droppings. Among MGEs, plasmids and transposons like Tn6072 and Tn4001 were the most abundant, playing a critical role in horizontal gene transfer. Bacterial genera including Bacteroides, Clostridium, and Escherichia were strongly associated with MGEs, indicating their role in the dissemination of resistance and virulence traits. Statistical analyses revealed significant differences in the abundance of ARGs, VFGs, and MGEs across sample types, with sediment and droppings identified as hotspots for gene exchange. These findings underscore the urgent need for improved antibiotic stewardship and waste management practices to limit the spread of antimicrobial resistance and pathogenic bacteria within integrated farming environments.},
}

Animals
*Chickens/microbiology
*Interspersed Repetitive Sequences/genetics
Aquaculture
Fishes
*Virulence Factors/genetics
*Drug Resistance, Microbial/genetics
*Bacteria/genetics/pathogenicity/drug effects
Gene Transfer, Horizontal
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
Virulence/genetics
Bangladesh

@article {pmid40595025,
year = {2025},
author = {Wedell, N},
title = {Harnessing lateral gene transfer and endosymbiosis for adaptation.},
journal = {Nature reviews. Genetics},
volume = {},
number = {},
pages = {},
pmid = {40595025},
issn = {1471-0064},
}

@article {pmid40594904,
year = {2025},
author = {Sayem, M and Rafi, MA and Mishu, ID and Mahmud, Z},
title = {Comprehensive genomic analysis reveals virulence and antibiotic resistance genes in a multidrug-resistant Bacillus cereus isolated from hospital wastewater in Bangladesh.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22915},
pmid = {40594904},
issn = {2045-2322},
mesh = {*Bacillus cereus/genetics/pathogenicity/isolation & purification/drug effects ; *Wastewater/microbiology ; Bangladesh ; *Drug Resistance, Multiple, Bacterial/genetics ; Phylogeny ; Hospitals ; Virulence/genetics ; Genome, Bacterial ; Whole Genome Sequencing ; Genomics/methods ; Anti-Bacterial Agents/pharmacology ; Virulence Factors/genetics ; Humans ; },
abstract = {Hospital wastewater represents a significant reservoir for antimicrobial-resistant bacteria, including multidrug-resistant (MDR) Bacillus cereus, a pathogen of growing concern due to its potential impact on public health and environmental safety. This study characterizes the genomic features, antimicrobial resistance (AMR) mechanisms, and virulence potential of Bacillus cereus MBC, isolated from hospital wastewater in Dhaka, Bangladesh. Using whole-genome sequencing (WGS) and advanced bioinformatics, we analyzed the isolate's taxonomy, phylogenetics, functional annotation, and biosynthetic potential. The genome, spanning 5.6 Mb with a GC content of 34.84%, contained 5,881 protein-coding sequences, including 1,424 hypothetical proteins, and 28 genes associated with AMR. Phylogenetic analysis revealed a close genetic relationship with Bacillus cereus ATCC 14579, sharing virulence factors such as hemolysin BL (HBL), non-hemolytic enterotoxin (NHE), and cytotoxin K (CytK), all contributing to its pathogenicity. The ability to form biofilms further enhances the strain's persistence and resistance in hospital environments. AMR profiling identified genes conferring resistance to beta-lactams (e.g., BcI, BcII, BcIII), tetracyclines (tetB(P)), glycopeptides (vanY), and fosfomycin, highlighting the bacterium's capacity to resist a wide array of antibiotics. Functional annotation revealed metabolic pathways involved in iron acquisition and the biosynthesis of siderophores such as petrobactin and bacillibactin, reinforcing the bacterium's adaptability in nutrient-limited environments. Mobile genetic elements, including prophages, CRISPR-Cas systems, and transposable elements, suggest significant horizontal gene transfer (HGT), enhancing genetic plasticity and resistance spread. Pangenomic analysis, involving 125 B. cereus strains, revealed a high degree of genetic diversity and close relationships with strains from clinical, food, and agricultural environments, emphasizing the overlap between clinical and environmental reservoirs of resistance. The strain's isolation from hospital wastewater underscores the complex interplay between environmental contaminants and bacterial evolution, which fosters MDR traits. Our findings underscore the urgent need for enhanced genomic surveillance and wastewater management strategies to mitigate the spread of MDR B. cereus and AMR genes in hospital environments.},
}

