@article {pmid40743960,
year = {2025},
author = {Wu, X and Tang, Z and Li, Y and Du, Z and Li, W and Wang, S and Huang, C},
title = {Biochar promotes removal of intracellular and extracellular antibiotic resistance genes in sludge compost: Reshaping microbial communities.},
journal = {Journal of environmental management},
volume = {392},
number = {},
pages = {126781},
doi = {10.1016/j.jenvman.2025.126781},
pmid = {40743960},
issn = {1095-8630},
abstract = {Antibiotic resistance genes (ARGs), as emerging pollutants, jeopardize ecological and public health. Extracellular ARGs (eARGs) pose heightened risks due to their mobility, accelerating resistance spread. However, studying eARGs remains challenging given extracellular DNA's environmental instability. While aerobic composting of sewage sludge reduces ARGs, resurgence of certain genes (e.g., sulfonamide resistance) in later stages may exacerbate resistance risks. This study investigated the effects of sludge-derived biochar and commercial biochar on the reduction of intracellular and extracellular sulfonamide ARGs during sludge composting. After the addition of both biochars, intracellular ARGs (iARGs) gradually decreased as composting progressed, while eARGs initially increased before subsequently declining. The biochars reshaped the microbial community in sludge composting, significantly increasing the number of differentially enriched microbial species, altering community assembly processes, and reducing bacterial diversity and richness-key factors in ARGs reduction. The addition of both biochars also decreased the abundance of intl1, and combined with the inactivation of certain microorganisms and disruption of cell membranes, effectively suppressed the horizontal gene transfer (HGT) of eARGs. However, compared to commercial biochar, the application of sludge-derived biochar led to an increase in potential host microorganisms for ARGs, highlighting a potential risk associated with the production of biochar from sludge. Additionally, the biochars modified environmental factors such as moisture and organic content, further enhancing eARG removal. This study proposes a "waste-to-waste" circular economy model. By reusing sludge-derived biochar in composting, it not only suppresses the spread of ARGs but also achieves high-value utilization of sludge, enabling synergistic pollution control.},
}

@article {pmid40743727,
year = {2025},
author = {Vinogradov, E and Zou, L and Stupak, J and Martynova, Y and Arbour, M and St Michael, F and Williams, D and Beaudoin, G and Li, J and Chen, W and Zou, W and Peters, DL},
title = {Capsular Polysaccharide of Acinetobacter baumannii MRSN 31196 (a KL1 Variant Strain) and its Degradation by a Recombinant Depolymerase from Bacteriophage vB_AbaP_B5.},
journal = {Carbohydrate research},
volume = {556},
number = {},
pages = {109621},
doi = {10.1016/j.carres.2025.109621},
pmid = {40743727},
issn = {1873-426X},
abstract = {Acinetobacter baumannii MRSN 31196 was assigned as KL1, but has now been reassigned as KL1-v as new polymerase wzy and acetyl transferase (atr25) genes are discovered outside of its gene locus due to horizontal gene transfer. Its capsular polysaccharide (CPS), namely K1v, was isolated by a standard water-phenol extraction and an aqueous base extraction. K1v is degradable by a recombinant phage depolymerase B5 which is known to hydrolyze A. baumannii K9 CPS. The structure of oligosaccharides obtained were determined by NMR and mass spectroscopic analysis. The results showed that the K1v structure is closely related to K1 CPS, with the same sugar composition and linkages except β-QuiNAcNR-(1-3)-GlcNAc in K1v replaced β-QuiNAcNR-(1-4)-GlcNAc in K1, due to an altered Wzy. However, the atr25 gene is likely silenced, or the transferase activity is inhibited, as K1v is not O-acetylated. We also found that the N-acetyl and N-3-hydroxybutyryl (HBu) substitutions (R) in QuiNAcNR has approximately a 1:1 ratio. The mass spectroscopic analysis provided evidence that structural blocks with consecutive QuiNAcNAc or QuiNAcNHBu are present in the polysaccharide. The K1v CPS structure has the following trisaccharide repeating unit.},
}

@article {pmid40743684,
year = {2025},
author = {Wang, H and Gao, J and Cui, Y and Wang, Y and Guo, Y and Chen, H},
title = {Short-chain per/polyfluoroalkyl substances alternatives enhance horizontal gene transfer risks in nitrification systems under quaternary ammonium compounds antimicrobials co-stress despite lower acute toxicity than perfluorooctanoic acid.},
journal = {Water research},
volume = {287},
number = {Pt A},
pages = {124274},
doi = {10.1016/j.watres.2025.124274},
pmid = {40743684},
issn = {1879-2448},
abstract = {The ecological risks posed by per/polyfluoroalkyl substances (PFAS) and quaternary ammonium compounds (QACs), as emerging contaminants, to the aquatic environment have recently attracted considerable attention. However, it is still unclear whether and how the combined stress of PFAS and QACs affects wastewater treatment system performance and modulates the transmission of resistance genes (RGs). In this paper, it was investigated that the ecological impacts of perfluorooctanoic acid (PFOA) and its alternatives, perfluorobutanesulfonic acid (PFBS) and perfluorohexanoic acid (PFHxA), on nitrification systems with/without diallyl dimethylammonium chloride (DADMAC), a typical QACs disinfectant, during 120 days. Results showed that 3 mg/L PFOA significantly reduced ammonia removal efficiency, while 0-3 mg/L PFBS and PFHxA had no significant impacts. Interestingly, the addition of 0.3 mg/L DADMAC mitigated the inhibitory effect of PFOA on ammonia oxidation and elevated the abundance of complete ammonia oxidizers amoA and ammonia-oxidizing bacteria amoA genes by 15.8 %-52.9 % and 45.0 %-113.9 %, respectively, through looser protein structures of extracellular polymeric substances and more RGs activated. Under single stress, the abundance of total RGs exhibited first decreasing and then increasing trends with increasing concentrations of all three PFAS, and 3 mg/L PFOA enriched the highest. Under combined stress, PFOA led to the highest abundance of RGs by adding 0.3 mg/L DADMAC, while PFBS resulted in the highest abundance of RGs by adding 3 mg/L DADMAC. Notably, the system with PFBS was observed to have the highest abundance of mobile genetic elements (MGEs), followed by PFHxA, particularly inducing intracellular MGEs in sludge to maintain richness and continuity during combined stress stages. Moreover, MGEs were found to have the most positive contribution to the multiplication of antibiotic resistance genes in all three systems. Overall, although PFBS and PFHxA are regarded as typical alternatives to PFOA and are significantly less toxic to the nitrification systems compared with PFOA, both alternatives resulted in higher levels of MGEs, especially posing a more severe risk of horizontal gene transfer in the combined stress environment. Thus, this requires a focus on the RGs transmission risks of using PFAS and its alternatives in disinfectant-intensive environments.},
}

@article {pmid40739812,
year = {2025},
author = {Nie, C and Liu, F and Li, Z and Shen, Y and Hou, Y and Han, P and Tong, M},
title = {Boosting Low-Dose Ferrate(VI) Activation by Layered FeOCl for the Efficient Removal of Antibiotic-Resistant Bacteria and Antibiotic Resistance Genes via Enhancing Fe(IV)/Fe(V) Generation.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c03869},
pmid = {40739812},
issn = {1520-5851},
abstract = {Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in aquatic environments pose threats to ecosystem safety and human health, which could not be efficiently removed by conventional disinfection techniques. Herein, layered FeOCl with coordinatively unsaturated Fe sites were fabricated and used to activate Fe(VI) for the efficient ARB/ARG removal in the present study. We found that highly reactive Fe(IV)/Fe(V) intermediates were generated in the FeOCl/Fe(VI) system, rapidly disinfecting 1 × 10[7] CFU mL[-1] ARB to below the limit of detection within only 6 min. Via the combination of in situ characterization and theoretical calculations, we revealed that Fe(VI) was preferentially adsorbed onto Fe sites on the (010) plane of FeOCl and subsequently activated to produce reactive Fe(IV)/Fe(V) through direct electron transfer. Meanwhile, O2[•-] generated from O2 activation on the FeOCl surface enhanced Fe(VI) conversion to Fe(IV)/Fe(V). During the disinfection process, intracellular/extracellular ARGs and DNA bases were simultaneously degraded, inhibiting the potential horizontal gene transfer process. The FeOCl/Fe(VI) system could effectively disinfect ARB under complex water matrices and in real water samples including tap water, lake water, and groundwater. When integrated into a continuous-flow reactor, the FeOCl/Fe(VI) system with excellent stability successively disinfected ARB. Overall, the FeOCl/Fe(VI) system showed great promise for eliminating ARB/ARGs from water.},
}

@article {pmid40738105,
year = {2025},
author = {Rodriguez-Rodriguez, L and Pfister, J and Schuck, L and Martin, AE and Mercado-Santiago, LM and Tagliabracci, VS and Forsberg, KJ},
title = {Metagenomic selections reveal diverse antiphage defenses in human and environmental microbiomes.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.07.005},
pmid = {40738105},
issn = {1934-6069},
abstract = {To prevent phage infection, bacteria have developed an arsenal of antiphage defenses. Evidence suggests that many examples in nature have not been described. Using plasmid libraries expressing small DNA inserts and functional selections for antiphage defense in Escherichia coli, we identified over 200 putative defenses from 14 bacterial phyla in 9 human and soil microbiomes. Many defenses were unrecognizable based on sequence or predicted structure and thus could only be identified via functional assays. In mechanistic studies, we show that some defenses encode nucleases that distinguish phage DNA via diverse chemical modifications. We also identify outer membrane proteins that prevent phage adsorption and a set of unknown defenses with diverse antiphage profiles and modalities. Most defenses acted against at least two phages, indicating that broadly acting systems are widely distributed. Collectively, these findings highlight the diversity and interoperability of antiphage defense systems.},
}

