Microbial Genomics最新文献

{"title":"An ode to the 16S rRNA gene: its history, importance, caveats and future in microbiome research.","authors":"F J Whelan, L J Hall","doi":"10.1099/mgen.0.001823","DOIUrl":"10.1099/mgen.0.001823","url":null,"abstract":"<p><p>The 16S rRNA gene has - and continues to - play an important role in microbiology. It's universality across prokaryotes and variation across species has allowed the sequencing of its hypervariable regions to be used to distinguish taxa within complex mixed bacterial communities. Although 16S rRNA gene sequencing has transformed our understanding of microbial communities, its use comes with important caveats and considerations, especially in light of the availability of whole-genome metagenomic sequencing. Within, we discuss the 16S rRNA gene and its important role in microbiome research, in the past, present, and future.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 8","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13505959/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148819024","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":"Integrated poultry production as a reservoir of <i>tet</i>(X4) and <i>mcr-1.1</i> encoding <i>Escherichia coli</i> in Pakistan.","authors":"Muhammad Ahmed Mushtaq, Peter Schierack, Muhammad Yousaf, Fariha Fatima, Tayyaba Qamar, Mashkoor Mohsin, Muhammad Moman Khan","doi":"10.1099/mgen.0.001800","DOIUrl":"10.1099/mgen.0.001800","url":null,"abstract":"<p><p>Plasmid-mediated colistin and tigecycline resistance threatens last-resort therapeutic options. We investigated the farm-to-fork dissemination of <i>Escherichia coli</i> encoding <i>mcr-1.1</i> and <i>tet</i>(X4) in a vertically integrated broiler production system. A total of 200 samples were collected in 2024, representing four sequential production stages: broiler breeders, day-old chicks, day-30 broilers and retail meat. All positive [<i>mcr-1.1</i> and/or <i>tet(X4</i>)] isolates underwent Illumina short-read sequencing, with long-read sequencing of three representatives. The study was enriched and analysed with <i>mcr-1.1</i> and <i>tet</i>(X4) encoding 213 publicly available <i>E. coli</i> genomes from Pakistan. Of 18 isolates, <i>tet</i>(X4) was detected in 11 and <i>mcr-1.1</i> in 7 isolates with a single breeder isolate (ST-398) co-harbouring both on separate plasmids. <i>tet</i>(X4) predominated breeders and day-30 broilers, whereas <i>mcr-1.1</i> was distributed across all four stages. ST-1011 exhibited a pattern of clonal farm-to-fork transmission of <i>tet</i>(X4) via IncFIB(AP001918)-IncFII providing molecular evidence suggestive of clonal transmission. Analysis of 231 genomes across 87 sequence types (STs) revealed contrasting evolutionary trajectories: <i>mcr-1.1</i> with post-mobilization stabilization marked by complete absence of ISApl1 and highly conserved IncI2 plasmid (93%), whereas <i>tet</i>(X4) retained active transposition within IS26-bounded elements. <i>tet</i>(X4) carriage was also associated with elevated resistance gene burden, driven by the IncF megaplasmids. All 18 isolates exhibited adhesion to chicken intestinal epithelial cells (CHIC-8E11), with high adhesion capacity among <i>tet</i>(X4)-positive isolates. This study demonstrates that <i>mcr-1.1</i> and <i>tet</i>(X4) disseminate through poultry production via distinct mechanisms. These findings highlight the need for integrated One Health surveillance of antimicrobial resistance dissemination.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 8","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13431907/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148663553","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":"Investigation of an outbreak of <i>Shigella sonnei bla</i> _CTX-M-3 among men in England, 2025-26, using long- and short-read whole-genome sequencing.","authors":"Jake D Turnbull, David R Greig, Clare R Barker, Satheesh Nair, Katherine Lock, Craig Swift, Marie A Chattaway, Kate S Baker, Claire Jenkins","doi":"10.1099/mgen.0.001817","DOIUrl":"https://doi.org/10.1099/mgen.0.001817","url":null,"abstract":"<p><p><b>Background.</b> Recent outbreaks of gastrointestinal symptoms among gay, bisexual and other men who have sex with men (GBMSM) have been caused by multidrug-resistant (MDR) <i>Shigella sonnei</i> carrying <i>bla</i> _CTX-M-27 or <i>bla</i> _CTX-M-15. To date, the <i>bla</i> _CTX-M-3 variant has not been associated with sexually transmitted shigellosis in the UK.<b>Methods.