*Bacillus cereus/genetics/pathogenicity/isolation & purification/drug effects
*Wastewater/microbiology
Bangladesh
*Drug Resistance, Multiple, Bacterial/genetics
Phylogeny
Hospitals
Virulence/genetics
Genome, Bacterial
Whole Genome Sequencing
Genomics/methods
Anti-Bacterial Agents/pharmacology
Virulence Factors/genetics
Humans

@article {pmid40592271,
year = {2025},
author = {Fan, Q and Bai, J and Jiao, T and Zhao, Z and Hou, F},
title = {Circular transmission network and reverse contribution pattern of antibiotic resistance genes in the Qinghai-Tibet Plateau ecosystem.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {139054},
doi = {10.1016/j.jhazmat.2025.139054},
pmid = {40592271},
issn = {1873-3336},
abstract = {The dissemination of antibiotic resistance genes (ARGs) poses a major global public health challenge, yet transmission mechanisms within extreme ecosystems are poorly understood. Using metagenomics and metagenome-assembled genome (MAG) analysis, we investigated ARG composition, risk, and pathways across a complete Qinghai-Tibet Plateau food chain (soil, earthworm, herbage, yak, pika, snowfinch, herdsman). Contrary to conventional theory, ARG assemblages correlated negatively with microbial diversity. Our MAG-centric approach provided direct evidence that Horizontal Gene Transfer (HGT), including striking bacteria-archaea cross-domain transfer of 18 ARGs, predominates ARG dissemination, with specialized 'ARG reservoir' host phyla (e.g., Pseudomonadota) decoupling ARG functional diversity from overall microbial community structure. Earthworms function as 'ARG bioamplifiers', enriching 79.81 % of soil ARGs and contributing 49.43 % to herbage. Crucially, apex consumers (snowfinches, herdsmen) are not merely recipients; their feces drive a significant 'reverse contribution' of high-risk ARGs back into the ecosystem, establishing a complete circular ARG feedback network. Herdsman feces contained all Rank I-IV high-risk ARGs, while snowfinch feces held Rank II/IV, highlighting human activities' impact on escalating ARG risks in this extreme setting. These findings, particularly the novel HGT mechanisms and host specialization insights, challenge the traditional unidirectional transmission model, presenting a new paradigm for managing antibiotic resistance risks in extreme ecosystems within the One Health framework.},
}

@article {pmid40592212,
year = {2025},
author = {Byczkowska-Rostkowska, Z and Gajewska, J and Chajęcka-Wierzchowska, W},
title = {Whole genome analysis and antimicrobial resistance assessment of Staphylococcus epidermidis isolated from food sources.},
journal = {The Science of the total environment},
volume = {993},
number = {},
pages = {179999},
doi = {10.1016/j.scitotenv.2025.179999},
pmid = {40592212},
issn = {1879-1026},
abstract = {Coagulase-negative staphylococci (CoNS), including Staphylococcus epidermidis, are commonly occurrence in a variety of food products. Historically considered non-pathogenic, these microorganisms were excluded from routine food safety monitoring protocols. However, their increasing involvement in nosocomial infections underscores their pathogenic potential. Emerging evidence suggests that the food chain may serve as a reservoir and transmission route for antibiotic-resistant bacteria. In this study, 26 S. epidermidis isolates obtained from ready-to-eat food were subjected to whole-genome sequencing and comprehensive bioinformatics analyses. The antimicrobial susceptibility of the isolates was also evaluated against a broad spectrum of agents including aminoglycosides, β-lactams, fluoroquinolones, glycopeptides, lincosamides, macrolides, nitrofurantoins, oxalidinones, phenicols, steroids, sulphonamides and tetracyclines. Sequence typing revealed the presence of 17 distinct sequence types (STs), with ST329 being the most frequently identified (8/26, 30.77 %), followed by ST88 and ST152 (each 2/26; 7.69 %). Notably, one isolate harbored a novel multi-locus sequence type. Phenotypically resistance to erythromycin was most prevalent (21/26, 80.77 %), followed by resistance to clindamycin (19/26, 73.08 %). Genomic analysis confirmed the presence of multiple antimicrobial resistance genes including norA/C, vanT, mecA, dfrC and multidrug resistance genes. The carrying of mobile genetic elements was demonstrated by 25/26 (96.15 %) strains. These findings indicate that S. epidermidis strains isolated from ready-to-eat foods not only exhibit multidrug resistance but also carry a diverse array of antimicrobial resistance genes. The potential for horizontal gene transfer to commensal or pathogenic bacteria highlights the need for increased surveillance and risk assessment concerning CoNS in the food supply.},
}

