Microbial Genomics最新文献

{"title":"Integrating genomic and transcriptomic analyses reveals virulence factors and bloodstream infection mechanisms of <i>Acinetobacter junii</i>.","authors":"Chenlu Xiao, Shuo Jiang, Zhenwei Guo, Pak-Leung Ho, Jing Dai, Huiluo Cao, Zhitao Yang","doi":"10.1099/mgen.0.001749","DOIUrl":"10.1099/mgen.0.001749","url":null,"abstract":"<p><p><i>Acinetobacter junii</i>, an emerging pathogen of the <i>Acinetobacter</i> genus, exhibits concerning environmental persistence and clinical virulence potential. Despite its growing significance in bloodstream infections (BSIs), the genetic determinants distinguishing pathogenic from environmental strains remain poorly characterized, limiting our understanding of its transmission dynamics and host adaptation mechanisms. We explored the diversity and population structure of <i>A. junii</i> using a comprehensive genome dataset, including four strains isolated from China, one of which (acj0210) was derived from BSIs. We analysed the pangenome of <i>A. junii</i> and characterized its virulence and antibiotic resistance profile. Bacterial genome-wide association studies (bGWAS) were performed to identify the virulence potential. The virulence potential for BSIs was further investigated through RNA-seq analysis under different conditions. Additionally, transmission dynamics of <i>bla</i> _NDM-carrying plasmids in carbapenem-resistant <i>A. junii</i> were inferred from plasmid network analysis. We identified seven lineages within <i>A. junii</i>, with BAPS1 as the dominant group. Discrepancies in accessory genes were observed between lineages, along with unique genes, particularly one novel capsular polysaccharide variant in acj0210. Using bGWAS, we uncovered key genetic differences, including transporter-encoding genes (<i>tauA</i>, <i>urtD</i>), regulatory mutations and exopolysaccharide-encoding genes that distinguish human and environmental strains. Transcriptomic analysis revealed potential virulence factors in BSIs, with distinct gene expression patterns between blood and immune cells, despite shared fatty acid metabolism profiles. As critical resistance determinants, <i>bla</i> _NDM genes may have been acquired from <i>A. baumannii. A. junii</i> has adapted to diverse geographical and ecological niches, particularly in BSIs, with lineage-specific virulence factors aligned with antibiotic resistance genes, especially those carried by <i>bla</i> _NDM harbouring plasmids.</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":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148619906","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":"Mitogenomics in <i>Amanita</i>, evolution, species delimitation and its utility at the species complex level.","authors":"Christian Quintero-Corrales, Roberto Garibay-Orijel","doi":"10.1099/mgen.0.001792","DOIUrl":"10.1099/mgen.0.001792","url":null,"abstract":"<p><p>Mitochondrial genomes are among the most powerful sources for resolving evolutionary relationships in eukaryotes; however, their application in fungal phylogenetics remains underutilized. In this study, we employed comparative genomics and phylogenomics to evaluate the utility of the mitogenome within the genus <i>Amanita</i>, specifically at the species complex level. Our results demonstrate that mitochondrial coding regions provide robust species-level resolution, while structural features - including intron dynamics, synteny breaks and ORFs - reveal evolutionary trajectories often obscured by traditional nuclear markers. We identified highly variable gene synteny patterns and significant fluctuations in intron and ORF content, particularly within the <i>cob</i> and <i>cox1</i> loci. Notably, these mitogenomic features varied considerably even among closely related species within the same section. Our findings underscore the dual utility of the mitochondrial genome for both interspecific inference and the identification of new cryptic lineages within established species complexes. Furthermore, we report a significant mitonuclear discordance, suggesting complex evolutionary histories such as ancestral hybridization or incomplete lineage sorting. These results highlight the necessity of integrating mitogenomics into fungal systematics to improve our understanding of species boundaries and evolutionary dynamics.