</b> Routine surveillance identified an outbreak <i>S. sonnei</i> among men in England in June 2025. Short-read sequencing data were analysed to identify antimicrobial resistance (AMR) determinants and to investigate the phylogenetic context of the outbreak. Long-read Oxford Nanopore Technology sequencing data were analysed to characterize the AMR-encoding plasmid content.<b>Results.</b> Of the 83 cases linked to the outbreak cluster, 91.5% were adult males and none reported recent travel outside Europe; these outbreak characteristics (specifically adult male, no travel) are consistent with transmission among European GBMSM networks (Mitchell <i>et al</i>. 2019, Mitchell <i>et al</i>. 2021). Phylogenetic analysis placed the outbreak cluster within a wider clade historically associated with travel to the Middle East. The outbreak isolates were MDR; 90.4% (<i>n</i>=75/83) had <i>bla</i> _CTX-M-3 located on an IncI1B/O plasmid. This is the first report of the IncI1B/O plasmid type and <i>bla</i> _CTX-M-3 in GBMSM-associated MDR <i>S. sonnei</i> in England.<b>Conclusions.</b> Acquisition of the IncI1B/O plasmid encoding <i>bla</i> _CTX-M-3 represents an independent evolutionary event, separate from previously described GBMSM epidemics driven by acquisition of IncFII plasmids encoding <i>bla</i> _CTX-M-27 or <i>bla</i> _CTX-M-15. This study provides further evidence of the parallel emergence of <i>bla</i> _CTX-M variants conferring resistance to the third-generation cephalosporins. Whole-genome sequencing based surveillance and routine susceptibility testing of MDR <i>S. sonnei</i> are essential, as this pathogen continues to diversify and spread.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 8","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13475751/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148760317","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":"Predicting the plastic biodegradation potential within microbial lineages and across global ecosystems.","authors":"Harmony Douwes, Zuzanna Dutkiewicz, Christian Rinke","doi":"10.1099/mgen.0.001814","DOIUrl":"10.1099/mgen.0.001814","url":null,"abstract":"<p><p>Plastic waste pollution is a global issue that threatens biodiversity and human health. Current plastic waste management practices are not sufficient to keep up with increasing plastic production rates. Microorganisms have the capacity to degrade different types of bio-based and synthetic plastics through enzymatic reactions, offering an alternative solution to traditional plastic recycling techniques. A limited number of plastic-degrading enzymes have been identified, sequenced and characterized; however, studies exploring the distribution of homologues of these enzymes across habitats and microbial taxa have remained scarce. Here, we applied analytical techniques to search for genes encoding potential plastic-degrading enzymes in environmental metagenome datasets and genomes of the Genome Taxonomy Database (GTDB) to explore the geographic and taxonomic distribution patterns of plastic-degrading microorganisms. Hidden Markov Models (HMMs) were constructed from amino acid sequences of known, experimentally verified and putative plastic-degrading enzymes. The HMMs were applied to landfill, soil, river, lake and ocean metagenomes and all archaeal and bacterial genomes in the GTDB. An abundance of hits was discovered across aquatic and terrestrial metagenomes with the majority occurring in polluted rivers, polar oceans and deep ocean samples. GTDB hits were mainly consistent with known plastic-degrading microbial lineages, while also revealing potential plastic-degrading archaeal taxa. The results of this study may be able to assist in the discovery of novel plastic-degrading enzymes for application in plastic waste biodegradation solutions.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 8","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13461043/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148707020","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":"Quantitative comparison of fungal genome assembly strategies using short and long reads from simulated and empirical sequencing data.","authors":"Gabriel Amorim de Albuquerque Silva, Temitope R Folorunso, Lori G Eckhardt, Janna R Willoughby","doi":"10.1099/mgen.0.001824","DOIUrl":"10.1099/mgen.0.001824","url":null,"abstract":"<p><p>High-quality fungal reference genomes are essential for comparative, functional and evolutionary studies, yet fungal genome features such