Microbial Genomics最新文献

{"title":"The poplar pathogen <i>Sphaerulina musiva</i> has a dynamic genome architecture marked by chromosomal inversions and changes in transposable element abundance.","authors":"Alex Z Zaccaron, Alexandre Lassagne, Kelsey L Søndreli, Martha A Sudermann, Ricardo I Alcalá Briseño, Niklaus J Grünwald, Alexandra J Weisberg, Jared M LeBoldus","doi":"10.1099/mgen.0.001603","DOIUrl":"10.1099/mgen.0.001603","url":null,"abstract":"<p><p>Fungal plant pathogens possess dynamic genomes, frequently shaped by transposable elements, that enable rapid adaptation to adverse conditions and host resistance mechanisms. However, assessing the adaptive significance of these genomic features remains challenging, in part due to the lack of high-quality genome assemblies for multiple members of a given species. To gain insights into genomic factors shaping pathogen evolution, we sequenced and assembled near-chromosome-scale genomes of 18 geographically diverse North American isolates of <i>Sphaerulina musiva</i>, a significant, important pathogen causing Septoria leaf spot and stem canker disease of poplar trees. Comparative genomic analyses indicated that all isolates possess 13 chromosomes with no evidence of accessory chromosomes. Transposable element (TE) content varied considerably among isolates (6.8 %-15.7 %), with a higher abundance in isolates from Oregon, British Columbia and Alberta, geographic regions outside the native range of <i>S. musiva</i>. The variation in TE content largely explained differences in genome size among isolates and suggested lineage-specific proliferation of TEs. Although a gene-based pangenome analysis indicated a relatively low percentage (9.5%) of accessory genes, this subset was enriched for candidate effectors. Our results indicate that <i>S. musiva</i> exhibits features of a 'one-speed genome' model. However, increased TE content is correlated with longer intergenic regions of candidate effector genes, suggesting that proliferation of TEs may be driving increased compartmentalization. Finally, synteny analysis revealed a total of 43 long chromosomal inversions with an average size of 293 kb that covered 34% of the <i>S. musiva</i> genome. These chromosomal inversions were more frequently observed in isolates from the pathogen's native range in the Eastern USA, and at least one inversion was predicted to affect the organization of a secondary metabolite gene cluster. These findings provide novel insights into the genome structure, TE dynamics and chromosomal rearrangements of the poplar pathogen <i>S. musiva</i>, offering a foundation for understanding its evolution and adaptation across diverse geographic regions and host species.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12778737/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145911804","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":"Novel features of <i>Mycoplasma genitalium</i> genomes identified through Oxford Nanopore sequence analysis of isolates from Australia.","authors":"Jose L Huaman, Catriona S Bradshaw, Teck-Phui Chua, Erica L Plummer, Jennifer A Danielewski, Lenka A Vodstrcil, Suzanne M Garland, Gerald L Murray","doi":"10.1099/mgen.0.001622","DOIUrl":"10.1099/mgen.0.001622","url":null,"abstract":"<p><p><i>Mycoplasma genitalium</i> is a fastidious human pathogen with increasing antimicrobial resistance, yet its genomic landscape remains poorly characterized due to difficulties with culture, including prolonged incubation periods and low DNA yields from both clinical and cultured samples. Consequently, there are few publicly available genome sequences. In this study, a Vero cell culture protocol was optimized to increase <i>M. genitalium</i> DNA yield and integrated with Oxford Nanopore technology. As a result, 22 complete genome sequences were generated with a mean sequencing depth of 51.01×. Comparative genomics revealed that 59% of isolates contained a translocated rRNA operon, with junction flanks showing ~90% identity to the <i>MgPar</i> repetitive regions known to be associated with genomic rearrangement. Phylogenetic analysis revealed multiple groups encompassing both recent and deeply branching lineages. High rates of macrolide (90.9%) and fluoroquinolone (45.5%) resistance were observed. All isolates with quinolone resistance mutations also carried macrolide resistance mutations. Notably, all three isolates with <i>mgpB</i> 161 allele had the same resistance profile: A2059G, H69R, S83I and M95I at 23S, L4, <i>parC</i> and <i>gyrA</i>, respectively. This work provides the first complete <i>M. genitalium</i> genome generated using Oxford Nanopore sequencing from Vero cell-propagated isolates, underscoring the novelty and technical advancement of this approach.