</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/PMC13424474/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148631027","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":"Evolutionary dynamics of the multidrug-resistant <i>Salmonella</i> Infantis harbouring the pESI megaplasmid across Europe.","authors":"Patricia Alba, Elena Lavinia Diaconu, Virginia Carfora, Antonio Battisti, Alessia Franco, Pieter-Jan Ceyssens, Cristina Graells-Garcia, Jannice Schau Slettemeås, Magdalena Zając, Magdalena Skarżyńska, Dariusz Wasyl, Lurdes Clemente, Manuela Caniça, Vera Manageiro, Stefan Börjesson, Eelco Franz, Emma Östlund, Robert Söderlund, Aurora Garcia-Fernandez, Laura Villa","doi":"10.1099/mgen.0.001787","DOIUrl":"10.1099/mgen.0.001787","url":null,"abstract":"<p><p>Multidrug-resistant <i>Salmonella enterica</i> subsp. <i>enterica</i> serovar Infantis clone, harbouring the pESI megaplasmid, first described in Israel in 2014, is consistently reported in poultry and humans worldwide. This study aimed to investigate the genomic epidemiology of <i>S</i>. Infantis collected by nine European Public Health Institutions from samples of different origins (human, food and animal sources) and understand the evolutionary dynamics of pESI-like in Europe. The resolved pESI-like sequences have also been compared with complete publicly available pESI-like sequences from other countries, in a One Health context. The circulation of a <i>S</i>. Infantis clone in Europe carrying the mosaic megaplasmid pESI-like has been associated with resistance to sulphonamides (<i>sul</i>)<i>,</i> tetracycline (<i>tet</i>)<i>,</i> streptomycin and spectinomycin (<i>aadA1</i>). In recent years, <i>bla</i> _CTX-M-1-positive pESI-like plasmids have been increasingly detected in the extended-spectrum beta-lactamase-producing <i>S</i>. Infantis clone. Using a combined short- and long-read sequencing approach, two main types of pESI variants have been identified, differing in the accessory gene content, including the <i>bla</i> _CTX-M variant, indicating a certain stability of pESI variants detected in different geographical regions and sources over time (2011-2021). Moreover, the differences were related to the acquisition of resistance, virulence or fitness-enhancing genes that would potentially benefit the <i>Salmonella</i> host.</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/PMC13361800/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148430649","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":"Comparative genomics and methylome profiling of <i>Pseudolactococcus laudensis</i> reveal signatures of niche adaptation and strain-level variation in mobile genetic elements and phage defence.","authors":"Axel Soto-Serrano, Tamas Vincze, Richard J Roberts, Lukasz Krych, Jennifer Mahony, Paulina Deptula","doi":"10.1099/mgen.0.001779","DOIUrl":"10.1099/mgen.0.001779","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Pseudolactococcus laudensis&lt;/i&gt; (formerly named &lt;i&gt;Lactococcus laudensis&lt;/i&gt;) is an emerging lactic acid bacterium first isolated from raw milk in 2015 and subsequently detected in vegetables and dairy mesophilic starter cultures. Despite its recurrent isolation from diverse environments, the genetic basis of its niche adaptation, horizontal gene transfer and phage defence remains unexplored. Here, we perform the first comparative genomic and epigenomic analysis of &lt;i&gt;P. laudensis&lt;/i&gt; using complete genomes of a plant-derived isolate (MCRI-603), a milk isolate (DSM 28961) and 20 strains from a Danish dairy mesophilic starter culture. Genomes were annotated and analysed using pangenomics, Clustering of Orthologous Genes and methylome profiling. Average nucleotide identity, pangenome and Clustering of Orthologous Genes analyses revealed niche-associated structure: dairy starter strains formed a tight cluster, while the plant isolate MCRI-603 and milk isolate DSM 28961 were more similar to each other than to the starter culture group. The pangenome comprised 4,946 genes, with 1,396 core genes. Dairy starter strains showed markedly elevated numbers of insertion sequences, pseudogenes, plasmids and genomic islands relative to MCRI-603, which was plasmid-free