as repeats, structural rearrangements, accessory chromosomes and intron-rich genes can complicate genome assembly and the selection of cost-effective sequencing strategies. Here, we benchmark fungal genome assembly performance using simulated and empirical short- and long-reads datasets to evaluate how sequencing depth, assembler choice and genome characteristics influence contiguity, completeness, accuracy and computational requirements. Using simulated reads from complete fungal genomes spanning diverse sizes and compositions, we evaluated short-reads (SR), long-reads (LR), hybrid and polished LR assemblies across sequencing depths from 10X to 100X. Key trends were validated using empirical sequencing data from 10 fungal isolates assembled with multiple strategies, including different Flye assembler parameter sensitivity and SR polishing. Across datasets, LR produced the largest improvements in contiguity, with most gains achieved at ~20-40X coverage and diminishing returns beyond moderate depth. SR polishing substantially improved base-level accuracy at relatively low cost, with ~10-20X coverage often sufficient to approach maximal error reduction. Hybrid assemblers showed strong algorithmic variability, with trade-offs between contiguity, error rates and computational demand. Genome architecture also influenced outcomes, as larger and more feature-dense genomes benefited more from long-read data while GC content had limited impact. Overall, our results suggest that moderate long-read coverage (~30-40X) combined with modest short-read polishing (~10-20X), particularly using Flye plus Polypolish, provides a strong balance of contiguity, completeness, accuracy and resource efficiency for generating high-quality fungal genome assemblies.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 8","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13514079/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148829972","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":"Emergent function, not microbial conformity: functional redundancy and the limits of taxonomic inference in microbiome genomics.","authors":"Rebecca Lewandowski","doi":"10.1099/mgen.0.001831","DOIUrl":"10.1099/mgen.0.001831","url":null,"abstract":"<p><p>Microbiome genomics has achieved remarkable resolution of community structure, yet composition alone remains an unstable basis for inferring host-relevant biology. That instability reflects a broader interpretive problem in which taxonomically distinct communities can converge on similar outputs, while superficially similar communities can diverge in behaviour because of strain variation, gene content, regulatory state, ecological context, spatial organization and host physiology. Functional redundancy is therefore better understood not as a reserve of interchangeable organisms but as a distributed functional architecture through which host-relevant outputs can persist across variation in membership. The central question for microbial genomics is not whether composition matters, but when community structure can be expected to predict function, host consequence or recovery. A more rigorous framework must distinguish membership from encoded capacity, realized activity, ecological interaction and host-relevant effect, while also recognizing that host physiology and spatial context shape which microbial functions become possible and which outputs are ultimately encountered. Progress will depend first on matching the evidentiary layer to the claim and then on selecting proportionate additions, from strain-resolved genomics and pathway-level interpretation to targeted metatranscriptomic, metaproteomic, metabolomic, spatial, perturbation-recovery or host-response measurements. In that framework, reproducibility may reside less in recurring taxa than in conserved biological outputs, and restoration less in compositional resemblance than in recovery of the functions and host-facing consequences that were actually disrupted.