@article {pmid40407375,
year = {2025},
author = {Lyra de Holanda Fonseca, D and Scheunemann, GS and Fortes, BN and Ishida, K and Galhardo, RS},
title = {Interaction of the SXT/R391 element ICEPmiJpn1 with its natural host Proteus mirabilis.},
journal = {Microbiology spectrum},
volume = {13},
number = {7},
pages = {e0033925},
pmid = {40407375},
issn = {2165-0497},
support = {2019/19435-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2020/00535-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2021/15170-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2021/10577-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2022/03986-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; finance code 01//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
mesh = {*Proteus mirabilis/genetics/pathogenicity/drug effects/physiology ; Conjugation, Genetic ; Gene Transfer, Horizontal ; Biofilms/growth & development ; Escherichia coli/genetics ; *DNA Transposable Elements/genetics ; Proteus Infections/microbiology ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; *Interspersed Repetitive Sequences ; Bacterial Proteins/genetics ; },
abstract = {Integrative and conjugative elements (ICEs) of the SXT/R391 family are mobile genetic elements that integrate into the bacterial host chromosome and can be transferred horizontally, spreading antimicrobial resistance genes. Our study aimed to evaluate aspects of the relationship between ICEPmiJpn1, one of the most widespread SXT/R391 variants, with its natural host Proteus mirabilis. For this investigation, we used isogenic strains (containing or not the ICEPmiJpn1) that enabled us to evaluate the influence of this element on several physiological aspects of P. mirabilis as well as the effect of different P. mirabilis genetic backgrounds on the conjugative transmission of the element. ICEPmiJpn1 did not impact the fitness, self-recognition, swarming, pathogenicity, and persistence abilities of this bacterium but increased biofilm formation in one strain. Additionally, conjugative transfer of the element to Escherichia coli is widely variable when different P. mirabilis strains are used as donors in mating assays. Our results indicate that ICEPmiJpn1 has no adverse effects on the physiology or pathogenicity of P. mirabilis, reflecting a stable association between this element and its host. Furthermore, the findings support the notion that ICE transfer between bacteria is influenced not only by element-specific regulators but also by strain-specific factors.IMPORTANCEMobile genetic elements play a key role in the spread of antimicrobial resistance, raising concerns about multidrug-resistant bacteria, yet their interactions with bacterial hosts are not well characterized. This study explores the relationship between ICEPmiJpn1, a globally distributed SXT/R391 integrative and conjugative element (ICE), and its natural host Proteus mirabilis, revealing minimal effects on bacterial fitness and pathogenicity. Nevertheless, strain-specific factors significantly influence conjugative transfer. These findings highlight the need for further research on host-dependent regulatory mechanisms that drive the spread of these elements. Understanding these dynamics is essential for developing strategies to mitigate the dissemination of antibiotic resistance in clinically relevant bacterial populations.},
}

*Proteus mirabilis/genetics/pathogenicity/drug effects/physiology
Conjugation, Genetic
Gene Transfer, Horizontal
Biofilms/growth & development
Escherichia coli/genetics
*DNA Transposable Elements/genetics
Proteus Infections/microbiology
Anti-Bacterial Agents/pharmacology
Drug Resistance, Multiple, Bacterial/genetics
*Interspersed Repetitive Sequences
Bacterial Proteins/genetics