and carried very few insertion sequence elements or genomic islands. DSM 28961 displayed pseudogene count similar to the dairy starter strains but markedly fewer transposases. These patterns are consistent with a plant-associated origin of &lt;i&gt;P. laudensis&lt;/i&gt; and progressive dairy specialization via mobile genetic element acquisition. The &lt;i&gt;P. laudensis&lt;/i&gt; mobilome was found to carry key niche-related traits. Lactose utilization operons were plasmid-encoded, whereas exopolysaccharide-encoding loci, &lt;i&gt;opp&lt;/i&gt; oligopeptide transport systems and several defence loci, including clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas), were consistently encoded within chromosomal integrative elements. All strains harboured prophage-like elements, including putatively intact prophages in 13 of them, and ~67% of 238 predicted antiphage systems resided on mobile genetic elements, underscoring their central role in phage defence. Restriction-modification systems dominated the defensome, and three strains encoded CRISPR-Cas systems (including type III-A and type I-C), indicating a higher prevalence than has been reported for &lt;i&gt;Lactococcus lactis&lt;/i&gt; and &lt;i&gt;Lactococcus cremoris&lt;/i&gt;, where CRISPR-Cas has rarely been observed. Methylome analysis identified 43 distinct motifs, of which 25 were novel. The &lt;i&gt;P. laudensis&lt;/i&gt; methylome was overwhelmingly dominated by N⁶-methyladenine, and most motifs were short, non-palindromic and largely associated with type III restriction-modification systems and some type I and II subtypes. Nearly all strains exhibited distinct methylation profiles, including those isolated from the same dairy starter culture, highlig","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/PMC13335696/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148391284","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":"Whole-genome sequencing of <i>Staphylococcus capitis</i> isolates from neonates with healthcare-associated bacteraemia in neonatal intensive care units in Taiwan: comparison between the NRCS-A strain and a non-NRCS-A multi-resistant strain.","authors":"Yu-Rou Yeh, Yi-Hsuan Huang, Chih-Jung Chen, Rey-In Lien, Ming-Chou Chiang, Yhu-Chering Huang","doi":"10.1099/mgen.0.001798","DOIUrl":"10.1099/mgen.0.001798","url":null,"abstract":"<p><p><i>Staphylococcus capitis</i> is a common pathogen causing late-onset sepsis in neonatal intensive care units (NICUs). A specific clone, <i>S. capitis</i> NRCS-A, which was first reported in 2012 from France, is spreading globally in NICU settings. The present study was carried out to explore the molecular characteristics and clinical features of <i>S. capitis</i> bacteraemia among infants hospitalized in NICUs in Taiwan. We retrieved and molecularly characterized 191 <i>S. capitis</i> bloodstream isolates from hospitalized patients of a medical centre in Taiwan between 2014 and 2021, with whole-genome sequencing (WGS) for 79 isolates. Seventy-three isolates were identified from 65 infants in neonatal units and 118 isolates from inpatients staying outside the neonatal units (non-neonates). Seventy-one (97%) of the 73 neonate isolates were characterized to 2 major pulsotypes: 16 out of 73 (22%) were pulsotype 300 which was similar to that of the NRCS-A strain, and 55 isolates were pulsotype 1300, while 27 pulsotypes were identified from 118 non-neonatal isolates. Seventy (96%) of 73 neonatal isolates were oxacillin-resistant. Of the 73 neonatal isolates and 6 selective non-neonatal isolates (pulsotype 300 for 5 isolates) selected for WGS, 69 neonatal isolates and 5 non-neonatal isolates clustered into four major clades (A to D), corresponding to the two major pulsotypes, 300 and 1300. By phylogenetic analysis, 15 neonatal isolates and 5 non-neonatal isolates, sharing pulsotype 300 and clades C/D, were embedded within the international isolates of the previously designated pandemic outbreak clone of the NRCS-A strain and also carried NRCS-A strain-related marker genes, confirmed as the NRCS-A strain. In addition to resistance to oxacillin and penicillin, the dominant clone (non-NRCS-A strain) exhibited additional resistance to erythromycin and clindamycin. Conclusively, in contrast to diverse genetic characteristics among non-neonatal isolates, over 95% of <i>S. capitis</i> bloodstream isolates from neonates in Taiwanese NICUs were resistant to oxacillin and belonged to two major clones, including the NRCS-A strain. The dominant clone was a non-NRCS-A strain and exhibited broader antibiotic resistance. Further surveillance is needed.