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 8","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13505790/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148819105","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":"Analysis of the genomes of a male-killing <i>Spiroplasma</i> and its co-infecting <i>Rickettsia</i> reveals a case of concerted genome expansion.","authors":"Emily A Hornett, Masayuki Hayashi, Keisuke Nagamine, Steve Paterson, Daisuke Kageyama, Gregory D D Hurst","doi":"10.1099/mgen.0.001766","DOIUrl":"10.1099/mgen.0.001766","url":null,"abstract":"<p><p>Maternally inherited symbionts are central to arthropod biology, functioning both as mutualistic partners and as reproductive parasites. Genomic analyses provide critical insight into these interactions. Here, we sequenced, assembled and examined the genomes of <i>Spiroplasma</i> and <i>Rickettsia</i> co-infecting the lacewing <i>Mallada desjardinsi</i>, with the aim of elucidating the male-killing phenotype of <i>Spiroplasma</i> and predicting potential phenotypes for <i>Rickettsia</i>. In <i>Spiroplasma</i>, we identified a set of candidate effector genes. However, Spaid-like genes, where present, lacked the functional domains previously demonstrated to be important for male-killing. The <i>Rickettsia</i> genome contained two <i>cifA/cifB</i> gene pairs, consistent with the capacity to induce cytoplasmic incompatibility (CI). Unexpectedly, both symbiont genomes were markedly expanded relative to congenerics. We describe this pattern - that contrasts with the classical trajectory of genome reduction in symbionts - as secondary genome expansion. Expansion was driven by extensive proliferation of mobile elements: <i>Rickettsia</i> harboured an exceptionally high number of insertion sequences, while <i>Spiroplasma</i> accumulated both insertion sequences and prophage regions. Collectively, our findings indicate that the canonical Spaid-mediated male-killing mechanism is not conserved in the <i>Spiroplasma</i> of <i>M. desjardinsi</i>, while <i>Rickettsia</i> may induce CI. Moreover, the parallel genome expansions observed suggest that secondary expansion events may be influenced by host-associated factors rather than occurring stochastically.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 7","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13375240/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148471429","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":"Evolving strategies for virus discovery.","authors":"Amanda Araujo Serrao de Andrade, Andrea Silverj, Theodore Josephs, Ann C Gregory","doi":"10.1099/mgen.0.001785","DOIUrl":"10.1099/mgen.0.001785","url":null,"abstract":"<p><p>Viruses interact with all domains of life and play fundamental roles in shaping biological systems from individual hosts to global ecosystems. Yet their identification remains difficult due to a lack of a universal marker gene and the extensive diversity of viral genomes. Despite this, the speed of viral discovery is quickly increasing, driven by the growing number of virome studies, improved sequencing technologies and the decreased cost of sequencing. In this review, we examine the evolution of virus identification approaches from classical and molecular methods to contemporary genome-resolved and computational frameworks. By aggregating genome-resolved virome studies from 2010 to early 2026 that meet defined criteria (<i>n</i>=502), we synthesize the current landscape of virus identification methods, including similarity-based, sequence-based artificial intelligence (AI) and hybrid approaches. We also highlight the key limitations of the current methods, particularly biases in reference databases that contribute to persistent viral 'dark matter'. Finally, we identify emerging opportunities for the field in structure-based and AI-driven approaches that extend detection beyond sequence similarity and outline how these integrative frameworks are poised to improve virus discovery across ecosystems.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 7","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13344882/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148405246","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 and enzymatic signatures underlying lifestyle diversity in <i>Xanthomonas arboricola</i>.","authors":"Sara Cuesta-Morrondo, Salvador Sastre, Jerson Garita-Cambronero, Jaime Cubero","doi":"10.1099/mgen.0.001782","DOIUrl":"10.1099/mgen.0.001782","url":null,"abstract":"<p><p><i>Xanthomonas arboricola</i> is a plant-associated bacterial species that comprises the pathovars pruni (<i>Xap</i>), juglandis (<i>Xaj</i>), corylina (<i>Xac</i>), which are of high economic concern; and the pathovars arracaciae, celebensis, fragariae and zantedeschiae, which are less relevant, meaning they have a lower economic impact, are less widely distributed, or cause less severe diseases in their host plants. Moreover, the species also includes strains without pathovar affiliation. The pathogenicity