Maria Juanpere-Borras, Jos Boekhorst, Peter van Baarlen, Sylvia Brugman, Adrià López Nadal
{"title":"A scalable and cost-effective nanopore workflow for 16S rRNA microbiome profiling validated in a zebrafish gut model.","authors":"Maria Juanpere-Borras, Jos Boekhorst, Peter van Baarlen, Sylvia Brugman, Adrià López Nadal","doi":"10.1099/mgen.0.001828","DOIUrl":"10.1099/mgen.0.001828","url":null,"abstract":"<p><p>Advancements in long-read sequencing technologies, such as those developed by Oxford Nanopore Technologies (ONT), have opened new possibilities for 16S rRNA gene profiling of microbial communities by enabling full-length sequencing. In this study, we optimized and validated a cost-effective, in-house ONT workflow for zebrafish gut microbiome analysis and compared its performance to the gold-standard Illumina NovaSeq platform. Using a PCR-based barcoding strategy, we successfully sequenced both the V3-V4 and V1-V9 regions of the 16S rRNA gene, achieving high read accuracy and balanced demultiplexing across samples. Our results demonstrate that ONT short-read (V3-V4) sequencing using the latest V14 chemistry and Dorado basecaller achieves resolution comparable to that of Illumina, supporting amplicon sequence variant classification. Rarefaction analysis confirmed that the sequencing depth (~240,000 reads/sample) was sufficient to capture microbial diversity in the zebrafish gut, a complex and taxonomically rich environment. Furthermore, taxonomic classifications and diversity metrics were consistent between platforms, supporting the reliability of ONT for microbiota profiling. While full-length (V1-V9) ONT sequencing yielded higher taxonomic richness through operational taxonomic units, it did not significantly improve species-level resolution, likely due to current database and bioinformatics limitations. Our custom library preparation protocol simplified multiplexing, reduced costs and improved scalability without compromising accuracy. Although 15 samples were conservatively multiplexed per flow cell in this study, the workflow has since been applied to larger-scale datasets with up to 75 samples per run and to additional amplicon targets, demonstrating its portability and adaptability across diverse biological contexts. These findings position ONT as a viable, scalable and field-deployable alternative to Illumina for microbiome research.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13623021/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149075175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Redundancy maintains microbial ecosystem functional potential despite taxonomic shifts between serpentine and nonserpentine soils.","authors":"Alexandria N Igwe, Michelle E Afkhami","doi":"10.1099/mgen.0.001835","DOIUrl":"10.1099/mgen.0.001835","url":null,"abstract":"<p><p>Environmental filtering and buffering are complementary processes responsible for stabilizing ecosystem services across landscapes. The extent to which either of these processes structures microbial composition and functions in extreme soil systems can be highly context-dependent, requiring site-specific examination to elucidate general principles of community function under stress. Serpentine soils have high amounts of heavy metals and magnesium and low levels of plant nutrients and exist in close proximity to nutrient-rich and plant-productive nonserpentine soils, making them an ideal system for evaluating selection and redundancy under stress. Combining biogeographical field surveys and shotgun metagenomic sequencing of microbiomes from 23 pairs of serpentine and nonserpentine soils across California, we investigated selection and functional redundancy between disparate soil types. We hypothesized that the strong selective pressure present in serpentine soils would result in distinct bacterial and functional profiles. Bacterial and fungal community taxonomic compositions were indeed distinct between serpentine and nonserpentine soils, while archaeal communities were similar between soil types. In contrast, functional repertoires of all microbial community groups were largely similar between soil types, with many of the same taxa carrying out functions across soil types. Still specialized functions in serpentine soils represented adaptations to stress in contrast to the carbon-rich environment of nonserpentine soils. For example, specialized functions - such as siderophore biosynthesis proteins, which are involved in the biosynthesis of iron-chelating compounds - were distinctive features of serpentine soils and specialized functions notably had similar functional redundancy but distinct taxa carrying out the functions across soil types. These results highlight taxa that perform the functions that have been selected for survival in an extreme soil ecosystem and the functions that are most at risk in the face of environmental disturbances.