</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/PMC13435550/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148620193","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":"Phylogenetically diverse Mucorales<i>-Mycetohabitans</i> endosymbiotic interactions identified from whole-genome sequencing using a targeted metagenomic assembly pipeline.","authors":"Jack B Gregory, Jamie W Harrison, Jessie K Uehling, Rhys A Farrer, Elizabeth R Ballou","doi":"10.1099/mgen.0.001746","DOIUrl":"10.1099/mgen.0.001746","url":null,"abstract":"<p><p>Endosymbiotic bacteria of the genus <i>Mycetohabitans</i> are obligate intracellular associates of Mucorales fungi, yet the understanding of their diversity, distribution and evolutionary dynamics is in its infancy. By screening 1,696 public sequencing datasets from Mucorales fungi, we detected <i>Mycetohabitans</i> in 46 fungal accessions spanning 5 host taxa across the fungal genera <i>Rhizopus</i> and <i>Apophysomyces</i>. These included 13 previously unreported associations. Genome reconstruction yielded 38 <i>Mycetohabitans</i> metagenome-assembled genomes (MAGs), of which 34 were of high quality. Incorporating these MAGs into genome-based species delimitation expanded known <i>Mycetohabitans</i> diversity from four to nine species-level clusters, including novel host-associated lineages. Re-examination of fungal host identities revealed frequent misidentification of isolates in fungal collection catalogues and/or misannotation in GenBank, with nearly a quarter of positive datasets requiring correction through internal transcribed spacer and genome-scale verification. Host-symbiont associations were non-random under this revised framework, with significant structure detected by contingency analysis and ParaFit. MAG-focused pangenome analysis revealed an open pangenome and mosaic lineage-associated functional traits, including variation in metabolism, secretion, cell-envelope systems, metal resistance, antimicrobial-resistance-associated functions and mobile elements. The most distinctive lineage comprised two <i>Apophysomyces</i>-associated MAGs, provisionally named <i>M. apophysomyceticola</i>, which showed pronounced genome reduction compared with other sampled <i>Mycetohabitans</i> spp. and loss of multiple central metabolic, nutrient assimilation, cofactor biosynthesis, catabolic, stress-response and defence pathways, consistent with reduced metabolic flexibility and increased host dependence. Together, these results show that <i>Mycetohabitans</i> symbioses are more geographically widespread, taxonomically diverse and functionally differentiated than previously recognized. More broadly, this work demonstrates the value of public sequencing repositories for uncovering hidden fungal-bacterial symbioses, while emphasizing that repository-derived patterns must be interpreted considering host misidentification, uneven sampling and incomplete metadata. Overall, our work establishes a global framework for <i>Mycetohabitans</i> diversity and function, with implications for fungal ecology, evolution and clinical mycology.</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/PMC13367373/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148437560","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":"Reproducible profiling of the gut microbiota using surplus clinical faecal immunochemical test samples.","authors":"Merel A van den Haak, Jakub T Zbikowski, Aliu Moomin, Joan Wilson, Chris Halsey, Charlie Gourley, Farhat Vn Din, Stephen T McSorley, Elaina S R Collie-Duguid, Graham Horgan, Alan W Walker, Alexandra M Johnstone, Anne E Kiltie","doi":"10.1099/mgen.0.001740","DOIUrl":"https://doi.org/10.1099/mgen.0.001740","url":null,"abstract":"<p><p><b>Background.</b> Numerous countries use the EXTEL HEMO-AUTO MC quantitative faecal immunochemical test (qFIT) to screen for faecal haemoglobin. We aimed to determine if bacterial 16S rRNA gene sequencing results from the leftover qFIT cassettes would be stable over time and comparable with larger volume faecal collection protocols.