@article {pmid40738074,
year = {2025},
author = {Yang, X and Heng, H and Zhang, H and Peng, M and Chan, EW and Shum, HP and Zhang, R and Chen, S},
title = {IncFIBK/FIIK conjugative iuc3-carrying virulence plasmids of clinical hypervirulent Klebsiella pneumoniae are multi-drug resistant.},
journal = {Microbiological research},
volume = {300},
number = {},
pages = {128288},
doi = {10.1016/j.micres.2025.128288},
pmid = {40738074},
issn = {1618-0623},
abstract = {Aerobactin encoding loci is the key virulence factor in the virulence plasmid of Klebsiella pneumoniae (Kp). The iuc1 and iuc2 loci are most commonly detected and well-studied, while the iuc3 lineage is less understood. The study investigated comprehensively the iuc3-carrying plasmids in Kp strains providing insights into the diversity, transmission potential and contribution to Kp virulence. The iuc3 was encoded on plasmids ranging from 177,328 bp to 249,880 bp, primarily of the IncFIBK/FIIK5 type, often carrying multi-drug resistance (MDR) regions. Conjugation experiments demonstrated the transferability of iuc3-carrying plasmids, conferring additional resistance to recipient strains. Siderophore production assays indicated that the iuc3 gene cluster significantly enhanced iron acquisition in transconjugants. Analysis of 69,969 Kp isolates from the NCBI Pathogen Detection database identified 872 iuc3-carrying strains across 205 STs and 69 KLs, indicating widespread genetic diversity. These strains were increasingly detected in human clinical samples over time, with additional reservoirs in animals, food, and the environment. The findings underscore the public health threat posed by iuc3-carrying Kp strains, emphasizing the need for surveillance and control measures to prevent the spread of MDR-HvKp clones. This study highlights the complex interplay between plasmid-mediated resistance, virulence, and the potential for horizontal gene transfer in Klebsiella spp.},
}

@article {pmid40738036,
year = {2025},
author = {Seethalakshmi, PS and Anas, A and Devika Raj, K and Jasmin, C and Menon, N and George, G and Sathyendranath, S},
title = {Genomic insights into antibiotic-resistant Vibrio species from clinical and coastal environmental sources in India.},
journal = {Marine pollution bulletin},
volume = {221},
number = {},
pages = {118496},
doi = {10.1016/j.marpolbul.2025.118496},
pmid = {40738036},
issn = {1879-3363},
abstract = {The occurrence and impact of pathogenic Vibrio sp. in coastal waters are strongly influenced by climate change indicators such as ocean warming, sea-level rise, and extreme weather events. This study aimed to compare the virulence and antimicrobial resistance (AMR) profiles of Vibrio cholerae from clinical and environmental sources across India's coastal regions. We also examined pathogenic traits in other marine Vibrio sp. We hypothesized that Vibrio spp. from different environments would show distinct virulence and AMR patterns shaped by their ecological context. To investigate this, we conducted antimicrobial susceptibility testing and whole-genome sequencing (WGS) on both clinical and environmental isolates. Our findings reveal that environmental V. cholerae from coastal waters possess genes promoting host adhesion and haemolytic activity. Similarly, Vibrio alginolyticus and Vibrio vulnificus harboured virulence factors aiding tissue attachment and invasion. Resistance profiling showed environmental V. cholerae were resistant to fluoroquinolones and macrolides, while clinical isolates were resistant to aminoglycosides and sulphonamides. The presence of antibiotic-resistant Vibrio in marine environments poses a significant public health risk, especially given frequent human interactions with coastal waters for recreation, fishing, and transport. Climate change may exacerbate the proliferation and movement of these pathogens across aquatic and terrestrial systems, increasing the likelihood of human exposure. Moreover, the potential for horizontal gene transfer of resistance genes among pathogenic marine bacteria further highlights the need for surveillance and mitigation strategies to address the growing threat of AMR in marine ecosystems.},
}

@article {pmid40737558,
year = {2025},
author = {Bhatt, S and Kumar, N and Akhter, Y and Chatterjee, S},
title = {Investigating RND efflux pumps in Sphingobium yanoikuyae P4: the role of nonpathogenic bacteria in antibiotic resistance gene spread amid environmental contamination.},
journal = {Journal of biomolecular structure & dynamics},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/07391102.2025.2540826},
pmid = {40737558},
issn = {1538-0254},
abstract = {The widespread and inappropriate application of antibiotics across human and veterinary medicine has generated pressing global health threats, principally the emergence of antimicrobial resistance (AMR) and the contamination of the environment with antibiotics. A fundamental mechanism fueling environmental AMR is the proliferation and horizontal dissemination of antibiotic resistance genes (ARGs), with efflux transporter proteins functioning as central intermediaries. Surprisingly, nonpathogenic bacteria, which are usually regarded as harmless, now pose a substantial risk to society due to the presence of efflux transporters, which make them AMR contributors. In this study, the genomic analysis of the nonpathogenic soil bacterium Sphingobium yanoikuyae P4 revealed an RND (Resistance-Nodulation-Division) efflux pump containing the relevant domains responsible for antibiotic efflux. Molecular docking studies revealed high affinities between the efflux pump and various antibiotics, including fluoroquinolones, beta-lactams, and sulfonamides, raising the possibility of their efflux into the environment. Antibiotic susceptibility tests showed reduced susceptibility due to the action of this efflux transporter. Furthermore, the genome analysis suggested the presence of mobile genetic elements and plasmid-associated sequences, indicating possible horizontal gene transfer. The data highlights that both nonpathogenic and pathogenic bacteria are crucial for capturing and transmitting antibiotic-resistance genes. These results confirm the disregard for existing concerns over the substantial role of nonpathogenic environmental bacteria in the ecological resistome and warrant the need to consider such microorganisms in monitoring and controlling AMR.},
}

@article {pmid40736339,
year = {2025},
author = {Tan, R and Song, Y and Yin, J and Shi, D and Li, H and Chen, T and Wang, Y and Jin, M and Li, J and Yang, D},
title = {Decoding the SCFA-CpxAR-OMP Axis as a Dietary Checkpoint against Antimicrobial Resistance Transmission across Gut-Environment Interfaces.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf156},
pmid = {40736339},
issn = {1751-7370},
abstract = {The transmission of environmental-originated antibiotic resistance genes (ARGs) into the human gut via the food chain or water has transformed the intestinal tract into a critical reservoir and dissemination hub for ARGs. Moreover, human to human oral-fecal transmission is likely to intensify this dissemination cycle. Gut microbiota harboring ARGs not only drive clinical infections but also exacerbate diverse pathologies, including inflammatory bowel disease and metabolic disorders. Furthermore, amplified ARGs can re-enter environmental compartments through fecal discharge, establishing a persistent bidirectional "gut-environment" resistance transmission cycle. In this study, we demonstrate that short-chain fatty acids (SCFAs), key metabolites derived from gut microbiota, potently suppress the horizontal transfer of ARGs. A high-fiber diet reshaped gut microbial composition, elevating SCFA production by 2.3-fold and reducing ARGs dissemination rates by up to 5.8-fold in vivo. The anti-conjugation activity of SCFAs was further validated through in vitro observations and in vivo models. Mechanistically, we propose the CpxAR-OMP pathway as a previously uncharacterized regulatory axis, wherein SCFAs inhibit ARGs transfer by downregulating conjugation-associated promoters (trfAp and trbBp) and disrupting membrane function via CpxAR-mediated suppression of OMPs expression. To our knowledge, this work provides comprehensive evidence of SCFAs in curbing exogenous ARGs dissemination within the gut ecosystem, deciphers the CpxAR-OMP-driven molecular mechanism, and proposes dietary fiber intervention as a feasible strategy to mitigate antimicrobial resistance across the "One-Health" continuum.},
}

@article {pmid40735512,
year = {2025},
author = {Boutzoukas, A and Doi, Y},
title = {The global epidemiology of carbapenem-resistant Acinetobacter baumannii.},
journal = {JAC-antimicrobial resistance},
volume = {7},
number = {4},
pages = {dlaf134},
pmid = {40735512},
issn = {2632-1823},
abstract = {Carbapenem-resistant Acinetobacter baumannii (CRAb) is a challenging, environmentally hardy organism with a propensity to spread within hospitals and a predilection to infect critically ill, vulnerable patients. With its potential for rapid transmission, limited treatment options, and substantial mortality, CRAb is recognized as a critical, top-priority pathogen. Since its initial discovery in 1985, CRAb has disseminated globally, presenting a significant public health threat. CRAb is now endemic in many regions in Europe, South America, Asia, and Africa and globally contributes to over 50 000 deaths each year. Its ability to adhere to hospital surfaces, withstand desiccation, and form biofilms leads to widespread outbreaks. At-risk populations include those hospitalized and ventilated, and the most frequent presentations are respiratory and bloodstream infections. Carbapenem resistance in CRAb is primarily mediated by plasmid-borne carbapenemase genes, especially bla OXA-23. These genes, carried by several epidemic international clones, including IC1 and IC2, have facilitated the global dissemination of CRAb through horizontal gene transfer in healthcare settings. Mortality rates are >20% and vary substantially by region and by type of infection, with bloodstream infections carrying >40% mortality. Despite its significant impact, the development of treatments for CRAb remains inadequate. The novel agent sulbactam-durlobactam holds promise for improved patient outcomes, but ongoing therapeutic development, infection prevention, and antimicrobial stewardship are critical to combat this formidable pathogen. Here, we review the emergence and dissemination of CRAb, its molecular epidemiology and resistance mechanisms, summarize contemporary global clinical epidemiology and patient outcomes, and briefly describe existing and future therapeutics.},
}