@article {pmid40590551,
year = {2025},
author = {Renno, AJ and Shields, RC and McLellan, LK},
title = {Bacterial evolution in the oral microbiome: the role of conjugative elements and horizontal gene transfer.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0006625},
doi = {10.1128/jb.00066-25},
pmid = {40590551},
issn = {1098-5530},
abstract = {As one of the most diverse bacterial populations within the human body, the oral microbiome encodes a wealth of genetic information. Horizontal gene transfer, driven by mobile genetic elements, takes advantage of this information to influence bacterial evolution and the spread of phenotypes (antibiotic resistances, virulence attributes, and metabolic capabilities) among oral microbes. Although widespread within microbial communities, fundamental aspects of the mobile elements that drive horizontal gene transfer within the oral cavity remain poorly understood. In this review, we explore what is known about the role of horizontal gene transfer in bacterial evolution within the oral microbiome and the elements that facilitate this transfer, with a specific focus on conjugative DNA transfer. Conjugative elements are found in virtually all bacterial phylogenetic clades, and some can mediate genetic exchange between distantly related organisms. This is of particular interest in the diverse microcosm of the oral cavity, specifically how it drives the evolution and virulence of dental pathogens. Finally, we highlight advances in our understanding of the unique biology within dental plaque and how these might influence our understanding of bacterial gene transfer, and thus human health and disease.},
}

@article {pmid40589066,
year = {2025},
author = {Collins, N and Levy, Y and Kolomeisky, AB},
title = {Theoretical Understanding of Target Search Dynamics in Horizontal Gene Transfer in Bacteria.},
journal = {The journal of physical chemistry. B},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jpcb.5c02436},
pmid = {40589066},
issn = {1520-5207},
abstract = {Horizontal gene transfer (HGT) is a fundamental process of increasing genetic diversity in microbial species. It allows bacterial cells to acquire new beneficial traits quickly by incorporating new genetic material into existing genomes. Despite the critical importance of HGT phenomena, the underlying molecular mechanisms are still poorly understood. Recent experiments investigated the dynamics of conjugation HGT processes in which DNA is transmitted directly from the donor to the recipient bacterial cell. It is accomplished by special mobile genetic particles known as integrative and conjugative elements (ICE). However, the molecular picture of how ICE can efficiently find the unique integration sites in a new genome is not yet clear. We present a novel theoretical model to explain the dynamic processes in HGT after ICE reaches the recipient cell. It is shown that the target search for integration sites can be viewed as a set of stochastic transitions between discrete states, allowing us to obtain an explicit description of the dynamic properties using analytical calculations supported by Monte Carlo computer simulations. Search times are found to depend on the location of integration sites, the size of the genome, the effective diffusion rate of mobile genetic elements, and the binding/unbinding transitions between ICE and DNA. Theoretical estimates for search times agree well with experimental observations for integration in Bacillus subtilis bacterial species. Physical-chemical arguments are presented to explain the dynamics of the ICE target search. This study clarifies some important mechanistic aspects of HGT phenomena.},
}

@article {pmid40588591,
year = {2025},
author = {Mancuso, CP and Baker, JS and Qu, EB and Tripp, AD and Balogun, IO and Lieberman, TD},
title = {Intraspecies warfare restricts strain coexistence in human skin microbiomes.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40588591},
issn = {2058-5276},
support = {1DP2GM140922//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
abstract = {Determining why only a fraction of encountered or applied strains engraft in a given person's microbiome is crucial for understanding and engineering these communities. Previous work has established that metabolic competition between bacteria can restrict colonization success in vivo, but other mechanisms may also prevent successful engraftment. Here we combine genomic analysis and high-throughput agar competition assays to demonstrate that intraspecies warfare presents a significant barrier to strain coexistence in the human skin microbiome by profiling 14,884 pairwise interactions between Staphylococcus epidermidis isolates cultured from 18 people from 6 families. We find that intraspecies antagonisms are abundant, mechanistically diverse, independent of strain relatedness and consistent with rapid evolution via horizontal gene transfer. Critically, these antagonisms are significantly depleted among strains residing on the same person relative to random assemblages, indicating a significant in vivo role. Wide variation in antimicrobial production and resistance suggests trade-offs between these factors and other fitness determinants. Together, our results emphasize that accounting for intraspecies warfare may be essential to the design of long-lasting probiotic therapeutics.},
}