<b>Methods.</b> Four qFIT probe samples were taken from each of sixteen fresh healthy volunteer stool samples, and sequencing results were compared after 0, 4, 7 and 14 days to provide a baseline control and mimic postage and sample processing conditions in cancer screening programmes. qFIT results were then compared to those of standard laboratory processing of larger whole-stool samples. DNA was extracted from 100 NHS surplus qFIT samples from symptomatic patients reporting rectal bleeding and quantified to assess suitability for 16S rRNA gene sequencing.<b>Results.</b> Bacterial composition and diversity from healthy volunteer qFITs remained stable over 14 days with only minor differences compared to baseline (day 0) and larger stool control samples; at least 75% of the symptomatic qFITs yielded sufficient DNA for 16S rRNA gene sequencing.<b>Conclusion.</b> qFIT samples were almost identical to control samples and stable over 14 days, allowing them to be used for large-scale, low-cost population-based intestinal microbiota studies.<b>Clinical Trial Registration.</b> The study was registered on clinicaltrials.gov (NCT06100549).</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":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148412323","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":"Phylogenetic analysis of serotype 19A-sequence type (ST)2331 <i>Streptococcus pneumoniae</i> associated with the Pneumococcal Molecular Epidemiology Network (PMEN)34 clone predominant in Japan after the introduction of the 7-valent pneumococcal conjugate vaccine (PCV7).","authors":"Shota Koide, Satoshi Nakano, Takao Fujisawa, Yutaka Ito, Bin Chang, Shigeru Suga, Yo Sugawara, Yukihiro Akeda, Motoyuki Sugai","doi":"10.1099/mgen.0.001808","DOIUrl":"10.1099/mgen.0.001808","url":null,"abstract":"<p><p>Following the introduction of the 7-valent pneumococcal conjugate vaccine (PCV7), serotype 19A <i>Streptococcus pneumoniae</i> emerged as a major cause of paediatric pneumococcal disease in Japan. Unlike global trends, in which multidrug-resistant serotype 19A-sequence type (ST)320 predominated, serotype 19A-ST2331 became one of the dominant lineages in Japan. The evolutionary origins of serotype 19A-ST2331 and the reasons for its domestic success remain unclear. To investigate the evolutionary origin and dissemination of the serotype 19A-ST2331 lineage, we analysed whole-genome sequences of 42 clonal complex (CC)2331 isolates collected in Japan between 2004 and 2017 and compared them with 825 genetically related global isolates. Phylogenetic analysis showed that Japanese serotype 19A-ST2331 isolates formed a distinct Japan-associated cluster within Global Pneumococcal Sequence Cluster 32 that was closely related to the globally disseminated Pneumococcal Molecular Epidemiology Network (PMEN)34 clone, typically represented by serotype 12F-ST218. Among the 42 Japanese CC2331 isolates, 40 were serotype 19A, whereas only two non-19A isolates were identified. Serotype 19A was absent from the 825 non-Japanese isolates, indicating that serotype 19A-ST2331 represents a globally rare, Japan-specific lineage. Most Japanese isolates remained susceptible to β-lactams, whereas 83.3% were erythromycin-resistant and carried either <i>mefA/E</i> or <i>ermB</i>. A highly clonal <i>mefA/E</i>-positive subclade was dated to a most recent common ancestor at ∼1998.5. These findings indicate that serotype 19A-ST2331 emerged before 2000 from an ST218-related ancestor through serotype switching and subsequently underwent local expansion in Japan. Although the ancestral intermediate was not represented in the present collection, the successful establishment of this clone may have been facilitated by the combined selective advantages conferred by the serotype 19A capsule and macrolide resistance in the post-PCV7 setting in Japan.