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13597068/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149025266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"CelluBase: a comprehensive genomic platform for advancing cellulose-producing bacteria.","authors":"Bashir A Akhoon, Lakshay Anand, Kendall R Corbin","doi":"10.1099/mgen.0.001825","DOIUrl":"10.1099/mgen.0.001825","url":null,"abstract":"<p><p>Bacterial cellulose (BC)-producing taxa constitute a functionally coherent yet phylogenetically heterogeneous assemblage of acetic acid bacteria distributed across evolutionary lineages within Alphaproteobacteria. Despite the importance of BC as a biomaterial in diverse biotechnological applications, a dedicated resource for the study and comparative analysis of cellulose-producing bacteria is currently lacking. To address this gap, we developed CelluBase - an integrated, user-friendly database for the study of bacteria from the genera <i>Komagataeibacter</i> and <i>Novacetimonas</i>. CelluBase is a domain-specific database dedicated to the genetic and functional dissection of BC synthesis. It integrates high-quality genome assemblies, functional annotations, operonic architectural analyses, multi-omics datasets and comparative genomics analyses for investigating the molecular mechanisms governing BC biosynthesis. Key features of the database include characterization of cellulose synthase gene organization, regulatory network architecture, metabolic pathway diversification and phylogenomic relationships across cellulose-producing lineages. Results generated within the CelluBase framework are available as text, interactive plots, and publication-ready figures. CelluBase (https://cellubase.shinyapps.io/cellubase/) is the first publicly accessible repository for BC genomics. CelluBase is designed to support comparative studies of cellulose-producing strains, in addition to providing the framework for future studies related to strain enhancement, cellulose yield improvement, and targeted metabolic engineering.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13584967/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148977222","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
C F C Zamunér, R Ragupathy, M S Terceti, R Zallot, J Redfern, J B Jones, F Behlau, H Ferreira, M C Enright
{"title":"Characterization of putatively lytic bacteriophages able to infect <i>Xanthomonas citri</i> subsp. <i>citri</i> and identification of novel putative exopolysaccharide depolymerases.","authors":"C F C Zamunér, R Ragupathy, M S Terceti, R Zallot, J Redfern, J B Jones, F Behlau, H Ferreira, M C Enright","doi":"10.1099/mgen.0.001821","DOIUrl":"https://doi.org/10.1099/mgen.0.001821","url":null,"abstract":"<p><p>Asiatic citrus canker (ACC), caused by the Gram-negative bacterium <i>Xanthomonas citri</i> subsp. <i>citri</i> (<i>X. citri</i>), leads to substantial economic losses in the global citrus industry, necessitating sustainable alternatives to conventional copper-based bactericides. In this study, we isolated and sequenced 72 putatively lytic bacteriophages (including 65 previously uncharacterized isolates from São Paulo, Brazil) and characterized their host range, stability and biocontrol potential. Genomic analysis revealed highly successful but low-diversity phage genomic signatures; 70 isolates shared ~95% DNA similarity and were closely related to the Japanese phage CP2, mirroring the clonal nature of the endemic <i>X. citri</i> population. These phages primarily belong to the <i>Autographiviridae</i> family, with the exception of the <i>Schitoviridae</i> isolate XacP77. Using HHsearch and AlphaFold structural modelling, we identified conserved tail-fibre genes predicted to encode putative exopolysaccharide depolymerases with structural homology to carbohydrate-binding modules (CBMs), which may facilitate the degradation of the bacterial xanthan gum capsule during infection. While the phages exhibited robust stability across a wide pH range (4-11) and temperatures up to 55 °C, they were highly sensitive to UV exposure, reaching total inactivation after 160 s. Greenhouse assays demonstrated that treatment with phage P27 reduced ACC lesion production by 60%, pointing to the potential of these viruses and their candidate CBM-containing proteins as components of a sustainable biocontrol development within integrated pest management strategies for <i>X. citri</i>.