@article {pmid40587929,
year = {2025},
author = {Chen, J and Guo, Y and Lin, Y and Zhang, Y and Qian, Q and Zhang, X and Lin, P and Chen, C and Xie, S},
title = {Fate, mobility and pathogenicity of antibiotic resistome in a full-scale drinking water treatment plant: Highlighting the chlorination risks.},
journal = {Journal of environmental management},
volume = {390},
number = {},
pages = {126425},
doi = {10.1016/j.jenvman.2025.126425},
pmid = {40587929},
issn = {1095-8630},
abstract = {Drinking water treatment plants (DWTPs) serve as the last barrier in preventing the spread of antibiotic resistance genes (ARGs) into tap water, yet the distribution and dissemination mechanisms of ARGs in DWTPs remain unclear. In this study, the antibiotic resistome of a full-scale DWTP using Nansi Lake (an important node of the South-to-North Water Diversion Project's eastern route, China) as water source was investigated based on metagenomic analysis. The results showed that coagulation and chlorination were the two crucial processes increasing the relative abundance of ARGs in the DWTP, and the former predominantly enhanced that of sulfonamide RGs, while the latter increased that of bacitracin, aminoglycoside and multidrug RGs. ARG hosts and mobile genetic elements (MGEs) both played significant roles in ARG compositions. The persistence of Sphingorhabdus during the conventional treatment stages and the dissemination potential of plasmids accounted for the relative abundance of sulfonamide RGs, while the chlorine and multidrug resistance of Acinetobacter, Acidovorax, and Pseudomonas, along with the coexistence of various MGEs, suggested the persistence and transmission risk of ARGs after chlorination. Ozonation and activated carbon filtration could eliminate some human-pathogenic bacteria (HPB), but the chlorination process significantly increased the relative abundance of HPB. The multidrug-resistant HPB such as Acinetobacter calcoaceticus and Acinetobacter haemolyticus were the key targets for risk control in the DWTP. Our findings provide new insights into the fate, mobility, and pathogenicity of ARGs in a typical DWTP, offering beneficial guidance for decision-making in the risk control of ARGs in DWTPs.},
}

@article {pmid40585299,
year = {2025},
author = {Chai, Z and Guo, Z and Chen, X and Yang, Z and Wang, X and Zhang, F and Kang, F and Liu, W and Liang, S and Ren, H and Yue, J and Jin, Y},
title = {Comprehensive profiling of integrative conjugative elements (ICEs) in Mollicutes: distinct catalysts of gene flow and genome shaping.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {2},
pages = {lqaf083},
pmid = {40585299},
issn = {2631-9268},
mesh = {*Genome, Bacterial ; Gene Transfer, Horizontal ; *Conjugation, Genetic ; *Gene Flow ; *Tenericutes/genetics ; Evolution, Molecular ; Phylogeny ; },
abstract = {Mollicutes, known as the simplest bacteria with streamlined genomes, were traditionally thought to evolve mainly through gene loss. Recent studies have highlighted their rapid evolutionary capabilities and genetic exchange within individual genomes; however, their evolutionary trajectory remains elusive. By comprehensive screening 1433 available Mollicutes genomes, we revealed widespread horizontal gene transfer (HGT) in 83.9% of investigated species. These genes involve type IV secretion systems and DNA integration, inferring the unique role of integrative conjugative elements (ICEs) or integrative and mobilizable elements (IMEs) as self-transmissible genetic elements. We systematically identified 263 ICEs/IMEs across most Mollicutes genera, being intact or fragmented, showing a strong correlation with HGT frequency (cor 0.573, P = .002). Their transfer tendency was highlighted across species sharing ecological niches, notably in livestock-associated mycoplasmas and insect-vectored spiroplasmas. ICEs/IMEs not only act as gene shuttles ferrying various phenotypic genes, but also promote increased large-scale chromosomal transfer events, shaping the host genomes profoundly. Additionally, we provided novel evidence that Ureaplasma ICE facilitates genetic exchange and the spread of antibiotic resistance gene tet(M) among other pathogens. These findings suggest that, despite the gene-loss pressure associated with the compact genomes of Mollicutes, ICEs/IMEs play a crucial role by introducing substantial genetic resources, providing essential opportunities for evolutionary adaptation.},
}

*Genome, Bacterial
Gene Transfer, Horizontal
*Conjugation, Genetic
*Gene Flow
*Tenericutes/genetics
Evolution, Molecular
Phylogeny