@article {pmid40733744,
year = {2025},
author = {Zahid, A and Ismail, H and Wilson, JC and Grice, ID},
title = {Bioengineering Outer-Membrane Vesicles for Vaccine Development: Strategies, Advances, and Perspectives.},
journal = {Vaccines},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/vaccines13070767},
pmid = {40733744},
issn = {2076-393X},
support = {NA//Earbus Foundation of Western Australia/ ; },
abstract = {Outer-membrane vesicles (OMVs), naturally secreted by Gram-negative bacteria, have gained recognition as a versatile platform for the development of next-generation vaccines. OMVs are essential contributors to bacterial pathogenesis, horizontal gene transfer, cellular communication, the maintenance of bacterial fitness, and quorum sensing. Their intrinsic immunogenicity, adjuvant properties, and scalability establish OMVs as potent tools for combating infectious diseases and cancer. Recent advancements in genetic engineering and biotechnology have further expanded the utility of OMVs, enabling the incorporation of multiple epitopes and antigens from diverse pathogens. These developments address critical challenges such as antigenic variability and co-infections, offering broader immune coverage and cost-effective solutions. This review explores the unique structural and immunological properties of OMVs, emphasizing their capacity to elicit robust immune responses. It critically examines established and emerging engineering strategies, including the genetic engineering of surface-displayed antigens, surface conjugation, glycoengineering, nanoparticle-based OMV engineering, hybrid OMVs, and in situ OMV production, among others. Furthermore, recent advancements in preclinical research on OMV-based vaccines, including synthetic OMVs, OMV-based nanorobots, and nanodiscs, as well as emerging isolation and purification methods, are discussed. Lastly, future directions are proposed, highlighting the potential integration of synthetic biology techniques to accelerate research on OMV engineering.},
}

@article {pmid40732295,
year = {2025},
author = {Bharathi, D and Lee, J},
title = {Recent Trends in Bioinspired Metal Nanoparticles for Targeting Drug-Resistant Biofilms.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {18},
number = {7},
pages = {},
doi = {10.3390/ph18071006},
pmid = {40732295},
issn = {1424-8247},
support = {RS-2025-00513239//National Research Foundation of Korea/ ; RS-2024-00450423//Korea Health Industry Development Institute/Republic of Korea ; },
abstract = {Multidrug-resistant (MDR) biofilm infections characterized by densely packed microbial communities encased in protective extracellular matrices pose a formidable challenge to conventional antimicrobial therapies and are a major contributor to chronic, recurrent and device-associated infections. These biofilms significantly reduce antibiotic penetration, facilitate the survival of dormant persister cells and promote horizontal gene transfer, all of which contribute to the emergence and persistence of MDR pathogens. Metal nanoparticles (MNPs) have emerged as promising alternatives due to their potent antibiofilm properties. However, conventional synthesis methods are associated with high costs, complexity, inefficiency and negative environmental impacts. To overcome these limitations there has been a global push toward the development of sustainable and eco-friendly synthesis approaches. Recent advancements have demonstrated the successful use of various plant extracts, microbial cultures, and biomolecules for the green synthesis of MNPs, which offers biocompatibility, scalability, and environmental safety. This review provides a comprehensive overview of recent trends and the latest progress in the green synthesis of MNPs including silver (Ag), gold (Au), platinum (Pt), and selenium (Se), and also explores the mechanistic pathways and characterization techniques. Furthermore, it highlights the antibiofilm applications of these MNPs emphasizing their roles in disrupting biofilms and restoring the efficacy of existing antimicrobial strategies.},
}

@article {pmid40732194,
year = {2025},
author = {Liu, F and Cao, B and Dai, H and Li, G and Li, S and Gao, W and Zhao, R},
title = {High-Resolution Core Gene-Associated Multiple Nucleotide Polymorphism (cgMNP) Markers for Strain Identification in the Wine Cap Mushroom Stropharia rugosoannulata.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071685},
pmid = {40732194},
issn = {2076-2607},
support = {2022YFD1200605//the National Key R&D Program of China project/ ; },
abstract = {Stropharia rugosoannulata, an ecologically valuable and economically important edible mushroom, faces challenges in strain-level identification and breeding due to limited genomic resources and the lack of high-resolution molecular markers. In this study, we generated high-quality genomic data for 105 S. rugosoannulata strains and identified over 2.7 million SNPs, unveiling substantial genetic diversity within the species. Using core gene-associated multiple nucleotide polymorphism (cgMNP) markers, we developed an efficient and transferable framework for strain discrimination. The analysis revealed pronounced genetic differentiation among cultivars, clustering them into two distinct phylogenetic groups. Nucleotide diversity (π) across 83 core genes varied significantly, highlighting both highly conserved loci under purifying selection and highly variable loci potentially associated with adaptive evolution. Phylogenetic analysis of the most variable gene, Phosphatidate cytidylyltransferase mitochondrial, identified 865 SNPs, enabling precise differentiation of all 85 cultivars. Our findings underscore the utility of cgMNP markers in addressing challenges posed by horizontal gene transfer and phylogenetic noise, demonstrating their robustness in cross-species applications. By providing insights into genetic diversity, evolutionary dynamics, and marker utility, this study establishes a foundation for advancing breeding programs, conservation strategies, and functional genomics in S. rugosoannulata. Furthermore, the adaptability of cgMNP markers offers a universal tool for high-resolution strain identification across diverse fungal taxa, contributing to broader fungal phylogenomics and applied mycology.},
}

@article {pmid40732100,
year = {2025},
author = {Mourão, AV and Fernandes, D and de Sousa, T and Calouro, R and Saraiva, S and Igrejas, G and Poeta, P},
title = {Aquatic Resistome in Freshwater and Marine Environments: Interactions Between Commensal and Pathogenic in the Context of Aquaculture and One Health.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071591},
pmid = {40732100},
issn = {2076-2607},
support = {UI/00772//Fundacao para a Ciencia e a Tecnologia/ ; LA/P/0059/2020//Fundacao para a Ciencia e a Tecnologia/ ; },
abstract = {Aquatic resistomes are important reservoirs of antibiotic resistance genes (ARGs) and their precursors, which can proliferate and dissipate in pathogenic microorganisms that affect humans and animals, especially due to anthropogenic pressures such as the intensive use of antibiotics in aquaculture, often without effective regulation. This review addresses the mechanisms of horizontal gene transfer (HGT) in the dissemination of ARGs through mobile genetic elements (MGEs). In freshwater, genera such as Aeromonas, Pseudomonas and Microcystis stand out as vectors of ARGs. In the context of One Health, it is essential to implement sound public policies and strict regulations on the use of antibiotics in aquaculture, and the use of monitoring tools such as environmental DNA (eDNA) and metagenomics allows for the early detection of ARGs, contributing to the protection of human, animal and environmental health.},
}

@article {pmid40730864,
year = {2025},
author = {McCallum, GE and Hall, JPJ},
title = {The hospital sink drain microbiome as a melting pot for AMR transmission to nosocomial pathogens.},
journal = {npj antimicrobials and resistance},
volume = {3},
number = {1},
pages = {68},
doi = {10.1038/s44259-025-00137-9},
pmid = {40730864},
issn = {2731-8745},
support = {MR/W02666X/1/MRC_/Medical Research Council/United Kingdom ; MR/W02666X/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {The hospital sink drain microbiome can harbour opportunistic pathogens and antimicrobial resistance genes (ARGs). Aspects of this habitat, such as exposure to disinfectants, antibiotics, nutrients, and body fluids could exacerbate horizontal gene transfer of ARGs and clinically impactful pathogen resistance. Here, we explore features of the hospital sink drain that may favour ARG acquisition and transmission, highlight studies providing evidence of transfer, and consider strategies to mitigate these risks.},
}

@article {pmid40729388,
year = {2025},
author = {Riaz, MR and Sosa Marquez, I and Lindgren, H and Levin, G and Doyle, R and Romero, MC and Paoli, JC and Drnevich, J and Fields, CJ and Geddes, BA and Marshall-Colón, A and Heath, KD},
title = {Mobile gene clusters and coexpressed plant-rhizobium pathways drive partner quality variation in symbiosis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {31},
pages = {e2411831122},
doi = {10.1073/pnas.2411831122},
pmid = {40729388},
issn = {1091-6490},
support = {IOS-1645875//NSF (NSF)/ ; DBI-2022049//NSF (NSF)/ ; IOS-2243821//NSF (NSF)/ ; na//Consejo Nacional de Humanidades, Ciencias y Tecnologías (Conahcyt)/ ; na//UofI | UIUC | Carl R. Woese Institute for Genomic Biology (IGB)/ ; IOS- 2243818//NSF (NSF)/ ; },
mesh = {*Symbiosis/genetics ; *Sinorhizobium meliloti/genetics ; *Multigene Family ; Root Nodules, Plant/microbiology/genetics ; Genetic Variation ; Transcriptome ; *Rhizobium/genetics ; Gene Regulatory Networks ; },
abstract = {Plant-microbe symbioses such as the legume-rhizobium mutualism are vital in the web of ecological relationships within both natural and managed ecosystems, influencing primary productivity, crop yield, and ecosystem services. The outcome of these interactions for plant hosts varies quantitatively and can range from highly beneficial to even detrimental depending on natural genetic variation in microbial symbionts. Here, we take a systems genetics approach, harnessing the genetic diversity present in wild rhizobial populations to predict genes and molecular pathways crucial in determining partner quality, i.e., the benefits of symbiosis for legume hosts. We combine traits, dual-RNAseq of both partners from active nodules, pangenomics/pantranscriptomics, and Weighted Gene Co-expression Network Analysis (WGCNA) for a panel of 20 Sinorhizobium meliloti strains that vary in symbiotic partner quality. We find that genetic variation in the nodule transcriptome predicts host plant biomass, and WGCNA reveals networks of genes in plants and rhizobia that are coexpressed and associated with high-quality symbiosis. Presence-absence variation of gene clusters on the symbiosis plasmid (pSymA), validated in planta, is associated with high or low-quality symbiosis and is found within important coexpression modules. Functionally our results point to management of oxidative stress, amino acid and carbohydrate transport, and NCR peptide signaling mechanisms in driving symbiotic outcomes. Our integrative approach highlights the complex genetic architecture of microbial partner quality and raises hypotheses about the genetic mechanisms and evolutionary dynamics of symbiosis.},
}

*Symbiosis/genetics
*Sinorhizobium meliloti/genetics
*Multigene Family
Root Nodules, Plant/microbiology/genetics
Genetic Variation
Transcriptome
*Rhizobium/genetics
Gene Regulatory Networks

