Microbial Genomics最新文献

{"title":"Molecular characterization and prevalence of plasmids co-harbouring <i>mcr</i> and ESBL genes.","authors":"K M G Houkes, V Weterings, J J Verweij, J L Murk, W van den Bijllaardt, J J J M Stohr","doi":"10.1099/mgen.0.001458","DOIUrl":"10.1099/mgen.0.001458","url":null,"abstract":"<p><p>Multidrug-resistant Enterobacterales isolates carrying extended-spectrum beta-lactamases (ESBLs) and mobile colistin resistance (<i>mcr</i>) genes pose a significant healthcare threat as they can lead to difficult-to-treat infections. This study investigates the prevalence of isolates co-harbouring ESBL and <i>mcr</i> genes and characterizes the plasmids co-harbouring those genes. ESBL-producing Enterobacterales (ESBL-E) isolates identified during point prevalence surveys (PPS) in a Dutch hospital were screened for <i>mcr</i> genes. Plasmids co-harbouring <i>mcr</i> and ESBL genes were identified using long- and short-read sequencing data, while detecting resistance and replicon genes using AMRFinderPlus and PlasmidFinder. The plasmid database PLSDB was searched for plasmids containing the same <i>mcr</i> and ESBL gene(s), and SNP and DCJ-Indel distance analyses were conducted to examine plasmid diversity. The most recent common ancestor (MRCA) was inferred through timed phylogeny analyses in BEAST, and putative composite transposons containing the <i>mcr</i> or ESBL genes were identified. Among 188 screened ESBL-E, 11 harboured <i>mcr</i> genes: 9 with <i>mcr-9</i> and 2 with <i>mcr-9</i> and <i>mcr-4.3</i>. All plasmids containing <i>mcr</i> and ESBL genes were IncHI plasmids harbouring <i>mcr-9</i>, <i>bla</i> _CTX-M-9 and/or <i>bla</i> _SHV-12. The plasmid database search resulted in 128 similar plasmids. SNP analysis showed ≤10 SNPs among the PPS study plasmids and up to 924 SNPs among all plasmids. Structural relatedness and phylogenetic analyses revealed clustering of the PPS study plasmids but no additional taxonomical or geographical clustering. The MRCA of the PPS study plasmids likely emerged between 1986 and 2008. Finally, composite transposon analysis indicated that matching complete insertion sequences rarely flanked <i>mcr-9</i> genes, whereas <i>bla</i> _CTX-M-9 and <i>bla</i> _SHV-12 frequently were. The prevalence of <i>mcr</i> genes among ESBL-E in this study is 5.9%, with <i>mcr-9</i> being the most prevalent. Limited plasmid diversity suggests a single introduction event followed by regional and global dissemination across related bacterial species. Persistent ESBL gene mobility suggests a more recent introduction of these genes compared to the <i>mcr-9</i> genes.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 7","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12306943/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144732108","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":"Multinuclear non-haem iron-dependent oxidative enzymes: landscape of their substrates, partner proteins and biosynthetic gene clusters.","authors":"R Antoine, L Leprevost, S Jünger, S Zirah, G Lippens, Y Li, S Dubiley, F Jacob-Dubuisson","doi":"10.1099/mgen.0.001462","DOIUrl":"https://doi.org/10.1099/mgen.0.001462","url":null,"abstract":"<p><p>Proteins of the multinuclear non-haem iron-dependent oxidative (MNIO) enzyme superfamily catalyse various modification reactions on the precursors of ribosomally synthesized post-translationally modified peptides (RiPPs). We recently identified two large families of MNIO-modified RiPPs called bufferins, which enhance bacterial growth under copper stress by chelating the excess metal ions. Here, we explored the diversity of potential MNIO substrates by performing extensive <i>in silico</i> studies. Analyses of MNIO-coding biosynthetic gene clusters (BGCs) identified various groups of putative precursors, most of which are characterized by specific Cys-containing motifs, throughout the eubacterial phylogenetic tree. The precursors of most MNIO-modified RiPPs harbour N-terminal Sec-dependent signal peptides, a rare feature among bacterial RiPPs. Some precursors are very long relative to those of typical RiPPs, indicating that MNIO enzymes could modify both peptide and protein substrates. We also identified a distinct family of integral membrane proteins with large predicted extra-cytoplasmic domains mostly found in <i>Actinomycetota</i>, frequently but not systematically associated with MNIOs. Most MNIO BGCs harbour genes coding for DUF2063 domain-containing proteins or structurally related proteins, serving as partners of the enzymes for precursor modification. We uncovered a correlation between the presence or the absence of Sec signal peptides in the precursors and the types of partner proteins of the MNIO enzymes. This study depicts the global landscape of potential MNIO-dependent natural products by unveiling groups of peptides and proteins genetically associated with MNIOs. It reveals a treasure trove of potential new RiPP precursors which likely represent a widespread bacterial strategy to deal with copper stress, and most likely other stresses, in natural environments.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 7","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144760508","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}