@article {pmid40584034,
year = {2025},
author = {Alhejaili, AY and Zhou, G and Halawa, H and Huang, J and Fallatah, O and Hirayban, R and Iftikhar, S and AlAsmari, A and Milner, M and Banzhaf, M and Alzaidi, AA and Rajeh, AA and Al-Otaiby, MA and Alabbad, SS and Bukhari, D and Aljurayyan, AN and Aljasham, AT and Alzeyadi, ZA and Alajel, SM and Alanazi, RH and Alghoribi, M and Almutairi, MM and Pain, A and Senok, A and Moradigaravand, D and Al Salem, W},
title = {Methicillin-resistant Staphylococcus aureus in Saudi Arabia: genomic evidence of recent clonal expansion and plasmid-driven resistance dissemination.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1602985},
pmid = {40584034},
issn = {1664-302X},
abstract = {OBJECTIVES: Staphylococcus aureus is a leading cause of hospital-acquired infections worldwide. Over recent decades, methicillin-resistant Staphylococcus aureus (MRSA), which is resistant to multiple antimicrobials, has emerged as a significant pathogenic strain in both hospital and community settings. The rapid emergence and dissemination of MRSA clones are driven by a dynamic and evolving population, spreading swiftly across regions on epidemiological time scales. Despite the vast geographical expanse and diverse demographics of the Kingdom of Saudi Arabia and the broader West Asia region, the population diversity of MRSA in hospitals in these areas remains underexplored.

METHODS: We conducted a large-scale genomic analysis of a systematic Staphylococcus aureus collection obtained from 34 hospitals across all provinces of KSA, from diverse body sites between 2022 and 2024. The dataset comprised 581 MRSA and 31 methicillin-susceptible Staphylococcus aureus (MSSA) isolates, all subjected to whole-genome sequencing. A combination of phylogenetic and population genomics approaches was utilized to analyze the genomic data. Hybrid sequencing approach was employed to retrieve the complete plasmid content.

RESULTS: The population displayed remarkable diversity, comprising 48 distinct sequence types (STs), with the majority harboring community-associated SCCmec loci (types IVa, V/VII, and VI). Virulence factors associated with community-acquired MRSA (CA-MRSA), including Panton-Valentine Leukocidin (PVL) genes, were identified in 12 distinct STs. Dominant clones, including ST8-t008 (USA300), ST88-t690, ST672-t3841, ST6-t304, and ST5-t311, were associated with infections at various body sites and were widely disseminated across the country. Linezolid and vancomycin resistance were mediated by cfr-carrying plasmids and mutations in the vraR gene (involved in cell-wall stress response) and the murF gene (involved in peptidoglycan biosynthesis) in five isolates, respectively. Phylodynamic analysis revealed rapid expansion of the dominant clones, with their emergence estimated to have occurred 10-20 years ago. Plasmidome analysis uncovered a diverse repertoire of blaZ-containing plasmids and the sharing of erm(C)-encoding plasmids among major clades. The acquisition of plasmids coincided with clonal expansion.

CONCLUSIONS: Our results highlight the recent concurrent expansion and geographical dissemination of CA-MRSA clones across hospitals. These findings also underscore the interplay between clonal spread and horizontal gene transfer in shaping the resistance landscape of MRSA.},
}