@article {pmid40727556,
year = {2025},
author = {Wang, Z and Zhao, S and Chen, G and Sun, S and Liu, Y and Chen, H and Meng, L and Han, Z and Zheng, D},
title = {Biodegradation of high-molecular-weight polycyclic aromatic hydrocarbons by a novel species of the genus Devosia isolated from the deep-sea region of the Kermadec Trench.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1584496},
pmid = {40727556},
issn = {1664-302X},
abstract = {Polycyclic aromatic hydrocarbons (PAHs) are categorized as persistent organic pollutants due to their high toxicity and environmental persistence. In this study, a deep-sea bacterium, designed Naph2[T], was isolated from the sediments of the Kermadec Trench using PAH-enriched cultures. A comparative analysis of Overall Genome Relatedness Indices (OGRI) values between Naph2[T] and closely related strains within the genus Devosia indicated that the isolate represents a novel species, designated as Devosia polycyclovorans sp. nov. (type strain Naph2[T] = MCCC 1K09447[T]). This conclusion is further supported by physiological and biochemical analyses. Naph2[T] exhibited the ability to degrade high-molecular-weight PAHs such as pyrene and benzo[a]pyrene, a feature not previously reported for any strain within the genus Devosia. The degradation degree of Naph2[T] for pyrene and benzo[a]pyrene reached 58 and 48% at a concentration of 300 mg/L and 200 mg/L, respectively, in 5 days. Genomic analysis revealed key genes associated with PAH degradation, including aromatic ring-hydroxylating dioxygenase (RHD), nagAa, and downstream gene clusters such as pht, pob, and pca. Comparative genomic studies showed that Naph2[T] harbors a greater number of PAH degradation genes than other species within the Devosia genus, demonstrate that it may have acquired these capabilities through horizontal gene transfer. Transcriptome data revealed significant upregulation of pcaG and pcaH, which encode enzymes involved in the degradation of 3,4-dihydroxybenzoic acid, a downstream intermediate of polycyclic aromatic hydrocarbon metabolism. These findings not only provide novel insights into the ecological roles of the genus Devosia, but also highlight the potential of this new species for PAH bioremediation applications.},
}

@article {pmid40725502,
year = {2025},
author = {Hu, T and Zhou, F and Wang, L and Hu, X and Li, Z and Li, X and Zhou, D and Wang, H},
title = {Mitogenome Characteristics and Intracellular Gene Transfer Analysis of Four Adansonia Species.},
journal = {Genes},
volume = {16},
number = {7},
pages = {},
doi = {10.3390/genes16070846},
pmid = {40725502},
issn = {2073-4425},
support = {No. 25L193//Integration and Optimization of Ancient Tree and Famous Tree Protection and Rural Tourism Development in Zhumadian City/ ; },
mesh = {*Genome, Mitochondrial/genetics ; Phylogeny ; Evolution, Molecular ; *Gene Transfer, Horizontal ; },
abstract = {Adansonia L. (1753) belongs to the family Malvaceae and is commonly known as the baobab tree. This species holds significant cultural and ecological value and is often referred to as the 'tree of life.' Although its nuclear genome has been reported, the mitogenome has not yet been studied. Mitogenome research is crucial for understanding the evolution of the entire genome. In this study, we assembled and analyzed the mitogenomes of four Adansonia species by integrating short-read and long-read data. The results showed that the mitogenomes of all four Adansonia species were resolved as single circular sequences. Their total genome lengths ranged from 507,138 to 607,344 bp and contained a large number of repetitive sequences. Despite extensive and complex rearrangements between the mitogenomes of Adansonia and other Malvaceae species, a phylogenetic tree constructed based on protein-coding genes clearly indicated that Adansonia is more closely related to the Bombax. Selection pressure analysis suggests that the rps4 gene in Adansonia may have undergone positive selection compared to other Malvaceae species, indicating that this gene may play a significant role in the evolution of Adansonia. Additionally, by analyzing intracellular gene transfer between the chloroplast, mitochondria, and nuclear genomes, we found that genes from the chloroplast and mitochondria can successfully transfer to each chromosome of the nuclear genome, and the psbJ gene from the chloroplast remains intact in both the mitochondrial and nuclear genomes. This study enriches the genetic information of Adansonia and provides important evidence for evolutionary research in the family Malvaceae.},
}

*Genome, Mitochondrial/genetics
Phylogeny
Evolution, Molecular
*Gene Transfer, Horizontal

@article {pmid40724928,
year = {2025},
author = {Mažeikienė, I and Frercks, B and Kurgonaitė, M and Rasiukevičiūtė, N and Mačionienė, I},
title = {Genomic Insights into Vaccinium spp. Endophytes B. halotolerans and B. velezensis and Their Antimicrobial Potential.},
journal = {International journal of molecular sciences},
volume = {26},
number = {14},
pages = {},
doi = {10.3390/ijms26146677},
pmid = {40724928},
issn = {1422-0067},
mesh = {*Endophytes/genetics/metabolism ; *Bacillus/genetics/metabolism/isolation & purification/classification ; *Genome, Bacterial ; *Anti-Infective Agents/pharmacology/metabolism ; Genomics/methods ; Phylogeny ; Blueberry Plants/microbiology ; Gene Transfer, Horizontal ; },
abstract = {Plant microbiota contributes to nutrient absorption, and the production of hormones and vitamins, and plays a crucial role in responding to environmental stress. We hypothesized that Vaccinium spp. harbour a unique microbiota that enables them to coexist in extreme environments such as saline, nutrient-poor, and waterlogged conditions. Upon examining Bacillus spp. endophytes isolated from blueberries, cranberries and lingonberries in vitro, we identified B. halotolerans (Bil-LT1_1, Bil-LT1_2) and B. velezensis (Cran-LT1_8, Ling-NOR4_15) strains that inhibit the growth of five pathogenic fungi and five foodborne bacteria. Whole-genome sequencing provided insights into genome organization and plasticity, helping identify mobile elements and genes potentially acquired through horizontal gene transfer. Functional annotation identified genes associated with plant colonization, stress tolerance, biocontrol activity, and plant growth promotion. Comparative genomic analyses revealed key biosynthetic gene clusters (BGCs) responsible for producing antifungal metabolites, including lipopeptides and polyketides. Genes supporting plant nutrition, growth, and environmental adaptation were present also in these strains. Notably, isolated endophytes exhibited particularly high levels of genomic plasticity, likely due to horizontal gene transfer involving gene ontology (GO) pathways related to survival in polymicrobial and foreign environments.},
}

*Endophytes/genetics/metabolism
*Bacillus/genetics/metabolism/isolation & purification/classification
*Genome, Bacterial
*Anti-Infective Agents/pharmacology/metabolism
Genomics/methods
Phylogeny
Blueberry Plants/microbiology
Gene Transfer, Horizontal

@article {pmid40724597,
year = {2025},
author = {Borgio, JF},
title = {Hybrid Genome and Clinical Impact of Emerging Extensively Drug-Resistant Priority Bacterial Pathogen Acinetobacter baumannii in Saudi Arabia.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/life15071094},
pmid = {40724597},
issn = {2075-1729},
abstract = {Acinetobacter baumannii is listed by the World Health Organization as an emerging bacterial priority pathogen, the prevalence and multidrug resistance of which have been increasing. This functional genomics study aimed to understand the drug-resistance mechanisms of an extensively drug-resistant (XDR) A. baumannii strain (IRMCBCU95U) isolated from a transtracheal aspirate sample from a female patient with end-stage renal disease in Saudi Arabia. The whole genome of IRMCBCU95U (4.3 Mbp) was sequenced using Oxford Nanopore long-read sequencing to identify and compare the antibiotic-resistance profile and genomic features of A. baumannii IRMCBCU95U. The antibiogram of A. baumannii IRMCBCU95U revealed resistance to multiple antibiotics, including cefepime, ceftazidime, ciprofloxacin, imipenem, meropenem and piperacillin/tazobactam. A comparative genomic analysis between IRMCBCU95U and A. baumannii K09-14 and ATCC 19606 identified significant genetic heterogeneity and mosaicism among the strains. This analysis also demonstrated the hybrid nature of the genome of IRMCBCU95U and indicates that horizontal gene transfer may have occurred between these strains. The IRMCBCU95U genome has a diverse range of genes associated with antimicrobial resistance and mobile genetic elements (ISAba1 and IS26) associated with the spread of multidrug resistance. The presence of virulence-associated genes that are linked to iron acquisition, motility and transcriptional regulation confirmed that IRMCBCU95U is a priority human pathogen. The plasmid fragment IncFIB(pNDM-Mar) observed in the strain is homologous to the plasmid in Klebsiella pneumoniae (439 bp; similarity: 99.09%), which supports its antimicrobial resistance. From these observations, it can be concluded that the clinical A. baumannii IRMCBCU95U isolate is an emerging extensively drug-resistant human pathogen with a novel combination of resistance genes and a plasmid fragment. The complex resistome of IRMCBCU95U highlights the urgent need for genomic surveillance in hospital settings in Saudi Arabia to fight against the spread of extensively drug-resistant A. baumannii.},
}

@article {pmid40724253,
year = {2025},
author = {Ortega-Sanz, I and Rajkovic, A},
title = {Microplastics-Assisted Campylobacter Persistence, Virulence, and Antimicrobial Resistance in the Food Chain: An Overview.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {14},
pages = {},
doi = {10.3390/foods14142432},
pmid = {40724253},
issn = {2304-8158},
support = {G000123N//Research Foundation - Flanders/ ; 965173//European Union/ ; },
abstract = {Recent studies have detected microplastics (MPs) in seafood and various food products worldwide, including poultry, fish, salt, beverages, fruits, and vegetables. This widespread contamination makes human exposure through consumption unavoidable and raises concerns for food safety and human health. MPs provide physical support to microorganisms for biofilm formation, protecting them from extreme conditions and facilitating their persistence in the environment. However, little is known about the impact of MPs in the transmission of foodborne pathogens and subsequent spread of infectious diseases like campylobacteriosis, the most common foodborne illness caused by a bacterium, Campylobacter. This review explores the sources of MP contamination in the food chain and offers a comprehensive overview of MP presence in animals, food products, and beverages. Moreover, we compile the available studies linking MPs and Campylobacter and examine the potential impact of these particles on the transmission of Campylobacter along the food chain with a particular focus on poultry, the main source and reservoir for the pathogen. While the environmental and toxicological effects of MPs are increasingly understood, their influence on the virulence of Campylobacter and the spread of antimicrobial resistance remains underexplored. Further studies are needed to develop standardized methods for isolating and identifying MPs, enabling comprehensive investigations and more effective monitoring and risk mitigation strategies.},
}