</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/PMC13426510/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148631038","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":"Home is where the host is: evolutionary history of geographic spread, host switching and adaptive genomic signatures in two generalist group B <i>Streptococcus</i> clonal group.","authors":"Antonia Hilbig, Chiara Crestani, Timothy Barkham, Swaine L Chen, Jiaying Ho, Claudia Cobo-Angel, Alejandro Ceballos-Marquez, Wanna Sirimanapong, Syafinaz Amin-Nordin, Nguyen Ngoc Phuoc, Tatiana Castro Abreu Pinto, Laura Oliveira, Chiara Anna Garbarino, Matteo Ricchi, Tiziana Lembo, Samantha Lycett, Roman Biek, Taya Forde, Ruth Nicolet Zadoks","doi":"10.1099/mgen.0.001745","DOIUrl":"10.1099/mgen.0.001745","url":null,"abstract":"<p><p>Group B <i>Streptococcus</i> (GBS) is a pathogen of global relevance in neonatal and maternal disease as well as bovine mastitis. Two closely related clonal group, denoted 103 and 314 (CG103/314), have been detected in humans and cattle on multiple continents in recent decades but are poorly characterized compared to other host-generalist clades. We examined their potential origins, host-switching events and the presence of a suite of genetic markers for antimicrobial resistance, virulence and host association using a newly assembled dataset of 248 CG103/314 genomes from humans, cattle and food originating from five continents. We detected multiple host switches between humans and cattle and significant regional differences in antimicrobial resistance gene distribution, possibly reflecting local differences in antimicrobial use across countries and hosts and indicating a capacity for regional adaptation to selective pressures. Across the evolutionary history of CG103/314 from both host species, the prevalence of the Lac.2 operon, a genetic marker associated with bovine host adaptation, was high, whereas the prevalence of the <i>scpB-lmb</i> gene pair, a genetic marker of human host adaptation in other GBS clonal group, was very low. All isolates with <i>scpB-lmb</i> were associated with human disease rather than carriage. Our dataset displayed biases typical of research into multi-host pathogens, when sampling is often focused on a specific host species or setting. Consistent, balanced, contemporaneous and sympatric sampling efforts across host species and sources are needed to fully understand the distribution and emergence of CG103/314 and similar multi-host pathogens that impact food safety and public health.</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/PMC13398308/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148562484","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":"New isolates from the 1970s to early 2000s provide insights into the evolution of <i>Acinetobacter baumannii</i> international clone 2 and its resistome.","authors":"Matthew Neil, Frédéric Grenier, Nancy Allard, Gemma C Langridge, Santiago Castillo-Ramírez, Louis-Patrick Haraoui, Benjamin A Evans","doi":"10.1099/mgen.0.001752","DOIUrl":"10.1099/mgen.0.001752","url":null,"abstract":"<p><p><i>Acinetobacter baumannii</i> remains a pervasive nosocomial pathogen, with international clone 2 (IC2) being the most successful lineage. IC2 is often discussed as a singular entity, and the genomic factors behind its success over other lineages are poorly characterized. This study aimed to track genomic changes occurring around the expansion of IC2 and further determine the within-clone population structure. A set of historical <i>A. baumannii</i> isolates from the 1970s to early 2000s was long-read sequenced and assembled into high-quality chromosomes. These were then used to supplement publicly available <i>A. baumannii</i> genomes, producing a dataset of 1,281 chromosomes derived from isolates collected across 6 continents. A recombination-free phylogeny was produced and combined with antimicrobial resistance gene presence/absence data. Analysis showed that IC2 became the dominant lineage around 2005, which coincides with the acquisition of <i>oxa23</i> and AbGRI3. Further, IC2 can be split into at least four distinct groups. Groups 1, 2 and 3 represent incremental evolution of the <i>A. baumannii</i> chromosome over time, while group 4 represents a separate evolutionary path distinct from the main IC2 lineage, which has recently been isolated at higher frequency.</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/PMC13324835/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148369128","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}