{"title":"Evolutionary dynamics in the genome of ocular <i>Chlamydia trachomatis</i> strains from Northern Tanzania following mass drug administration.","authors":"Ehsan Ghasemian, Athumani Ramadhani, Anna Harte, Elias Mafuru, Tamsyn Derrick, Tara Mtuy, Patrick Massae, Aiweda Malissa, Judith Breuer, Harry Pickering, Robin L Bailey, David Mabey, Matthew J Burton, Martin J Holland","doi":"10.1099/mgen.0.001431","DOIUrl":"10.1099/mgen.0.001431","url":null,"abstract":"<p><p>Trachoma, caused by <i>Chlamydia trachomatis</i> (Ct), remains a leading cause of preventable infection-induced blindness worldwide. We conducted a 4-year longitudinal study in three trachoma-endemic villages in Northern Tanzania, tracking infection dynamics and factors influencing trachomatous scarring progression and persistence pre- and post-mass drug administration (MDA) interventions. We analysed 118 whole genomes of Ct originating from ocular swabs of children. Sample collection was conducted at 3-month intervals over 4 years, encompassing 15 timepoints. We studied Ct phylogeny and patterns of SNP accumulation within sequences in the Ct genotype A (CtA) and Ct genotype B (CtB) phylogenetic clades, with the association of clinical signs of trachoma and scarring progression. Of the samples analysed, 71 (60.2%) were identified as CtA and 47 (39.8%) as CtB. We observed a significant shift in genotype prevalence: CtB predominated in pre-MDA samples (36 out of 40, 90%), whilst CtA became the dominant genotype after the first MDA round (67 out of 78, 85.9%) (<i>P</i><0.0001). Phylogenetic analysis revealed two distinct CtA clades: clade 1 (29 sequences) was primarily found pre-MDA and shared a common ancestor with Tanzanian CtA reference genomes, whilst clade 2 (42 sequences) emerged post-MDA and exhibited a characteristic ~6 kbp reduction in the plasticity zone (PZ). Similarly, CtB sequences formed two distinct clades, both sharing ancestry with a Tanzanian CtB reference genome. Notably, we identified variable genome reduction in the PZ (~4 and ~10 kbp) amongst 13 CtB sequences distributed across both clades. We documented a significant shift in Ct genotype distribution following the first round of MDA, characterized by the emergence of CtA strains with distinct genetic profiles compared to pre-MDA strains. The observed reductions in Ct genome size suggest ongoing evolutionary processes shaping these bacterial populations. Additional research is needed to understand the dynamic changes in Ct lineage composition before and after antibiotic interventions and to determine how variations in genome size influence Ct biology and its susceptibility to azithromycin treatment.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 7","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12222737/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144553964","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":"Genomic features of three major diarrhoeagenic <i>Escherichia coli</i> pathotypes in India.","authors":"Yuki Hoshiko, Goutam Chowdhury, Kei Kitahara, Debjani Ghosh, Debora Satie Nagano, Ayumu Ohno, Shin-Ichi Miyoshi, Miki Okuno, Takeshi Yamamoto, Shanta Dutta, Asish K Mukhopadhyay, Yoshitoshi Ogura","doi":"10.1099/mgen.0.001430","DOIUrl":"10.1099/mgen.0.001430","url":null,"abstract":"<p><p><b>Background.</b> Diarrhoea remains a major threat to children in developing nations, with diarrhoeagenic <i>Escherichia coli</i> (DEC) being the primary causative agent. Characterizing prevalent DEC strains is crucial, yet comprehensive genomic analyses of major DEC strains, including enteropathogenic <i>E. coli</i> (EPEC), enteroaggregative <i>E. coli</i> (EAEC) and enterotoxigenic <i>E. coli</i> (ETEC), are lacking in India.<b>Methods.</b> We sequenced 24 EAEC and 23 EPEC strains from Indian patients with diarrhoea and conducted an extensive database search for DEC human isolates from India. Detailed phylogenetic analyses, virulence gene subtyping and examinations of accessory virulence and antimicrobial resistance (AMR) genes were performed.<b>Results.