@article {pmid40723966,
year = {2025},
author = {Atriano Briano, RA and Badillo-Larios, NS and Niño-Moreno, P and Pérez-González, LF and Turrubiartes-Martínez, EA},
title = {Molecular Characterization of Vancomycin-Resistant Enterococcus spp. from Clinical Samples and Identification of a Novel Sequence Type in Mexico.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/antibiotics14070663},
pmid = {40723966},
issn = {2079-6382},
abstract = {Background:Enterococcus spp. is the third leading cause of healthcare-associated infections in the American continent, often because of the virulence factors that protect the bacterium against host defenses and facilitate tissue attachment and genetic material exchange. In addition, vancomycin, considered a last-resort treatment, has shown reduced efficacy in Enterococcus spp. strains. However, the relationship between bacterial resistance and virulence factors remains unclear. This study intends to evaluate the prevalence of glycopeptide-resistant genotypes and virulence factors in Enterococcus spp. strains. Methods: Over six months, 159 Enterococcus spp. strains causing nosocomial infections were analyzed. Multiplex PCR was performed to identify species, glycopeptide-resistant genotypes, and 12 virulence factors. Results: The most abundant species identified were Enterococcus faecalis and E. faecium. Vancomycin resistance was observed in 10.7% of the isolates, and the vanA genotype was present in 47% of resistant samples. The main virulence factors detected were acm (54%), which is related to cell adhesion; gel E (66%), a metalloproteinase linked to tissue damage; and the sex pheromones cpd (64%) and ccf (84%), which are involved in horizontal gene transfer. A significant association was found between the prevalence of acm, ccf, and cpd in VRE isolates, indicating the potential dissemination of genes to emerging strains via horizontal gene transfer. In addition, a new E. faecium, which displayed five virulence factors and harbored the vanA sequence type, was identified and registered as ST2700. Conclusions:Enterococcus faecalis and E. faecium are clinically critical due to multidrug resistance and virulence factors like acm, which aids host colonization. Genes ccf and cpd promote resistance spread via horizontal transfer, while the emerging ST2700 strain requires urgent monitoring to curb its virulent, drug-resistant spread.},
}

@article {pmid40723946,
year = {2025},
author = {Saengsawang, P and Tanonkaew, R and Kimseng, R and Nissapatorn, V and Wintachai, P and Rodríguez-Ortega, MJ and Mitsuwan, W},
title = {Whole Genome Sequence Analysis of Multidrug-Resistant Staphylococcus aureus and Staphylococcus pseudintermedius Isolated from Superficial Pyoderma in Dogs and Cats.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/antibiotics14070643},
pmid = {40723946},
issn = {2079-6382},
support = {RGNS 65-187//Office of the Permanent Secretary, Ministry of Higher Education, Science, Research and Innova-tion (OPS MHESI), Thailand Science Research/ ; WU-COE-65-05//Centre of Excellence in Innovation of Essential Oil and Bioactive Compounds/ ; },
abstract = {Background: Pyoderma is a superficial bacterial infection that is considered the formation of pus-containing lesions on the skin occurring in animals. Staphylococci, including Staphylococcus aureus and Staphylococcus pseudintermedius, that cause pyoderma in pet animals is a global health concern. The objectives of this study were to investigate antibiotic-resistant staphylococci isolated from pyoderma in dogs and cats and to analyse whole genome sequences of multidrug-resistant (MDR) staphylococci. Methods: A total of 56 pyoderma swabbing samples from 42 dogs and 14 cats located in Southern Thailand was collected to isolate staphylococci. Antibiotic susceptibility and antibiotic-resistant genes of staphylococcal isolates were investigated. Furthermore, the representative MDR isolates were investigated using whole genome sequence analysis. Results: 61 isolates were identified as staphylococci, which can be classified into 12 different species, mostly including 13 S. intermedius (13.26%), 13 S. saprophyticus (13.26%), 8 S. sciuri (8.16%), and Staphylococcus cohnii (8.16%). Remarkably, the main pyoderma-causing species that were isolated in this study were S. aureus (5.10%) and S. pseudintermedius (3.06%). Most staphylococci were resistant to penicillin G (30%), and the blaZ gene was found to be the highest prevalence of the resistance genes. Both MDR-S. aureus WU1-1 and MDR-S. pseudintermedius WU48-1 carried capsule-related genes as main virulence factor genes. Interestingly, MDR-S. pseudintermedius WU48-1 was resistant to seven antibiotic classes, which simultaneously carried blaZ, mecA, aac, dfrK, aph3, and tetM. Genes related to antibiotic efflux were the highest proportion of the mechanism found in both representatives. Remarkably, SCCmec cassette genes were found in both isolates; however, the mecA gene was found only in MDR-S. pseudintermedius WU48-1. In addition, these were mostly carried by macrolide- and tetracycline-resistance genes. Mobile gene transfer and horizontal gene transfer events frequently contain genes involved in the antibiotic target alteration mechanism. Conclusions: This study found that MDR staphylococci, especially S. aureus and S. pseudintermedius, are important in animals and owners in terms of One Health concern. The information on whole genome sequences of these MDR staphylococci, particularly antimicrobial resistance genes, mobile genetic elements, and horizontal gene transfer events, can help to understand gene transmission and be applied for antibiotic resistance surveillance in veterinary medicine.},
}

@article {pmid40723873,
year = {2025},
author = {Gatto, KP and Targueta, CP and Vittorazzi, SE and Lourenço, LB},
title = {Could Horizontal Gene Transfer Explain 5S rDNA Similarities Between Frogs and Worm Parasites?.},
journal = {Biomolecules},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/biom15071001},
pmid = {40723873},
issn = {2218-273X},
support = {2014/23542-6//Fapesp/ ; },
mesh = {Animals ; *Gene Transfer, Horizontal ; Phylogeny ; *RNA, Ribosomal, 5S/genetics ; *DNA, Ribosomal/genetics ; *Anura/genetics ; *Xenopus laevis/genetics/parasitology ; },
abstract = {Horizontal gene transfer (HGT), the non-Mendelian transfer of genetic material between organisms, is relatively frequent in prokaryotes, whereas its extent among eukaryotes remains unclear. Here, we raise the hypothesis of a possible cross-phylum HGT event involving 5S ribosomal DNA (rDNA). A specific type of 5S rDNA sequence from the anuran Xenopus laevis was highly similar to a 5S rDNA sequence of the genome of its flatworm parasite Protopolystoma xenopodis. A maximum likelihood analysis revealed phylogenetic incongruence between the gene tree and the species trees, as the 5S rDNA sequence from Pr. xenopodis was grouped along with the sequences from the anurans. Sequence divergence analyses of the gene region and non-transcribed spacer also agree with an HGT event from Xenopus to Pr. xenopodis. Additionally, we examined whether contamination of the Pr. xenopodis genome assembly with frog DNA could explain our findings but found no evidence to support this hypothesis. These findings highlight the possible contribution of HGT to the high diversity observed in the 5S rDNA family.},
}

Animals
*Gene Transfer, Horizontal
Phylogeny
*RNA, Ribosomal, 5S/genetics
*DNA, Ribosomal/genetics
*Anura/genetics
*Xenopus laevis/genetics/parasitology

@article {pmid40723416,
year = {2025},
author = {Zhang, H and Wu, T and Ruan, H},
title = {Unveiling Genomic Islands Hosting Antibiotic Resistance Genes and Virulence Genes in Foodborne Multidrug-Resistant Patho-Genic Proteus vulgaris.},
journal = {Biology},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/biology14070858},
pmid = {40723416},
issn = {2079-7737},
support = {2022KJ004//Tianjin Education Commission Scientific Research Project/ ; },
abstract = {Proteus vulgaris is an emerging multidrug-resistant (MDR) foodborne pathogen that poses a significant threat to food safety and public health, particularly in aquaculture systems where antibiotic use may drive resistance development. Despite its increasing clinical importance, the genomic mechanisms underlying antimicrobial resistance (AMR) and virulence transmission in foodborne Proteus vulgaris remain poorly understood, representing a critical knowledge gap in One Health frameworks. To investigate its AMR and virulence transmission mechanisms, we analyzed strain P3M from Penaeus vannamei intestines through genomic island (GI) prediction and comparative genomics. Our study provides the first comprehensive characterization of mobile genetic elements in aquaculture-derived Proteus vulgaris, identifying two virulence-associated GIs (GI12/GI15 containing 25/6 virulence genes) and three AMR-linked GIs (GI7/GI13/GI16 carrying 1/1/5 antibiotic resistance genes (ARGs)), along with a potentially mobile ARG cluster flanked by IS elements (tnpA-tnpB), suggesting horizontal gene transfer capability. These findings elucidate previously undocumented genomic mechanisms of AMR and virulence dissemination in Proteus vulgaris, establishing critical insights for developing One Health strategies to combat antimicrobial resistance and virulence in foodborne pathogens.},
}

@article {pmid40722006,
year = {2025},
author = {Qiu, J and Tao, H and Li, H and Liu, X and Liu, R and Nawaz, MN and Wang, X and Ma, L},
title = {The environmental adaptation of acidophilic archaea: promotion of horizontal gene transfer by genomic islands.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {696},
doi = {10.1186/s12864-025-11875-5},
pmid = {40722006},
issn = {1471-2164},
support = {42277193//National Natural Science Foundation of China/ ; 42277193//National Natural Science Foundation of China/ ; },
mesh = {*Gene Transfer, Horizontal ; *Genomic Islands ; *Archaea/genetics/physiology ; Genome, Archaeal ; *Adaptation, Physiological/genetics ; Base Composition ; Phylogeny ; Genomics ; RNA, Transfer/genetics/chemistry ; },
abstract = {Acid mine drainage (AMD) is an extremely acidic leachate highly contaminated with metal ions, yet it harbors a significantly high abundance of archaea. Genomic islands (GIs), as one of the productions of horizontal gene transfer (HGT), play an important role in the environmental adaptation and evolutionary processes of archaea. However, the distribution, structure, and function of GI within the genomes of archaea remain poorly understood. In this study, through the bioinformatic analysis of archaea in AMD, including Ferroplasma acidiphilum ZJ isolated from laboratory and 25 acidophilic archaea collected from NCBI database, 176 GIs were predicted and annotated. Furthermore, we analyzed their structural features and provided insights into the role of HGT in environmental adaptation. The size and distribution of GIs in the genomes were found to be random. In the majority of GIs, the GC content was lower than the average GC content of the strain genome, suggesting that GIs were typically looped out of the genomes with poor stability and transferred into those with higher stability. tRNAs with classical stem-loop secondary structures have been found at the ends of several GIs, suggesting that GIs frequently integrate near tRNAs. In contrast to functional genes directly involved in cellular life processes, GIs were more likely to carry genes related to genetic information and metabolism. Several GIs were identified to carry genes involved in iron oxidation, mercury reduction, and various toxin-antitoxin systems, which enhance the adaptability of the strains to highly acidic environments.},
}