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148977185","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Karolina Mercoulia, Jake Lacey, George Taiaroa, Sally Dougall, Francesca Azzato, Stuart Adcock, Maryza Graham, Evelyn Wong, Norelle Sherry, Timothy P Stinear, Benjamin P Howden, Andrew H Buultjens, Torsten Seemann
{"title":"Pathogen genome enrichment sequencing to support a city-wide Legionnaires' disease outbreak investigation.","authors":"Karolina Mercoulia, Jake Lacey, George Taiaroa, Sally Dougall, Francesca Azzato, Stuart Adcock, Maryza Graham, Evelyn Wong, Norelle Sherry, Timothy P Stinear, Benjamin P Howden, Andrew H Buultjens, Torsten Seemann","doi":"10.1099/mgen.0.001836","DOIUrl":"10.1099/mgen.0.001836","url":null,"abstract":"<p><p>Pathogen genomics can provide high-confidence source attribution for epidemiological investigations of Legionnaires' disease (LD) outbreaks. However, the utility of culture-based genomics can be undermined by long lead times for <i>Legionella pneumophila</i> culture or a lack of isolates when dealing with non-culturable bacteria or low-biomass specimens. Here, during a large 2024 LD outbreak in Melbourne, Australia, we compared direct specimen, hybridization-based enrichment sequencing with traditional culture-based whole-genome sequencing of 18 clinical and 5 environmental <i>L. pneumophila</i> specimens. Informed by the <i>L. pneumophila</i> global population structure, the method used 28,061 RNA bait hybridization probes to enrich >170,000 known genome-wide informative SNP sites directly from clinical and environmental specimens. Genome enrichment sequencing detected <i>L. pneumophila</i> with high sensitivity, achieving genome-wide coverage at 100 c.f.u. ml<sup>-1</sup>. Using sequence enrichment data with phylogenomic and machine learning approaches, we identified that a single cooling tower was likely responsible for the outbreak. Genome enrichment sequencing has the potential to enable faster and more comprehensive source tracking, thereby enhancing public health responses to outbreaks of environmental pathogens, permitting earlier, more confident interventions.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13618814/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149069838","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Applications of transposon-insertion sequencing for understanding bacterial physiology.","authors":"Emily C A Goodall, Stineke van Houte","doi":"10.1099/mgen.0.001796","DOIUrl":"10.1099/mgen.0.001796","url":null,"abstract":"<p><p>Transposon-insertion sequencing (Tn-seq) couples transposon mutagenesis with next-generation sequencing to identify the transposon insertion site for thousands of mutants in parallel. It is a powerful technology with a myriad of uses beyond the identification of essential genes required for a cell to grow and divide. Tn-seq is particularly useful as a high-throughput method to assign function to function-unknown genes, which have increased steadily with the abundance of newly sequenced bacterial genomes. Tn-seq has now been adapted for use in over 100 bacterial species. Here, we summarize the applications of Tn-seq for querying bacterial physiology and discuss some of the possible applications for the future.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13541208/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148887922","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Transcriptomic shift in ethanol and amino acid metabolic genes regulated by Med15 during alcoholic fermentation.","authors":"David G Cooper, Emma Grunkemeyer, Jan S Fassler","doi":"10.1099/mgen.0.001811","DOIUrl":"10.1099/mgen.0.001811","url":null,"abstract":"<p><p>Organisms that thrive in extreme environments provide natural experiments in evolution, revealing the genetic regulators that orchestrate complex phenotypic change. Wine yeast (WY) are specialized strains that are adapted to survive in the wine