</b> The analysed DEC strains included 32 EAEC, 25 EPEC, 32 ETEC and 1 each of the EPEC/ETEC-hybrid and ETEC/EAEC-hybrid pathotypes. These strains were predominantly classified into phylogroups A (35.2%) and B1 (41.8%) and dispersed within these phylogroups without pathotype-specific clustering. One ETEC strain was classified into cryptic clade 1. Subtypes of hallmark virulence genes varied substantially amongst strains in each pathotype, and 31 accessory virulence genes were detected either specifically within certain pathotypes or across multiple pathotypes at varying frequencies, indicating diversification of the virulence gene repertoire within each pathotype. Acquired AMR genes were found in 73.6% of the strains, with frequent identification of AMR genes for aminoglycosides (40.0%), <i>β</i>-lactams (64.8%), sulphonamides (49.5%) and trimethoprim (42.9%). Known quinolone-resistant mutations were found in 74.7% of the strains, whereas AMR genes for macrolide (30.8%), phenicol (11.0%) and tetracycline (27.4%) were less frequent.<b>Conclusions.</b> The diverse virulence potential and trends in AMR gene prevalence amongst major DEC strains in India are highlighted in this study. Continuous monitoring of DEC strain characteristics is essential for the effective control and treatment of DEC infections in India.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 7","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12282231/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144575790","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":"skDER and CiDDER: two scalable approaches for microbial genome dereplication.","authors":"Rauf Salamzade, Aamuktha Kottapalli, Lindsay R Kalan","doi":"10.1099/mgen.0.001438","DOIUrl":"10.1099/mgen.0.001438","url":null,"abstract":"<p><p>An abundance of microbial genomes have been sequenced in the past two decades. For fundamental comparative genomic investigations, where the goal is to determine the major gain and loss events shaping the pangenome of a species or broader taxon, it is often unnecessary and computationally onerous to include all available genomes in studies. In addition, the over-representation of specific lineages due to sampling and sequencing bias can have undesired effects on evolutionary analyses. To assist users with <i>genomic dereplication</i>, we developed skDER and CiDDER (https://github.com/raufs/skDER) to select a subset of representative genomes for downstream comparative genomic investigations. skDER is a nucleotide-based genomic dereplication tool that can dereplicate thousands of microbial genomes leveraging recent advances in average nucleotide identity (ANI) inference. CiDDER dereplicates microbial genomes based on saturation assessment of distinct protein-coding genes. To support usability, auxiliary functionalities are incorporated for testing the number of representative genomes resulting from applying various clustering parameters, automated downloading of genomes belonging to a bacterial species or genus, clustering non-representative genomes to their closest representative genomes and filtering plasmids and phages prior to dereplication. From benchmarking against other ANI-based dereplication tools, skDER, when run in the default mode, was efficient and achieved comparable pangenome coverage and strictly adhered to user-defined cutoffs for both ANI and aligned fraction (AF). Further, we showcase that CiDDER is a convenient alternative to ANI-based dereplication that allows users to more directly optimize the selection of representative genomes to cover a large breadth of a taxon's pangenome.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 7","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12245536/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144600937","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":"Dissemination of extended-spectrum beta-lactamase-producing <i>Escherichia coli</i> in poultry in Zimbabwe.","authors":"Peter Katsande, Alistair R Davies, Tom Chisnall, Kudzaishe Vhoko-Tapesana, Sam Willcocks, Chenai S Majuru, Tendayi Mubau, Richard A Stabler, Roderick M Card","doi":"10.1099/mgen.0.001454","DOIUrl":"10.1099/mgen.0.001454","url":null,"abstract":"<p><p>Extended-spectrum beta-lactamase (ESBL)-producing <i>Escherichia coli</i> 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 <i>E. coli</i> in poultry. In this study, we screened for ESBL-<i>E. coli</i> at farms (<i>n</i>=50) and markets (<i>n</i>=10) using MacConkey agar supplemented with 4 µg ml^-1 ceftriaxone. ESBL-<i>E. coli</i> 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 <i>bla</i> _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-<i>E. coli</i>. 