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12852374/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146064540","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":"Unravelling the genomic landscape of Canadian <i>Borrelia burgdorferi</i>: a comparison across global strains.","authors":"Anthony Piot, Iain L Mainprize, Justin Wood, Jeff Gauthier, Cezar M Khursigara, Karine Thivierge, Melanie K B Wills, Roger C Levesque","doi":"10.1099/mgen.0.001606","DOIUrl":"10.1099/mgen.0.001606","url":null,"abstract":"<p><p>The main agent of Lyme borreliosis (LB) in North America, the bacteria <i>Borrelia burgdorferi</i>, is spreading in Canada following the northward expansion of its primary tick vectors, <i>Ixodes scapularis</i> and <i>Ixodes pacificus</i>. Despite the importance of this pathogen for human health, the precise geographical origin and genome structure of Canadian <i>B. burgdorferi</i> strains remain to be determined, and no complete genome sequence from this region is available. The complex genome structure of <i>Borrelia</i> species makes their assembly challenging, but the latest long-read sequencing technologies and bioinformatics software now enable <i>de novo</i> assembly of <i>Borrelia</i> genomes with high efficacy. In this study, we sequenced and assembled the genomes of six Canadian <i>B. burgdorferi</i> strains to compare their content and structure to additional <i>Borrelia</i> genomes from the USA and Europe. We successfully reconstructed the genome, comprising chromosomes and plasmids of the six Canadian strains. These genomes showed an overall similar structure compared to other <i>B. burgdorferi</i> strains. Phylogenetic inferences highlighted topological differences in the placement of <i>B. burgdorferi</i> strains between the chromosome and the cp26 and lp54 plasmids. Synteny analyses revealed important replicon sequence conservation across strains while highlighting a high proportion of shared gene sequences among the replicons of the same strain, especially for cp32 plasmids. We describe the first complete genomes of Canadian <i>B. burgdorferi</i> strains and present a strategy for the assembly, annotation, comparative analysis of plasmids and their evolution in the same bacterial genus. While the genome content and structure of Canadian strains are similar to other <i>B. burgdorferi</i> strains, the information in the plasmids and genes they harbour will be useful to elucidate the origins and evolution of LB in Canada.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12813429/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145933961","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":"Decoding the interconnected splicing patterns of hepatitis B virus and host using large language and deep learning models.","authors":"Chun Shen Lim, Chris M Brown","doi":"10.1099/mgen.0.001616","DOIUrl":"10.1099/mgen.0.001616","url":null,"abstract":"<p><p>Hepatitis B virus (HBV) infection causes one million deaths annually and remains a major driver of hepatocellular carcinoma. Despite its compact 3.2 kb genome, HBV exhibits extensive alternative splicing. HBV splice variants contribute to immune evasion and reduce the likelihood of achieving a functional cure. Here, we show that HBV splicing efficiency - quantified from 279 RNA-sequencing libraries of HBV-associated liver biopsies and cultured cells - correlates more strongly with disease progression than the overall proportion of spliced HBV RNA, the latter of which has been proposed as an emerging biomarker. All HBV splice sites are embedded within protein-coding regions, forming a gene structure distinct from typical host splice sites. To decode the sequence determinants of HBV splicing, we apply SpliceBERT and OpenSpliceAI to 4,706 HBV genomes. These models reveal that HBV splice donor sites share features with host splice donor sites, whereas HBV splice acceptor sites are more cryptic. These patterns likely reflect constraints imposed by HBV's compact genome, which must accommodate overlapping protein-coding regions. Motif conservation and splicing propensity analyses across HBV genomes reveal context- and genotype-specific splicing patterns, indicating regulation by sequence context. HBV genotypes may have coevolved with their human hosts to exploit suboptimal but spliceable host-like motifs without disrupting their gene structure, supporting mechanisms of viral persistence and immune evasion. This study demonstrates the utility of artificial intelligence in decoding viral splicing patterns and provides a framework for investigating co-transcriptional processes in other clinically important viruses.