making environment while producing high concentrations of ethanol. In addition to large genomic changes that differentiate WY from yeast used in other industries, SNP and polyglutamine tract polymorphism in the transcriptional regulator Med15 are associated with the fermentation efficiency and stress response phenotypes of WY. In this study, we investigated the transcriptional differences during wine fermentation in transgenic lab strain yeast having integrated WY <i>MED15</i> alleles. Compared to the unmodified lab strain (<i>MED15</i> <sub>LAB</sub>), the same strain in which the <i>MED15</i> locus was replaced with a <i>MED15</i> allele from yeast isolated from palm wine, the fermented sap of palm (oil, date, coconut) trees (<i>MED15</i> <sub>WY23</sub>), exhibited enhanced expression of amino acid biosynthesis genes as well as stress resistance and metabolic adaptation genes. Our experimental data confirm the role of arginine in efficient fermentation and suggest that certain <i>MED15</i> alleles alter the expression patterns of arginine pathway genes in some cases improving carbon flux under nitrogen stress. The global benefits conferred by natural polymorphisms in a single transcriptional regulator highlight Med15 as a target for engineering of strains devoted to various types of alcohol production.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13541290/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148887949","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Samantha K Lindberg, Ana Beatriz Garcez Buiatte, Odion O Ikhimiukor, Leticia Roberta Martins Costa, Samantha E Wirth, Kimberlee A Musser, Lisa A Mingle, Cheryl P Andam
{"title":"Presence of globally prominent multidrug-resistant genotypes of <i>Salmonella enterica</i> serovar Typhi in New York State, 2016-2023.","authors":"Samantha K Lindberg, Ana Beatriz Garcez Buiatte, Odion O Ikhimiukor, Leticia Roberta Martins Costa, Samantha E Wirth, Kimberlee A Musser, Lisa A Mingle, Cheryl P Andam","doi":"10.1099/mgen.0.001816","DOIUrl":"10.1099/mgen.0.001816","url":null,"abstract":"<p><p>The human-restricted enteric pathogen <i>Salmonella enterica</i> serovar Typhi (<i>S</i>. Typhi) is the causative agent of the life-threatening typhoid fever. Although <i>S</i>. Typhi incidence is relatively low in the USA, routine surveillance of <i>S</i>. Typhi is critical to track the emergence and spread of high-risk lineages in non-endemic areas. In this study, we analysed 151 genomes of <i>S</i>. Typhi isolates from patients who were clinically confirmed with typhoid fever across New York State between 2016 and 2023. We used the GenoTyphi classification scheme and identified established multidrug-resistant and extensively drug-resistant lineages. We detected the presence of the globally widespread genotype 4.3.1 (haplotype 58) and its derivative 4.3.1.1.P1, which recently emerged in Pakistan, as well as the Bangladesh-restricted lineages 3.3.2.Bd1 and 3.3.2.Bd2 in our dataset. Ten mutations and 14 acquired genes associated with antimicrobial resistance (AMR) were present across the entire population, with 86.8% of the genomes possessing at least one of these AMR determinants. The <i>gyrA</i> S83F mutation conferring quinolone and triclosan resistance was the most frequently detected (94 genomes). Combinations of <i>dfrA7+catA1</i> (resistance to trimethoprim and chloramphenicol, respectively) and <i>sul2+aph(3″)-Ib+aph(6)-Id</i> (resistance to sulphonamide and aminoglycosides, respectively) co-occurred frequently and were associated with IncQ and IncY plasmid replicons. Phylogenetic contextualization against a global dataset of 1,643 genomes from 20 countries across five continents, including other parts of the USA, from the same time period showed geographic intermingling, suggesting the spread of high-risk genotypes of international origins to New York State. Altogether, these findings reveal the presence of globally dominant resistant genotypes that are likely facilitated by human travel in New York State, where typhoid fever is not endemic. Long-term genomic surveillance is critical to AMR profiling, identifying genotypic shifts in regional <i>S</i>. Typhi populations, monitoring transmission routes and guiding effective public health interventions.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13537747/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148880989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lama Koumaty, Stéphanie Dan, Allan De Clercq, Grégory Destras, Hadrien Regue, Antoine Oblette, Adrien Le Meur, Alexandre Gaymard, Vanessa Escuret, Maude Bouscambert-Duchamp, Emmanuel Chanard, Margaux Fabre, Vincent Vieillefond, Benoit Visseaux, Antonin Bal, Laurence Josset