*Gene Transfer, Horizontal
*Genomic Islands
*Archaea/genetics/physiology
Genome, Archaeal
*Adaptation, Physiological/genetics
Base Composition
Phylogeny
Genomics
RNA, Transfer/genetics/chemistry

@article {pmid40721230,
year = {2025},
author = {Chen, A and Liu, K and Wu, X and Qi, T and Lv, Z and Lu, Y and Tao, Y and Liu, C},
title = {Proliferation of Resistance Genes in Wastewater Pipe Under Tetracycline and Cu Stress.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {97},
number = {7},
pages = {e70155},
doi = {10.1002/wer.70155},
pmid = {40721230},
issn = {1554-7531},
support = {51808285//National Natural Science Foundation of China/ ; SJCX 24-0503//Postgraduate Research & Practice Innovation Program of Jiangsu Province/ ; },
mesh = {*Copper/toxicity/pharmacology ; *Tetracycline/pharmacology/toxicity ; *Wastewater/microbiology ; *Water Pollutants, Chemical/toxicity ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects ; },
abstract = {Antibiotics and heavy metals can accumulate in wastewater pipe, and they could affect the proliferation of resistance genes in pipe. This study investigated the effects of tetracycline (TC) and Cu stress on extracellular polymeric substances (EPS) of sediments and the proliferation process and mechanism of typical antibiotic resistance genes (ARGs) and heavy metal resistance genes (HMRGs) in pipe. The results showed that TC and Cu induced microorganisms to secrete more tightly bound EPS (TB-EPS) in sediments. Under the 20 days exposure of 10,000 μg/L TC, TB-EPS increased by 49.38% compared with that without TC. Under TC and Cu stress, microorganisms secreted more functional groups associated with proteins and polysaccharides, and the secondary structure of proteins (α-helix and β-sheet) was changed, which improved the stability and aggregation of cell structure. Under the single and combined stress of TC and Cu, the relative abundance of most resistance genes in the sediment of wastewater pipe increased significantly (p ≤ 0.05). And TC and Cu stress increased the abundance of genes encoding for efflux pumps (tet(A), tet(G), copA, and copB) and promoted intl1-mediated horizontal gene transfer. This study could provide the theoretical basis for reducing the further spread of resistance genes in wastewater pipe.},
}

*Copper/toxicity/pharmacology
*Tetracycline/pharmacology/toxicity
*Wastewater/microbiology
*Water Pollutants, Chemical/toxicity
*Anti-Bacterial Agents/pharmacology
Genes, Bacterial
*Drug Resistance, Bacterial/genetics
Bacteria/genetics/drug effects

@article {pmid40719986,
year = {2025},
author = {Pandey, M and Rajput, M and Singh, P and Shukla, VK and Dixit, R},
title = {Human long non-coding RNAs acquired from bacteria via horizontal gene transfer promote gallbladder cancer.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {762},
doi = {10.1007/s11033-025-10870-z},
pmid = {40719986},
issn = {1573-4978},
mesh = {Humans ; *RNA, Long Noncoding/genetics ; *Gene Transfer, Horizontal/genetics ; *Gallbladder Neoplasms/genetics/microbiology ; Phylogeny ; *Bacteria/genetics ; Gene Expression Regulation, Neoplastic ; Evolution, Molecular ; Transcriptome/genetics ; Gene Expression Profiling/methods ; },
abstract = {BACKGROUND: Gallbladder cancer, the most common malignancy of the bile duct, has a poorly understood etiopathogenesis. Non-coding RNAs are implicated in various cancers, but their role in gallbladder carcinogenesis remains unclear.

METHODS: Transcriptomic data from gallbladder cancer patients were analyzed to identify differentially expressed long non-coding RNAs (lncRNAs). These data underwent cross-species phylogenetic analysis and BLAST comparison with bacterial and ancient human genomes, including Homo heidelbergensis and Homo neanderthalensis. Pathway analysis, gene-gene interactions, and data and text mining were performed for non-conserved, non-coding genes.

RESULTS: Of 16 differentially expressed lncRNAs, seven showed phylogenetic links to bacterial genomes, suggesting acquisition through horizontal gene transfer (HGT) during human evolution. These lncRNAs were present in ancient human species with sequence variations. Functional analysis revealed their role in regulating biological and genetic processes, potentially promoting gallbladder carcinogenesis.

CONCLUSIONS: This is the first study to propose that seven human lncRNAs, likely of bacterial origin, were acquired through HGT during evolution. These lncRNAs regulate transcriptional and post-transcriptional processes, potentially inducing gallbladder carcinogenesis, thus highlighting a novel link between evolutionary genetics and cancer.},
}

Humans
*RNA, Long Noncoding/genetics
*Gene Transfer, Horizontal/genetics
*Gallbladder Neoplasms/genetics/microbiology
Phylogeny
*Bacteria/genetics
Gene Expression Regulation, Neoplastic
Evolution, Molecular
Transcriptome/genetics
Gene Expression Profiling/methods

@article {pmid40719955,
year = {2025},
author = {Purohit, HV},
title = {Nucleoid-associated proteins: molecular mechanisms in microbial adaptation.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {8},
pages = {277},
pmid = {40719955},
issn = {1573-0972},
abstract = {Nucleoid-associated proteins (NAPs) are essential regulators of bacterial chromosomal organization and gene expression, enabling microbes to adapt to environmental fluctuations. Bacteria are under increasing pressure from oxidative stress, temperature changes, osmotic fluctuations, and nutritional constraints, all of which are consequences of climate change. Major NAPs including H-NS, Fis, HU, IHF, Lrp, and Dps contribute significantly to microbial resilience by regulating genes that respond to stress and reshape chromosomal architecture. The ability to withstand extreme environments depends on these proteins, which mediate gene silencing, transcriptional activation, and DNA protection. In addition to their essential function in stress adaption, NAPs have tremendous promise for biotechnological developments. Their ability to regulate gene expression in reaction to stimuli in the environment can be used to create microbial strains that are more resistant to stress, which would be useful in fields such as bioremediation, farming, and industrial fermentation. Their impact on dormancy regulation and horizontal gene transfer opens doors for better microbial engineering techniques and the fight against antibiotic resistance. Enhancing heterologous gene expression, optimizing metabolic pathways, and designing biosensors responsive to changing environmental conditions are all possible through fine-tuning NAP activity in synthetic biology. Extremophilic NAP variations, their relationships with global regulators, and their possible utility in developing microbial systems that can withstand climate change are the topics of new research. An in-depth molecular-level understanding of these proteins may provide novel approaches to maintaining microbial-driven activities in dynamic ecosystems. Researchers can help with worldwide sustainability initiatives by creating more resilient microbial systems that can adapt to changing conditions by combining biotechnology with environmental microbiology and NAP-driven regulatory mechanisms.},
}

@article {pmid40717244,
year = {2025},
author = {Mishra, S and Lercher, MJ},
title = {Horizontal Gene Transfer Inference: Gene Presence-Absence Outperforms Gene Trees.},
journal = {Molecular biology and evolution},
volume = {42},
number = {7},
pages = {},
doi = {10.1093/molbev/msaf166},
pmid = {40717244},
issn = {1537-1719},
support = {//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Horizontal gene transfer is a fundamental driver of prokaryotic evolution, facilitating the acquisition of novel traits and adaptation to new environments. Despite its importance, methods for inferring horizontal gene transfer are rarely systematically compared, leaving a gap in our understanding of their relative strengths and limitations. Validating horizontal gene transfer inference methods is challenging due to the absence of a genomic fossil record that could confirm historical transfer events. Without an empirical gold standard, new inference methods are typically validated using simulated data; however, these simulations may not accurately capture biological complexity and often embed the same assumptions used in the inference methods themselves. Here, we leverage the tendency of horizontal gene transfer events to involve multiple neighboring genes to assess the accuracy of diverse horizontal gene transfer inference methods. We show that methods analyzing gene family presence/absence patterns across species trees consistently outperform approaches based on gene tree-species tree reconciliation. Our findings challenge the prevailing assumption that explicit phylogenetic reconciliation methods are superior to simpler implicit methods. By providing a comprehensive benchmark, we offer practical recommendations for selecting appropriate methods and indicate avenues for future methodological advancements.},
}

@article {pmid40715782,
year = {2025},
author = {Tonkin-Hill, G and Ruis, C and Bentley, SD and Lythgoe, KA and Bryant, JM},
title = {Within-host bacterial evolution and the emergence of pathogenicity.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40715782},
issn = {2058-5276},
support = {2025515//Department of Health | National Health and Medical Research Council (NHMRC)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; },
abstract = {The use of whole-genome sequencing to monitor bacterial pathogens has provided crucial insights into their within-host evolution, revealing mutagenic and selective processes driving the emergence of antibiotic resistance, immune evasion phenotypes and adaptations that enable sustained human-to-human transmission. Deep genomic and metagenomic sequencing of intra-host pathogen populations is also enhancing our ability to track bacterial transmission, a key component of infection control. This Review discusses the major processes driving bacterial evolution within humans, including both pathogenic and commensal species. Initially, mutational processes, including how mutational signatures reveal pathogen biology, and the selective pressures driving evolution are considered. The dynamics of horizontal gene transfer and intra-host pathogen competition are also examined, followed by a focus on the emergence of bacterial pathogenesis. Finally, the Review focuses on the importance of within-host genetic diversity in tracking bacterial transmission and its implications for infectious disease control and public health.},
}