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12811152/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145989830","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":"The Resistance-Nodulation-Division efflux pump EefABC is highly conserved within lineages of <i>E. coli</i> commonly associated with infection.","authors":"Hannah L Pugh, Elizabeth M Darby, Leah Burgess, Abigail L Colclough, Asti-Rochelle Meosa John, Steven Dunn, Christopher Connor, Eoughin A Perry, Alan McNally, Vassiliy N Bavro, Jessica M A Blair","doi":"10.1099/mgen.0.001593","DOIUrl":"10.1099/mgen.0.001593","url":null,"abstract":"<p><p>Resistance-nodulation-division (RND) efflux pumps confer multidrug resistance in Gram-negative bacteria and are critical for many physiological functions including virulence and biofilm formation. The common <i>Escherichia coli</i> laboratory strain, K-12 MG1655, has six recognized RND transporters (AcrB, AcrD, AcrF, CusA, MdtBC and MdtF). However, by studying >20,000 <i>E</i>. <i>coli</i> assemblies, we show that <i>E. coli</i> belonging to phylogroups B2, D, E, F and G, which are commonly associated with infection, possess an additional, seventh RND transporter, EefB. It is found in a five-gene operon, <i>eefRABCD</i>, which also encodes a TetR family transcription factor, a periplasmic adapter protein, an outer membrane factor and major facilitator superfamily pump. In contrast, <i>E. coli</i> from phylogroups A, B1 and C, generally containing environmental/commensal strains, do not encode the operon. Where the <i>eefRABCD</i> operon is present, it was highly conserved. In fact, conservation levels were comparable to that of the major RND efflux system AcrAB-TolC, suggesting an important biological function. Protein modelling shows that this pump is distinct from endogenous <i>E. coli</i> RND systems with unique structural features. However, unlike other RND efflux systems, EefABC does not appear to transport antimicrobials and instead may be important for infection or survival in the host environment.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12817139/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145952245","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":"The natural history of the emergence of sexually transmissible shigellosis.","authors":"Lewis C E Mason, Fariha Jawed, Angelika Fruth, Roberto Vivancos, Claire Jenkins, Kate S Baker","doi":"10.1099/mgen.0.001607","DOIUrl":"10.1099/mgen.0.001607","url":null,"abstract":"<p><p>Shigellosis is a gastrointestinal illness caused by bacteria belonging to one of four species of <i>Shigella</i>. Sexually transmissible (ST) shigellosis was first reported in 1974, but recently there has been a global increase in the transmission of extensively drug-resistant (XDR) strains. Here, we sought to characterise the natural history of ST shigellosis through literature review and genomic epidemiological analysis of early outbreaks. The literature review revealed a significant gap in reporting of ST shigellosis between the first report in 1974 and the early 2000s, after which reporting increased. To better understand this sustained emergence of ST shigellosis in the 21st century, we explored potential pathogen factors and linked these with changes in host populations. Specifically, we analysed the genomic epidemiology of preserved strains from outbreaks in both Berlin (2000-2002) and London (2004-2006). Both outbreaks were <i>Shigella sonnei</i> Genotype 3.1, an ancestral branch of the globally disseminated lineage III subtype, which is distinct from the currently globally dominant XDR forms (Genotypes 3.6.1.1.2 and 3.6.1.1) circulating in sexual transmission networks. We also describe the variable antimicrobial resistance, conserved colicin genes and differing virulence and plasmid profiles between the London and Berlin outbreaks. Finally, we conducted temporal reconstruction of Genotype 3.1 and found that the most recent common ancestor occurred in 1999 (95% highest posterior density 1997-2000), which is coincident with the introduction of highly active antiretroviral therapy (HAART) for human immunodeficiency virus. This suggests that changes associated with the introduction of HAART may have contributed to the re-emergence of ST shigellosis in the 21st century.