of the less economically relevant pathovars as well as the non-affiliated strains has been debated. The present study analysed all the <i>X. arboricola</i> genomes deposited in GenBank by March 2025, focusing on type III secretion system (T3SS), type III effectors (T3Es), cell wall-degrading enzymes (CWDE), amylases and hydrolytic activity.The average nucleotide identity analysis showed that strains belonging to the three main pathovars clustered according to their pathovar designation, harbouring both T3SS and a large T3Es repertoire. However, strains belonging to pathovars of lower economic relevance or with no pathovar affiliation were clustered into two groups, G1 and G2. Remarkably, strains belonging to these less relevant pathovars were scattered along these two groups, exhibiting notable genetic diversity. Moreover, strains in G1 generally displayed T3SS but a limited set of T3Es, whereas strains in G2 lacked a T3SS and exhibited an even more reduced T3Es repertoire. Regarding CWDE, differences in the amount and profiles of cellulolytic, hemicellulolytic and pectinolytic enzymes were observed. While <i>Xap</i> and <i>Xaj</i> possessed the highest counts of hemicellulolytic enzymes, strains in G1 and G2 harboured the highest numbers of cellulolytic and pectinolytic enzymes. Moreover, hydrolytic activities were assayed in a set of strains comprising the three main pathovars and G1 and G2 clusters. It was demonstrated that G1 and G2 strains caused soft rot in pepper fruits, while the main pathovars did not. Furthermore, all the <i>X. arboricola</i> strains analysed hydrolysed starch, except for <i>Xap</i>, which also harboured a reduced set of amylolytic enzymes. The doubtful, atypical or weak pathogenicity, the genomic diversity, the limited content of T3Es, together with the soft rot capacity, the higher counts of cellulolytic and pectinolytic enzymes and the literature, suggest that strains in G1 and G2 would probably be commensal or saprophytic strains that may behave as opportunistic pathogens under certain conditions.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 7","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13375143/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148471408","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":"Comprehensive identification of sequence types belonging to <i>Acinetobacter baumannii</i> clonal complexes.","authors":"Ruth M Hall, Christopher J Harmer","doi":"10.1099/mgen.0.001772","DOIUrl":"10.1099/mgen.0.001772","url":null,"abstract":"<p><p><i>Acinetobacter baumannii</i> is a major nosocomial pathogen, with multiply antibiotic-resistant (MAR) isolates primarily belonging to two globally disseminated clonal complexes, Global Clone 1 (GC1) and Global Clone 2 (GC2). <i>A. baumannii</i> has two MLST schemes: the Pasteur and the Oxford scheme. However, the Pasteur scheme identifies clones more simply. Under the Pasteur MLST scheme, these clones centre on sequence types 1 (ST1) and 2 (ST2), respectively, but both encompass related single-locus variants (SLVs) and double-locus variants (DLVs) and even some triple-locus variants (TLVs). Despite their clinical importance, no systematic and up-to-date catalogue of sequence types (STs) belonging to GC1 or GC2 was available.A workflow was developed using a custom Python workflow to identify SLVs and DLVs of founder STs. This identified 63 STs associated with ST1 and 163 associated with ST2. The impact of accounting for these additional ST was evaluated by analysing 41,951 publicly available <i>A. baumannii</i> genome assemblies from GenBank. Inclusion of SLVs and DLVs increased the number of GC1 genomes significantly from 1,083 ST1 to 1,428 genomes total, but GC2 only from 26,962 to 28,002 genomes. Relatively few SLVs or DLVs found in PubMLST were represented among genome assemblies (22 out of 64 for ST1 and 65 out of 164 for ST2), suggesting incomplete genome coverage or erroneous MLST profiles. Other successful clones, including ST25, ST79, ST85 and ST499, each showed diversification. This framework provides a method for consistent clone definition across clinically important <i>A. baumannii</i> clonal complexes and can be applied more broadly to other important MAR bacteria such as <i>Klebsiella pneumoniae</i>.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 7","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13322331/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148361123","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}