@article {pmid40434128,
year = {2025},
author = {Zhao, R and Nawrocki, A and Møller-Jensen, J and Liu, G and Olsen, JE and Thomsen, LE},
title = {Mechanistic divergence between SOS response activation and antibiotic-induced plasmid conjugation in Escherichia coli.},
journal = {Microbiology spectrum},
volume = {13},
number = {7},
pages = {e0009025},
pmid = {40434128},
issn = {2165-0497},
support = {//China Scholarship Council/ ; },
mesh = {*SOS Response, Genetics/drug effects ; *Escherichia coli/genetics/drug effects/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Plasmids/genetics/metabolism ; *Conjugation, Genetic/drug effects ; Escherichia coli Proteins/genetics/metabolism ; Cefotaxime/pharmacology ; Ciprofloxacin/pharmacology ; Gene Expression Regulation, Bacterial/drug effects ; Mitomycin/pharmacology ; Gene Transfer, Horizontal ; },
abstract = {The SOS response is a critical DNA damage repair mechanism in bacteria, designed to counteract genotoxic stress and ensure survival. This system can be activated by different classes of antimicrobial agents, each inducing the SOS response through different mechanisms. Moreover, it has been observed that certain antibiotics can enhance conjugative plasmid transfer frequencies. However, while previous studies have suggested that the SOS response contributes to horizontal transfer of certain genes, its role in plasmid conjugation remains unclear. In this study, we investigated the relationship between the SOS response and conjugation of IncI1 and IncFII plasmids harboring various blaCTX-M resistance genes. Results showed that cefotaxime and mitomycin C induced both the SOS response and conjugation, while ciprofloxacin induced the SOS response without affecting conjugation frequencies. Further analysis of SOS mutants, ranging from constitutively inactive to hyper-induced states, revealed no correlation between SOS levels and conjugation frequencies, despite upregulation of tra gene expression in a SOS hyper-induced strain. Proteomic analysis revealed that cefotaxime-induced conjugation was associated with increased transfer and pilus protein expression. In contrast, the SOS hyper-induced strain displayed limited upregulation of plasmid-encoded proteins, suggesting post-transcriptional regulation. Additionally, putative LexA binding sites on the IncI1 plasmid revealed potential SOS-mediated regulation of plasmid genes, highlighting the interaction between the SOS response and plasmid, although it did not significantly affect conjugation.IMPORTANCEPlasmids play a critical role in the dissemination of antibiotic resistance through conjugation. Recent research suggests that the use of antibiotics not only selects for already resistant variants but further increases the rate of plasmid-encoded conjugative transmission by increasing expression of the conjugative system. At the same time, these antibiotics are known to induce the stress-related SOS response in bacteria. To be able to counteract an antibiotic-induced increase in conjugative transfer of resistance plasmid, there is a need for a fundamental understanding of the regulation of transmission, including whether this happens through activation of the SOS response. In this research, we show that antibiotic-induced conjugation and induction of the SOS response happen through different mechanisms, and thus that future strategies to control the spread of antibiotics cannot interfere with the SOS response as its target.},
}

*SOS Response, Genetics/drug effects
*Escherichia coli/genetics/drug effects/metabolism
*Anti-Bacterial Agents/pharmacology
*Plasmids/genetics/metabolism
*Conjugation, Genetic/drug effects
Escherichia coli Proteins/genetics/metabolism
Cefotaxime/pharmacology
Ciprofloxacin/pharmacology
Gene Expression Regulation, Bacterial/drug effects
Mitomycin/pharmacology
Gene Transfer, Horizontal

@article {pmid40408992,
year = {2025},
author = {Zhang, S and Li, J and Lai, J and Zhang, Q and Zhao, Z and Li, B},
title = {Transfer dynamics of intracellular and extracellular last-resort antibiotic resistome in hospital wastewater.},
journal = {Water research},
volume = {283},
number = {},
pages = {123833},
doi = {10.1016/j.watres.2025.123833},
pmid = {40408992},
issn = {1879-2448},
mesh = {*Wastewater/microbiology ; Hospitals ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; },
abstract = {The increasing prevalence of last-resort antibiotic resistance genes (LARGs) has posed severe public health hazards. Previous studies focused primarily on the profiles of intracellular LARGs (iLARGs) in hospital wastewater (HWW), while largely neglecting the expression patterns of iLARGs and the presence of extracellular LARGs (eLARGs). Currently, wastewater resistomes and transfer dynamics of LARGs are still poorly characterized. This study integrates Nanopore-metagenomic and metatranscriptomic sequencing to conduct the comprehensive longitudinal analysis of both iLARGs and eLARGs in HWW. Our study firstly revealed the distinct seasonal patterns of iLARGs and eLARGs. Specifically, iLARGs showed higher abundance during colder seasons, whereas eLARGs showed higher abundance in warm seasons. Both clinical pathogens and functional bacteria of wastewater treatments were identified as important hosts of LARGs, while clinical pathogens played predominant roles in the high expression levels of LARGs. Acinetobacter spp. was identified as major host of blaNDM-1 in HWW, which is unrestricted by plasmid host range compatibility. However, HWW treatments could not remove LARGs effectively and instead facilitated their transmission by enhancing the expression and horizontal transfer of mobile genetic element (MGE)-derived LARGs. Our study provides comprehensive insights for the atlas and transfer dynamics of LARGs in HWW for the development of control strategies under worldwide spread of antibiotic resistance.},
}

*Wastewater/microbiology
Hospitals
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Microbial/genetics
*Drug Resistance, Bacterial/genetics
Gene Transfer, Horizontal