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12824643/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146011029","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":"Machine learning-based lineage prediction from antimicrobial susceptibility testing phenotypes for <i>Escherichia coli</i> sequence type 131 clade C surveillance across infection types.","authors":"Theodor A Ross, Anna K Pöntinen, Einar Holsbø, Ørjan Samuelsen, Kristin Hegstad, Michael Kampffmeyer, Jukka Corander, Rebecca A Gladstone","doi":"10.1099/mgen.0.001608","DOIUrl":"10.1099/mgen.0.001608","url":null,"abstract":"<p><p>Rising antimicrobial resistance (AMR) in <i>Escherichia coli</i> bloodstream infections (BSIs) in high-income settings has typically been dominated by one clone, the sequence type (ST)131. More specifically, ST131 clade C (ST131-C) is associated with fluoroquinolone resistance and extended-spectrum <i>β</i>-lactamases (ESBLs). Even though urinary tract infections (UTIs) are a known common precursor to BSIs, there is currently limited knowledge on the longitudinal prevalence of ST131-C in UTIs and, therefore, the temporal link between the two infection types. Leveraging available genomic and antimicrobial susceptibility test (AST) data for ciprofloxacin, gentamicin and ceftazidime in 2,790 <i>E. coli</i> BSI isolates, we trained Random Forest and extreme gradient boosting (XGBoost) classifiers to predict if an <i>E. coli</i> isolate belongs to ST131-C using only AST data. These models were used to predict the yearly prevalence of ST131-C in 22942 UTI and 24866 BSI isolates from Norway. The XGBoost classifier achieved a prediction F1-score of over 70% on a highly unbalanced dataset where only 4.3% of the genomic BSI isolates belonged to ST131-C. The predicted prevalence of ST131-C in UTIs exhibited a similar annual trend to that of BSIs, with a stable infection burden for 8 years after its rapid expansion, confirming that the persistence of ST131-C in BSIs is largely driven by ST131-C UTIs. However, a higher prevalence of ST131-C in BSIs (~7 %) compared to UTIs (~4 %) suggests a subsequent enrichment of ST131-C. Our study highlights how existing epidemiological knowledge can be supplemented by utilizing extensive data from AMR surveillance efforts without genomic markers.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12816985/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145998451","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":"A <i>nirK</i>-cbb3 genomic region links SAR11 to nitrogen loss in the northern Benguela Upwelling System.","authors":"Robert M Morris, Timothy E Mattes, Kunmanee Bubphamanee, Mike C Sadler, Luke A Calderaro, Jen Karolewski, Karen L Casciotti, Olivia U Mason","doi":"10.1099/mgen.0.001620","DOIUrl":"10.1099/mgen.0.001620","url":null,"abstract":"<p><p>Denitrification leads to nitrogen loss from marine oxygen minimum zones. The complete metabolic pathway for denitrification reduces nitrate to dinitrogen gas in four sequential steps. Many facultatively anaerobic bacteria are capable of the initial step of nitrate reduction to nitrite. Far fewer contribute to nitrogen loss by reducing nitrite to nitric oxide, nitrous oxide or dinitrogen gas. We sequenced the genomes of 24 bacteria isolated from low-oxygen waters (23 µM) in the northern Benguela Upwelling System (nBUS) to identify species with the genetic potential for denitrification. Most isolates have the genetic potential for partial denitrification, including ten SAR11 strains with a genomic region that codes for a copper-containing nitrite reductase (NirK) and a high-affinity cbb3-type cytochrome c oxidase. Evidence that nBUS SAR11 have the potential to respire nitrite in low-dissolved-oxygen waters suggests that they could have a more direct role in marine nitrogen loss.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12816887/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146003701","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":"Exploring the IS-capades of <i>Klebsiella pneumoniae</i>: insertion sequences drive metabolic loss in obscure sub-lineages.","authors":"Ben Vezina, Claire White, Helena B Cooper, Kathryn E Holt, Jane Hawkey, Kelly L Wyres, Margaret M C Lam","doi":"10.1099/mgen.0.001612","DOIUrl":"10.1099/mgen.0.001612","url":null,"abstract":"<p><p><b>Introduction.