{"title":"Emergence of a genetically distinct cluster of influenza A(H3N2) viruses within subclade J.2.2 associated with hospitalization during the 2024-2025 season in Auvergne-Rhône-Alpes, France.","authors":"Lama Koumaty, Stéphanie Dan, Allan De Clercq, Grégory Destras, Hadrien Regue, Antoine Oblette, Adrien Le Meur, Alexandre Gaymard, Vanessa Escuret, Maude Bouscambert-Duchamp, Emmanuel Chanard, Margaux Fabre, Vincent Vieillefond, Benoit Visseaux, Antonin Bal, Laurence Josset","doi":"10.1099/mgen.0.001810","DOIUrl":"10.1099/mgen.0.001810","url":null,"abstract":"<p><p>During the 2024-2025 influenza season in Auvergne-Rhône-Alpes, France, a genetically distinct cluster of A(H3N2) viruses within subclade J.2.2 was found to be significantly overrepresented in hospitalized patients compared with community patients. Circulating mainly in November and December 2024, this genetically distinct cluster harboured HA1:G62R and S145N mutations, both linked to immune escape, as well as P239Q, located near key antigenic sites and warranting further investigation. The findings highlight the importance of monitoring influenza genome diversity in both hospital and community settings to identify emerging genetically distinct clusters with potential for increased severity.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13597097/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149025182","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Anna K Pöntinen, Nguyen Vinh Trung, Sudaraka Mallawaarachchi, Rebecca A Gladstone, Juri Kuronen, Ørjan Samuelsen, Huynh Xuan Yen, Phung Le Kim Yen, Nguyen Phu Huong Lan, Nguyen Thanh Dung, Nguyen Van Vinh Chau, Julian Parkhill, Gerry Tonkin-Hill, Ngo Thi Hoa, Jukka Corander
{"title":"Mapping the evolutionary path towards multi-drug resistance in the pandemic <i>Escherichia coli</i> ST131 lineage.","authors":"Anna K Pöntinen, Nguyen Vinh Trung, Sudaraka Mallawaarachchi, Rebecca A Gladstone, Juri Kuronen, Ørjan Samuelsen, Huynh Xuan Yen, Phung Le Kim Yen, Nguyen Phu Huong Lan, Nguyen Thanh Dung, Nguyen Van Vinh Chau, Julian Parkhill, Gerry Tonkin-Hill, Ngo Thi Hoa, Jukka Corander","doi":"10.1099/mgen.0.001795","DOIUrl":"10.1099/mgen.0.001795","url":null,"abstract":"<p><p><i>Escherichia coli</i> sequence type (ST) 131 is the most widely studied genetic lineage of the species to date, originally identified in the early 2000s as an increasingly common cause of human urinary tract and bloodstream infections worldwide. This lineage is subdivided into four extant main subclades A, B, C1 and C2 that exhibit distinct features in terms of invasiveness, antibiotic resistance and transmissibility. However, the evolutionary pathway from the generally susceptible ST131-B to the drug-resistant ST131-C clades remains poorly mapped. To fill this knowledge gap, we analysed in detail human clinical isolates obtained in Vietnam, designated as belonging to the generally neglected minor clade ST131-B0. We sequenced them using both short- and long-read technology and combined these data with a recently published high-resolution genomic collection to provide further insight into the evolutionary process and its timeline. Extensive genomic analyses established ST131-B0 as an intermediary progenitor in the evolutionary path leading from ST131-B to the ST131-C clades, associated with multiple type I pili switches, as well as the loss and gain of specific chromosomal genes representing diverse core functions such as metabolism, transcription, DNA binding and type II toxin-antitoxin systems. Furthermore, all Vietnamese isolates of ST131-B0 unprecedentedly harboured <i>bla</i> <sub>CTX-M</sub> genes encoding extended-spectrum β-lactamases, a trait dominant in ST131-C clades and not previously observed in ST131-B0. Our study supports the hypothesis that the ST131-C clades have gradually evolved from ST131-B by reducing the host range with better adaptation to colonizing humans under selective conditions.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13600687/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149030799","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}