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 <i>bla</i> _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 <i>bla</i> _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-<i>E. coli</i> 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-<i>E. coli</i> 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 <i>E. coli</i>.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 7","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12284406/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144659621","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":"Characterization of a <i>Listeria monocytogenes</i> plasmid with antibiotic and stress resistance genes.","authors":"Clare R Barker, David R Greig, Israel Olonade, Craig Swift, Adam Crewdson, Anaïs Painset, Nigel Pittock, Dunstan Rajendram, Gauri Godbole, Paolo Ribeca","doi":"10.1099/mgen.0.001445","DOIUrl":"10.1099/mgen.0.001445","url":null,"abstract":"<p><p>Listeriosis is a predominantly foodborne infection causing severe, invasive disease in the immunocompromised, with the causative agent being <i>Listeria monocytogenes</i>. While <i>L. monocytogenes</i> possesses innate resistance to several classes of antibiotics, acquired antibiotic resistance is low compared with other foodborne pathogens. Conversely, plasmids possessing stress tolerance mechanisms are common and contribute to their ability to persist in food production environments. However, very few have been identified, which also carry antibiotic resistance genes, particularly multidrug resistance regions. We scanned a UK collection of <i>L. monocytogenes</i> genomes and detected an isolate with the <i>dfrD</i>, <i>lnuG</i> and <i>mphB</i> genes, encoding predicted resistance to trimethoprim, lincosamides and macrolides, respectively. This isolate also possessed a <i>Listeria repA</i> family plasmid replication gene, as well as multiple chromosomal and plasmid-associated stress tolerance factors. Long-read sequencing confirmed the presence of a single 120,420 bp plasmid, which notably is a composite of a highly conserved <i>Listeria</i> plasmid backbone with a novel 35 kb resistance region. Comparative genomic analyses revealed that the plasmid-borne resistance region was likely acquired from other Gram-positive species over several events. The island containing the <i>lnuG</i> and <i>mphB</i> genes has links to porcine and bovine origins, while the <i>dfrD</i> gene is located on a Tn<i>3</i>-like transposon associated with multiple resistance genes, and both elements can move to the chromosome of <i>L. monocytogenes</i> strains from food and human disease. This work furthers the understanding of plasmid-mediated antibiotic resistance as well as the wider circulation of mobile genetic elements among <i>L. monocytogenes</i> and other bacterial species within the food chain.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 7","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12282311/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144575789","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":"ChiVariARIBA: a modular, editable workflow and database for characterising chitin gene variation in <i>Vibrio</i> spp. and related bacteria.","authors":"Evan P Naughton, Matthew J Dorman","doi":"10.1099/mgen.0.001439","DOIUrl":"10.1099/mgen.0.001439","url":null,"abstract":"<p><p>Chitin is a highly abundant biopolymer of bioeconomic, biochemical and commercial importance. This carbohydrate is a source of nutrients for chitinolytic bacteria and can influence natural competence, surface adsorption and other fundamental aspects of prokaryote physiology. Bacterial enzymatic degradation of chitin is mediated by a well-studied set of hydrolytic enzymes, transcriptional regulators and carbohydrate transport proteins. Many of these gene products have been functionally characterized <i>in vitro</i> or <i>in vivo</i>, but there is a reliance on <i>in silico</i> genomic approaches to study the variation of these metabolic components amongst diverse bacteria. Computational surveys of bacterial genomes to date have tended to focus on determining the presence and absence of chitin metabolism genes in diverse genomes, but not on the diversity of sequences amongst these gene families. To enable future research into chitin metabolism variation in vibrios and other bacteria, we present ChiVariARIBA, a workflow for extracting chitin metabolism genes from published genome sequences of chitinolytic <i>Vibrio</i> species and their relatives, compatible with the rapid gene-finding and variant-characterizing tool ARIBA, with which to describe the presence of chitin-metabolising genes in genomes of interest and to characterize the sequence variation of these genes across diverse bacteria.