</b> <i>Klebsiella pneumoniae</i> is an opportunistic pathogen that causes a wide spectrum of infections within healthcare settings and the community. Four <i>K. pneumoniae</i> sub-lineages, defined using core gene multi-locus sequence types, are known to cause distinct infections of the nasal and/or upper respiratory passages: SL91 and SL10031 (also referred to as subspecies <i>ozaenae</i>), SL10032 (subspecies <i>rhinoscleromatis</i>) and SL82. These sub-lineages have also demonstrated reduced carbon source utilization, which, in other species, has been linked with high loads of insertion sequences (ISs).<b>Methods.</b> We performed comparative genomics, analysed IS composition and loads and constructed genome-scale metabolic models for available public sequences from these four sub-lineages. These were then compared with other sub-lineages from the wider <i>K. pneumoniae</i> population.<b>Results.</b> The four focal sub-lineages displayed significantly higher IS loads (median range, 88-120 per genome) than other <i>K. pneumoniae</i> sub-lineages (median range, 12-73). Notably, each <i>K. pneumoniae</i> sub-lineage had unique IS profiles, consistent with distinct evolutionary trajectories of IS acquisition and expansion. Across sub-lineages, higher IS loads were inversely associated with the number of metabolic model genes per genome (R²=0.16; <i>P</i><0.001), as well as predicted aerobic substrate utilization for phosphorus sources (R²=0.39; <i>P</i><0.001), as per a second-degree polynomial regression model (<i>n</i>=1,664 genomes). Additionally, the four IS-dense sub-lineages displayed a combination of convergent, sub-lineage-specific substrate utilization losses, including the parallel loss of 3-phospho-d-glycerate, d-glycerate-2-phosphate and phosphoenolpyruvate utilization as carbon/phosphorus sources. Finally, inspection of IS insertion sites demonstrated frequent and non-destructive insertion next to transcriptional, carbohydrate and amino acid metabolism genes.<b>Conclusions.</b> IS accumulation in <i>K. pneumoniae</i> was significantly associated with reduced metabolic substrate usage, consistent with an inverse relationship between IS load and metabolic capacity. Despite these losses, the affected lineages still demonstrate substantial metabolic breadth, consistent with early-stage, ongoing reductive evolution.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12828178/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146018989","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":"A public resource of 15 genomically characterized representative strains of <i>Shigella sonnei</i>.","authors":"Sydney L Miles, Jane Hawkey, Ben Vezina, Vincenzo Torraca, Claire Jenkins, François-Xavier Weill, Stephen Baker, Kate S Baker, Serge Mostowy, Kathryn E Holt","doi":"10.1099/mgen.0.001596","DOIUrl":"10.1099/mgen.0.001596","url":null,"abstract":"<p><p><i>Shigella sonnei</i> is rapidly emerging as the dominant agent of shigellosis, an enteric disease responsible for a significant burden of morbidity and mortality worldwide. Whole-genome sequencing of <i>S. sonnei</i> isolated over the last three decades has revealed phylogenomic diversity within the population and the emergence of multiple lineages associated with distinct epidemiological patterns such as resistance to critical antimicrobials and/or transmission within different groups. However, most experimental work on <i>S. sonnei</i> biology and pathogenicity has focused on a single laboratory strain (53G), which is phylogenetically distant from currently circulating strains. Here, we introduce a set of phylogenetically diverse and epidemiologically relevant <i>S. sonnei</i> isolates made available through publicly accessible culture collections as a resource for laboratory science. We present their complete whole-genome sequences, including the pINV invasion plasmid (missing from a large proportion of public genome data due to loss during laboratory culture). Finally, the characterization and comparison of these complete genome sequences highlight evidence for ongoing adaptive evolution in <i>S. sonnei</i>, featuring the accumulation of insertion sequences, gene pseudogenization and structural variation.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12795559/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145952611","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}