@article {pmid40582582,
year = {2025},
author = {Munshi, ID and Mathuria, A and Sharma, H and Acharya, M and Chaudhary, A and Jain, K and Ragini, and Dahiya, S and Arora, R and Singh, V and Saini, A and Mani, I},
title = {Emerging concept of genomic islands in bacterial adaptation and pathogenicity.},
journal = {Research in microbiology},
volume = {},
number = {},
pages = {104303},
doi = {10.1016/j.resmic.2025.104303},
pmid = {40582582},
issn = {1769-7123},
abstract = {Genomic Islands (GEIs) are distinct DNA segments acquired through horizontal gene transfer (HGT), driving bacterial evolution and adaptation. These include Pathogenicity Islands (PAIs), Symbiosis Islands, Antibiotic Resistance Islands, Xenobiotic-Degradation Islands, and Nitrogen Fixation Islands. GEIs contribute to genetic diversity, enhancing bacterial pathogenicity, symbiosis, antibiotic resistance, and xenobiotic degradation. Characterized by variations in GC content, codon bias, and integration sites, they distinguish themselves from the core genome. Advances in genome sequencing and bioinformatics have deepened our understanding of GEIs in bacteria like Salmonella, Vibrio, E. coli, and many more, offering insights into microbial evolution, pathogenicity, and antibiotic resistance mechanisms.},
}

@article {pmid40581000,
year = {2025},
author = {Fraikin, N and Samuel, B and Burstein, D and Lesterlin, C},
title = {Strategies for zygotic gene expression during plasmid establishment.},
journal = {Plasmid},
volume = {},
number = {},
pages = {102754},
doi = {10.1016/j.plasmid.2025.102754},
pmid = {40581000},
issn = {1095-9890},
abstract = {Conjugative plasmids are key drivers of horizontal gene transfer and the spread of antimicrobial resistance. Their successful establishment in new hosts requires overcoming diverse bacterial defence mechanisms, such as restriction-modification systems, CRISPR-Cas systems, and the SOS response. Plasmids achieve this through a leading region-encoded zygotic program of anti-defence genes expressed early in conjugation. This program employs diverse strategies, including single-stranded promoters, repressed double-stranded promoters, and protein translocation. This review explores the diversity of these zygotic programs, the mechanisms underlying their timely regulation, and the array of anti-defence functions they encode. Further investigation of leading region genes is crucial for discovering novel counter-defence strategies and understanding their tailored regulation across diverse plasmid and bacterial species, ultimately enabling us to better understand and potentially manipulate plasmid transfer.},
}

@article {pmid40580037,
year = {2025},
author = {},
title = {Correction to 'GutMetaNet: an integrated database for exploring horizontal gene transfer and functional redundancy in the human gut microbiome'.},
journal = {Nucleic acids research},
volume = {53},
number = {12},
pages = {},
doi = {10.1093/nar/gkaf654},
pmid = {40580037},
issn = {1362-4962},
}

@article {pmid40579721,
year = {2025},
author = {O'Donnell, S and Rezende, G and Vernadet, JP and Snirc, A and Ropars, J},
title = {Harbouring Starships: The accumulation of large Horizontal Gene Transfers in Domesticated and Pathogenic Fungi.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf125},
pmid = {40579721},
issn = {1759-6653},
abstract = {Human-related environments, including food and clinical settings, present microorganisms with atypical and challenging conditions that necessitate adaptation. Several cases of novel horizontally acquired genetic material associated with adaptive traits have been recently described, contained within giant transposons named Starships. While a handful of Starships have been identified in domesticated species, their abundance has not yet been systematically explored in human-associated fungi. Here, we investigated whether Starships have shaped the genomes of two major genera of fungi occurring in food and clinical environments, Aspergillus and Penicillium, providing a unique opportunity to study several independent events of adaptation to similar niches. We found in all cases that the domesticated strains or species exhibited significantly greater Starship content compared with close relatives from non-human-related environments, containing an enrichment in genes involved in adaptation to food. We found a similar pattern in clinical contexts. Our findings have clear implications for agriculture, human health and the food industry as we implicate Starships as a widely recurrent mechanism of gene transfer aiding the rapid adaptation of fungi to novel environments.},
}