@article {pmid40714442,
year = {2025},
author = {Hong, YL and Xi, WM and Wang, YT and Yuan, Y and Shen, ZZ and Tian, M and Clarke, JL and Xie, WY and Zhao, FJ},
title = {Soil co-occurring bacterial communities serve as assembly hubs of antibiotic resistance determinants under organic fertilization.},
journal = {Journal of environmental management},
volume = {392},
number = {},
pages = {126708},
doi = {10.1016/j.jenvman.2025.126708},
pmid = {40714442},
issn = {1095-8630},
abstract = {Environmental transmission of antibiotic resistance poses a significant threat to human health by undermining the efficacy of therapeutic interventions against bacterial infections. Agricultural practices, particularly the application of organic fertilizers derived from animal manure, are major contributors to the spread of antibiotic resistance determinants (ARDs) in soil ecosystems. However, the fates of ARDs and their bacterial hosts in soil following organic fertilization as well as the impact of water management regimes remain poorly understood. We investigated the attenuation and persistence of ARDs in soil following organic fertilization under water management practices of upland, continuous flooding, and intermittent flooding. Most ARDs introduced via the organic fertilizer exhibited significant attenuation, with half-lives ranging from 19 to 50 days, primarily due to the decline of fertilizer-derived bacterial hosts. Specific ARDs, such as aph(3')-IIIa and tetO, persisted across all treatments. Upland conditions accelerated the attenuation of ARDs and their pathogenic hosts compared to flooding conditions, which prolonged their survival and promoted horizontal gene transfer. The divergent responses of ARD composition and soil bacterial communities to the environmental variables revealed a unique dissemination pattern, wherein the soil co-occurring bacterial communities served as critical hubs for the dissemination of ARDs and their bacterial hosts from organic fertilizers. The soil co-occurring bacterial communities exhibited strong interspecies interactions and high sensitivity to environmental changes. Targeted strategies to disrupt these assembly hubs may provide an effective way to mitigate the spread of antibiotic resistance from organic fertilizers to soil ecosystems.},
}

@article {pmid40714172,
year = {2025},
author = {Fan, Y and Du, M and Zhang, W and Deng, W and Yang, E and Wang, S and Yan, L and Zhang, L and Kang, S and Steenwyk, JL and An, Z and Liu, X and Xiang, M},
title = {The genomes of nematode-trapping fungi provide insights into the origin and diversification of fungal carnivorism.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108423},
doi = {10.1016/j.ympev.2025.108423},
pmid = {40714172},
issn = {1095-9513},
abstract = {Nematode-trapping fungi (NTF), most of which belong to a monophyletic lineage in Ascomycota, cannibalize nematodes and other microscopic animals, raising questions regarding the types and mechanisms of genomic changes that enabled carnivorism and adaptation to the carbon-rich and nitrogen-poor environment created by the Permian-Triassic extinction event. To address these questions, we conducted comparative genomic analyses of 21 NTF and 21 non-NTFs. Carnivorism-associated changes include expanded genes for nematode capture, infection, and consumption (e.g., adhesive proteins, CAP superfamily, eukaryotic aspartyl proteases, and serine-type peptidases). Although the link between secondary metabolite (SM) production and carnivorism remains unclear, we found that the number of SM gene clusters in NTF was significantly lower than that in non-NTF. Significantly expanded cellulose degradation gene families (GH5, GH7, AA9, and CBM1) and contracted genes for carbon-nitrogen hydrolases (enzymes that degrade organic nitrogen to ammonia) are likely associated with adaptation to carbon-rich and nitrogen-poor environments. Through horizontal gene transfer events from bacteria, NTF acquired the Mur gene cluster (participating in synthesizing peptidoglycan of the bacterial cell wall) and Hyl (a virulence factor in animals). Disruption of MurE reduced NTF's ability to attract nematodes, supporting its role in carnivorism. This study provides new insights into how NTF evolved and diversified, presumably after the Permian-Triassic mass extinction event.},
}

@article {pmid40712959,
year = {2025},
author = {Zhang, W and Guan, A and Qi, W and Mu, X and Hu, C and Qu, J},
title = {Cumulative Effects of Sulfamethoxazole and Its Metabolite on Nitrogen Reduction and Antibiotic Resistance in Constructed Wetlands: Microbial Mechanisms and Ecological Risks.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122426},
doi = {10.1016/j.envres.2025.122426},
pmid = {40712959},
issn = {1096-0953},
abstract = {Antibiotic residues in the tailwater of wastewater treatment plants (WWTPs) threaten nitrogen removal in constructed wetlands (CWs), yet the long-term impacts of fluctuating sulfamethoxazole (SMX) and its metabolite N-acetylsulfamethoxazole (N-SMX) remain unclear. Here, the dual effects of dynamic recovery in microbial nitrogen-removal functions and irreversible accumulation of antibiotic resistance genes (ARGs) under gradient SMX+N-SMX exposure (10-1000 μg·L[-1] with 30-day stepwise increments) in lab-scale CWs were systematically revealed. At ≤ 100 μg·L[-1], denitrification and anammox rates could recover to baseline levels, whereas 1 mg·L[-1] exposure triggered a short-term surge and then cumulative inhibition of nitrogen reduction (e.g., denitrification rates was 34.7% lower than the controls even after the SMX+N-SMX concentration reduction). Notably, sulfonamide resistance genes (sul1/sul2) increased steadily over 180 days despite the decline in SMX+N-SMX exposure (from 1 mg·L[-1] to 10 μg·L[-1] from day 120 to day 180), probably driven by horizontal gene transfer. Microbial analysis identified Burkholderia and Anaerolineales as dual-functional taxa linking nitrogen metabolism with ARGs propagation. Furthermore, sustained exposure suppressed the expression of denitrification genes (narG/nirK) of Methylotenera, despite its role in degrading SMX/N-SMX. These findings highlight a critical threshold: exposures < 100 μg·L[-1] allow the functional recovery of nitrogen reduction, but ≥ 1 mg·L[-1] induces irreversible ARGs enrichment and disrupts microbial nitrogen cycling. This study provides mechanistic insights into the ecological risks of antibiotic fluctuations, advocating stricter control of high-concentration SMX/N-SMX in WWTP tailwater to mitigate the dissemination of resistance genes.},
}

@article {pmid40712912,
year = {2025},
author = {Zhang, X and Ding, W and Yang, J and Gao, L and Wang, Q and Wang, J and Luo, Y and Yuan, X and Sun, B and Yang, J and Zhou, Y and Sun, L},
title = {Mechanisms of outer membrane vesicles in bacterial drug resistance: Insights and implications.},
journal = {Biochimie},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.biochi.2025.07.024},
pmid = {40712912},
issn = {1638-6183},
abstract = {The emergence of antibiotic resistance has rendered the treatment of bacterial infections exceedingly challenging, with diseases caused by resistant strains often resulting in significant morbidity and mortality. Consequently, it is crucial to investigate the mechanisms underlying antibiotic resistance. Outer membrane vesicles (OMVs) are nanoscale spheres characterized by a double membrane structure, released by Gram-negative bacteria (GNB). While the mechanisms governing OMV biogenesis remain under investigation, three models have been proposed. These vesicles have been implicated in enhancing bacterial survival during antibiotic treatment and contributing to the onset and development of drug resistance through various pathways. OMVs function as a secretion system, delivering cargo that mediates intercellular communication to neighboring cells, and their closed structure facilitates this molecular delivery. Vesicles released into the extracellular compartment can protect bacteria from antibiotic treatment by promoting horizontal gene transfer, inactivating or binding antibiotics, influencing biofilm formation, and mediating bacterial gene mutations, among other mechanisms. Many studies have demonstrated that OMVs play a critical role during antibiotic exposure. An in-depth understanding of the mechanisms of OMVs in the development of bacterial drug resistance could help develop more effective therapeutic strategies to prevent persistent bacterial infections. This review focuses on summarising the latest evidence on the involvement of OMVs in the development of drug resistance, to provide ideas for future studies.},
}

@article {pmid40712751,
year = {2025},
author = {Zhang, J and Wang, H and Ni, Y and Yan, Z and Chi, D and Li, K and Zhang, R},
title = {Comparative Epidemiology and Resistance Mechanisms of Carbapenem-, Tigecycline-, and Polymyxin-Resistant Enterobacteriaceae in Pediatric Diarrhea, 2017 and 2023.},
journal = {International journal of antimicrobial agents},
volume = {},
number = {},
pages = {107580},
doi = {10.1016/j.ijantimicag.2025.107580},
pmid = {40712751},
issn = {1872-7913},
abstract = {The increasing prevalence of antimicrobial resistance (AMR) infections in children is becoming a growing global concern. AMR poses a significant challenge in pediatric diarrhea, where multidrug-resistant Enterobacteriaceae threaten treatment efficacy. This study investigates the prevalence, resistance mechanisms, and genetic characteristics of carbapenem-, tigecycline-, and polymyxin-resistant Enterobacteriaceae isolated from pediatric diarrhea cases , in 2017 (n=1059) and 2023 (n=367). The prevalence of mcr-1-positive strains declined significantly from 2.36% (25/1059) in 2017 to 0.82% (3/367) in 2023, while tet(X4)-positive strains rose from 0% to 1.91% (7/367). Carbapenemase-producers remained rare (0.28% in 2017; 1.63% in 2023), with blaNDM as the dominant carbapenemase gene. Whole genome sequencing revealed diverse antimicrobial resistance genes (ARGs) and evolving plasmid types. Notably, by 2023 all mcr-1 were carried on IncI2 plasmids. Conjugation experiments confirmed plasmids carrying mcr-1, blaNDM-5, and tet(X4) are transferable to a recipient strain, highlighting the potential for horizontal gene transfer. Our findings demonstrate a significant shift in pediatric diarrhea-associated Enterobacteriaceae resistance profiles from 2017 to 2023. The decline in mcr-1 mirrors the impact of reduced polymyxin use, whereas the rise of tet(X4) signals a new challenge. These findings underscore the dynamic nature of AMR in pediatric Enterobacteriaceae and emphasize the need for stringent antimicrobial stewardship and surveillance. A One Health approach, integrating clinical, agricultural, and environmental efforts, is crucial to mitigating AMR spread and protecting pediatric health globally.},
}