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 7","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12282291/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144659620","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":"Serotyping of <i>Actinobacillus pleuropneumoniae</i> based on whole genome sequencing: validation of a bioinformatic tool.","authors":"Øystein Angen, Kasper Thystrup Karstensen, Anna Vilaró, Lina Maria Cavaco, Paul R Langford, Lorenzo Jose Fraile Sauce, Lourdes Migura-Garcia, Charlotte Mark Salomonsen, Yanwen Li, Janine T Bossé","doi":"10.1099/mgen.0.001434","DOIUrl":"10.1099/mgen.0.001434","url":null,"abstract":"<p><p>Serovar detector is a new bioinformatic tool for determining the serovar of <i>Actinobacillus pleuropneumoniae</i> using whole genome sequencing. The composition of <i>cps</i> genes of isolates is compared to those of the serovar reference strains, and the outcome is determined both by the number of common genes and the similarities between the homologous genes. The validation of the bioinformatic tool utilized a broad collection of 732 isolates, including representatives from all described serovars. The isolates included had been characterized by conventional serotyping, PCR tests or different bioinformatic tools. The collection also includes isolates that have been difficult to allocate to a serovar using serology to test the performance of the Serovar detector when potential new varieties or combinations of <i>cps</i> genes are present. Out of the 732 isolates included in the investigation, only 36 isolates (4.9%) could not be allocated to the 19 recognized serovars. The validation showed that the Serovar detector is a robust method for determining the serovar of an isolate and a valuable tool for further characterization of the genetic heterogeneity both within serovars and within the <i>A. pleuropneumoniae</i> species.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 7","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12263286/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144637433","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":"<i>Vibrio cholerae</i> lineage and pangenome diversity vary geographically across Bangladesh over 1 year.","authors":"Chuhan Qin, Patrick Lypaczewski, Md Abu Sayeed, Aline Cuénod, Lindsey Brinkley, Ashton Creasy-Marrazzo, Emilee T Cato, Kamrul Islam, Md Imam Ul Khabir, Md Taufiqur R Bhuiyan, Yasmin Begum, Manasi N Kamat, Laura S Bailey, Kari B Basso, Firdausi Qadri, Ashraful I Khan, Eric J Nelson, B Jesse Shapiro","doi":"10.1099/mgen.0.001437","DOIUrl":"10.1099/mgen.0.001437","url":null,"abstract":"<p><p>Cholera is an acute diarrhoeal disease caused by <i>Vibrio cholerae</i>. It remains a major public health challenge worldwide, and particularly in the endemic region around the Bay of Bengal. Over decadal time scales, one lineage typically dominates and spreads in global pandemic waves. However, it remains unclear to what extent diverse lineages co-circulate during a single outbreak. Defining the pool of diversity over finer time-scales is important because the selective pressures that impact <i>V. cholerae</i>, namely antibiotics and phages, are dynamic on these scales. To study the nationwide diversity of <i>V. cholerae</i>, we long-read sequenced 273 <i>V</i>. <i>cholerae</i> genomes from seven hospitals over 1 year (2018) in Bangladesh. Four major <i>V. cholerae</i> lineages were identified: three known lineages, BD-1, BD-2a and BD-2b, and a novel lineage that we call BD-3. In 2022, BD-1 caused a large cholera outbreak in Dhaka, at which point it had replaced BD-2 as the most common lineage in Bangladesh. We show that, in 2018, BD-1 was already predominant in the five northern regions, including Dhaka, consistent with an origin from northern India. By contrast, we observed a higher diversity of lineages in the two southern regions near the coast. The four lineages differed in pangenome content, including integrative and conjugative elements (ICEs) and genes involved in resistance to bacteriophages and antibiotics. Notably, BD-2a lacked an ICE and is predicted to be more sensitive to phages and antibiotics, yet persisted throughout the sampling period. Genes previously associated with antibiotic resistance in <i>V. cholerae</i> isolated from Bangladesh in the prior decade were entirely absent from all lineages in 2018-2019, suggesting shifting costs and benefits of encoding these genes. Our results highlight the diverse nature of the <i>V. cholerae</i> pangenome and geographic structure within a single outbreak season. This diversity provides the raw material for adaptation to antibiotics, phages and other selective pressures.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 7","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144708059","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}