@article {pmid40712095,
year = {2025},
author = {Sarre, LA and Gastellou Peralta, GA and Romero Charria, P and Ovchinnikov, V and de Mendoza, A},
title = {Repressive cytosine methylation is a marker of viral gene transfer across divergent eukaryotes.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf176},
pmid = {40712095},
issn = {1537-1719},
abstract = {Cytosine DNA methylation patterns vary widely across eukaryotes, with its ancestral roles being understood to have included both transposable element silencing and host gene regulation. To further explore these claims, in this study, we reevaluate the evolutionary origins of DNA methyltransferases and characterise the roles of cytosine methylation on underexplored lineages, including the amoebozoan Acanthamoeba castellanii, the glaucophyte Cyanophora paradoxa, and the heterolobosean Naegleria gruberi. Our analysis of DNA methyltransferase evolution reveals a rich ancestral eukaryotic repertoire, with several eukaryotic lineages likely subsequently acquiring enzymes through lateral gene transfer (LGT). In the three species examined, DNA methylation is enriched on young transposable elements and silenced genes, suggesting an ancestral repressive function, without the transcription-linked gene body methylation of plants and animals. Consistent with this link with silencing, methylated genomic regions co-localise with heterochromatin marks, including H3K9me3 and H3K27me3. Notably, the closest homologues of many of the silenced, methylated genes in diverse eukaryotes belong to viruses, including giant viruses. Given the widespread occurrence of this pattern across diverse eukaryotic groups, we propose that cytosine methylation was a silencing mechanism originally acquired from bacterial donors which was used to mitigate the expression of both transposable and viral elements, and that this function may persist in creating a permissive atmosphere for LGT in diverse eukaryotic lineages. These findings further highlight the importance of epigenetic information to annotate eukaryotic genomes, as it helps delimit potentially adaptive LGTs from silenced parasitic elements.},
}

@article {pmid40711446,
year = {2025},
author = {Ngoepe, MP and Schoeman, S and Roux, S},
title = {Challenges Associated With the Use of Metal and Metal Oxide Nanoparticles as Antimicrobial Agents: A Review of Resistance Mechanisms and Environmental Implications.},
journal = {Biotechnology journal},
volume = {20},
number = {7},
pages = {e70066},
pmid = {40711446},
issn = {1860-7314},
support = {//Department of Science and Innovation/ ; C2136/2021//Nelson Mandela University/ ; },
mesh = {*Metal Nanoparticles/chemistry/toxicity ; *Bacteria/drug effects ; *Drug Resistance, Bacterial/drug effects ; *Oxides/pharmacology/chemistry ; *Anti-Infective Agents/pharmacology ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Metals/pharmacology ; },
abstract = {The use of metal and metal oxide nanoparticles has been suggested as a means of combating antibiotic-resistant bacteria (ARB). This is due to the ability of nanoparticles to target numerous sites inside the bacterial cell. Microbes can, however, develop a resistance to hazardous environments. Soil microorganisms have evolved resistance to specific metals in soil by employing alternative survival strategies, like those adopted against antibiotics. Because of this survival mechanism, bacteria have been able to develop defense mechanisms to deal with metallic nanoparticles. Resistance has evolved in human pathogens to therapies that use metallic nanoparticles, such as silver nanoparticles. Metallic nanoparticles and antibiotics have currently been proven to be ineffective against several infections. Due to these concerns, scientists are investigating whether nanoparticles might cause environmental harm and potentially breed microbes that are resistant to both inorganic and organic nanoparticles. The increased use of inorganic nanoparticles has thus been shown to result in contaminations in wastewater, facilitating horizontal gene transfer among bacterial populations. The resistance mechanism of metallic nanoparticles, role in antibiotic resistance, and a potential solution to the environment's toxicity from nanoparticles are all discussed in this review.},
}

*Metal Nanoparticles/chemistry/toxicity
*Bacteria/drug effects
*Drug Resistance, Bacterial/drug effects
*Oxides/pharmacology/chemistry
*Anti-Infective Agents/pharmacology
Humans
*Anti-Bacterial Agents/pharmacology
*Metals/pharmacology

@article {pmid40708915,
year = {2025},
author = {Li, M and Zhan, A and Rahman, TT and Jiang, T and Hou, L},
title = {From wastewater to resistance: characterization of multidrug-resistant bacteria and assessment of natural antimicrobial compounds.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1612534},
pmid = {40708915},
issn = {1664-302X},
abstract = {The development and spread of antibiotic resistance in wastewater pose significant threats to both the environment and public health. Bacteria harboring multiple antibiotic resistance genes (ARGs), including those associated with horizontal gene transfer (HGT), can serve as persistent reservoirs and vectors for antimicrobial resistance in natural ecosystems. In this study, nine antibiotic-resistant bacterial strains (U1-U9) were isolated from a wastewater treatment plant (WWTP) effluent. The isolates were identified using 16S rRNA gene sequencing and whole-genome sequencing (WGS), and their antibiotic susceptibility profiles were evaluated. All isolates exhibited resistance to multiple antibiotics, and WGS revealed that U1, U2, U4, and U7 harbored diverse ARGs, including β-lactamase genes, efflux pumps, and resistance determinants for sulfonamides, tetracyclines, and, quinolones, confirming the presence of multidrug-resistant bacteria in WWTP effluent. Phylogenetic analysis classified them into Microbacterium spp. (Actinobacteria), Chryseobacterium spp. (Bacteroidetes), Lactococcus lactis spp. (Firmicutes), and Psychrobacter spp. (Proteobacteria). To explore mitigation strategies, eleven natural compounds were screened for their effects on cell growth, biofilm formation, and motility in selected multi-drug-resistant bacteria. Among the tested compounds, curcumin and emodin showed the most consistent inhibitory activity, particularly against Microbacterium spp. strains U1 and U2, and Lactococcus lactis sp. U4. In contrast, Chryseobacterium sp. U7, a Gram-negative strain, exhibited strong resistance to all tested natural compounds, highlighting the challenge of controlling Gram-negative ARBs in wastewater settings. These findings underscore the environmental risks posed by multidrug-resistant and HGT-associated ARG-harboring bacteria in WWTP effluent. They also demonstrate the potential of natural products, such as curcumin and emodin, as alternative or complementary agents for mitigating antibiotic resistance in water systems.},
}

@article {pmid40707455,
year = {2025},
author = {Sato, Y and Bex, R and van den Berg, GCM and Santhanam, P and Höfte, M and Seidl, MF and Thomma, BPHJ},
title = {Starship giant transposons dominate plastic genomic regions in a fungal plant pathogen and drive virulence evolution.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6806},
pmid = {40707455},
issn = {2041-1723},
mesh = {*DNA Transposable Elements/genetics ; *Genome, Fungal/genetics ; Phylogeny ; Virulence/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Ascomycota/genetics/pathogenicity ; *Plant Diseases/microbiology ; Verticillium ; },
abstract = {Starships form a recently discovered superfamily of giant transposons in Pezizomycotina fungi, implicated in mediating horizontal transfer of diverse cargo genes between fungal genomes. Their elusive nature has long obscured their significance, and their impact on genome evolution remains poorly understood. Here, we reveal a surprising abundance and diversity of Starships in the phytopathogenic fungus Verticillium dahliae. Remarkably, Starships dominate the plastic genomic compartments involved in host colonization, carry multiple virulence-associated genes, and exhibit genetic and epigenetic characteristics associated with adaptive genome evolution. Phylogenetic analyses suggest extensive horizontal transfer of Starships between Verticillium species and, strikingly, from distantly related Fusarium fungi. Finally, homology searches and phylogenetic analyses suggest that a Starship contributed to de novo virulence gene formation. Our findings illuminate the profound influence of Starship dynamics on fungal genome evolution and the development of virulence.},
}

*DNA Transposable Elements/genetics
*Genome, Fungal/genetics
Phylogeny
Virulence/genetics
*Evolution, Molecular
Gene Transfer, Horizontal
*Ascomycota/genetics/pathogenicity
*Plant Diseases/microbiology
Verticillium

@article {pmid40706788,
year = {2025},
author = {Ayaz, M and Oon, YS and Oon, YL and Khan, K and Deng, M and Li, L and Song, K and Jiang, X and Xia, Z},
title = {Microplastics transport and impact on nitrogen cycling and N2O emissions in estuaries.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126869},
doi = {10.1016/j.envpol.2025.126869},
pmid = {40706788},
issn = {1873-6424},
abstract = {Microplastic pollution in estuarine ecosystems disrupts nitrogen cycling and enhances nitrous oxide (N2O) emissions, reinforcing the role of estuaries as greenhouse gas (GHG) hotspots. This review integrates mechanisms that modulate microplastic-induced disruptions to nitrogen cycling processes and transform estuarine biogeochemistry. It elucidates key mechanistic pathways whereby microplastic dynamics influence microbial nitrogen transformations and alter GHG fluxes. Microplastics affect nitrogen cycling through multiple mechanisms, including adsorption of nitrogenous compounds, restructuring of microbial communities, and modulation of enzymatic processes that control nitrogen transformations. Within plastisphere biofilms, microplastics foster microbial interactions that promote incomplete denitrification and nitrifier-driven N2O production, intensifying N2O fluxes from estuarine sediments and waters. The review synthesizes recent findings on microplastic degradation, genetic drift, and horizontal gene transfer, which may further reshape nitrogen cycling capacity over time. Recent advancements in microplastic characterization, including aptamer-based sensors, flow cytometry, and improved extraction methods, enhance the ability to quantify and trace microplastic impacts in estuarine environments. This review proposes an integrative conceptual model for microplastic-mediated amplification of N2O emissions in estuaries and identifies critical research and policy directions. Addressing microplastic-induced disruptions of nitrogen cycling and GHG dynamics will require integrated mitigation strategies, targeted regulatory interventions, and interdisciplinary research to support sustainable estuarine management.},
}

@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