{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T23:45:32Z","timestamp":1790639132682,"version":"4.1.0"},"reference-count":48,"publisher":"Microbiology Society","issue":"10","license":[{"start":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T00:00:00Z","timestamp":1760659200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Wellcome","award":["206194"],"award-info":[{"award-number":["206194"]}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"crossref","award":["INV-003570"],"award-info":[{"award-number":["INV-003570"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001061","name":"Rebecca L. Cooper Medical Research Foundation","doi-asserted-by":"crossref","award":["Rebecca Cooper Fellowship"],"award-info":[{"award-number":["Rebecca Cooper Fellowship"]}],"id":[{"id":"10.13039\/501100001061","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,10,17]]},"abstract":"<jats:p>\n                    The unprecedented number of\n                    <jats:italic>Streptococcus pneumoniae<\/jats:italic>\n                    (the pneumococcus) genomes sequenced in recent years has accelerated the discovery of novel serotypes and highlighted the genetic diversity both between and within each serotype. A novel serotype should demonstrate a distinct\n                    <jats:italic>cps<\/jats:italic>\n                    locus, capsular structure and serological profile. In only the past 4\u2009years, nine new serotypes have been identified. Accurate and timely serotyping of pneumococcal isolates is key to understanding their global distribution, evolution and the response of the bacterial population to vaccination. However, current bioinformatics serotyping tools are infrequently updated and struggle to accommodate the rapid discovery of new serotypes in a timely manner. To address these limitations, we built a comprehensive and curated library (SeroBAnk) encompassing all known pneumococcal serotypes; this resource is presented as an atlas on a dedicated publicly accessible webpage (\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/www.pneumogen.net\/gps\/\" xlink:type=\"simple\">https:\/\/www.pneumogen.net\/gps\/<\/jats:ext-link>\n                    <jats:named-content content-type=\"#000000\">#\/serobank<\/jats:named-content>\n                    ). Building upon this resource, we developed SeroBA(v2.0), a tool with an easy-to-update database that can accurately identify 102 of 107 known pneumococcal serotypes (except for serotypes 24B, 24C, 24F, 7D and 6H) and 18 genetic subtypes within serotypes 6A, 6B, 11A, 19A, 19F and 33F. We validated SeroBA(v2.0) on 26,306 genomes from the Global Pneumococcal Sequencing project, reference isolates and simulated reads derived from the reference genetic sequences of capsular polysaccharide biosynthetic (\n                    <jats:italic>cps<\/jats:italic>\n                    ) locus. We showed that SeroBA(v2.0) can reliably detect the nine recently discovered serotypes. Additionally, we show that\n                    <jats:italic>in silico<\/jats:italic>\n                    serotypes inferred by SeroBA(v2.0) had high concordance with phenotypic serotypes determined by either Quellung or latex agglutination at the serotype level (88.9%; 15,945\/17,933) and at the serogroup level (91.9%; 16,480\/17,933). Finally, we propose a community-contribution-based approach to ensure that SeroBA(v2.0) is maintained and updated as novel serotypes continue to be discovered. The global community can submit putative novel serotypes through our public repository on GitHub (\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/GlobalPneumoSeq\/seroba\/issues\" xlink:type=\"simple\">https:\/\/github.com\/GlobalPneumoSeq\/seroba\/issues<\/jats:ext-link>\n                    ). The submitted putative novel serotypes will be curated based on the genetic sequence of the\n                    <jats:italic>cps<\/jats:italic>\n                    region, capsular structure and serological profile by people of relevant expertise in the field. SeroBA(v2.0) can be accessed at\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/GlobalPneumoSeq\/seroba\" xlink:type=\"simple\">https:\/\/github.com\/GlobalPneumoSeq\/seroba<\/jats:ext-link>\n                    <jats:named-content content-type=\"#000000\">.<\/jats:named-content>\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.001483","type":"journal-article","created":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T14:16:52Z","timestamp":1760710612000},"source":"Crossref","is-referenced-by-count":5,"title":["SeroBA(v2.0) and SeroBAnk: a robust genome-based serotyping scheme and comprehensive atlas of capsular diversity in Streptococcus pneumoniae"],"prefix":"10.1099","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3018-4336","authenticated-orcid":false,"given":"Oliver","family":"Lorenz","sequence":"first","affiliation":[{"name":"Parasites and Microbes, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4100-3657","authenticated-orcid":false,"given":"Alannah C.","family":"King","sequence":"additional","affiliation":[{"name":"Parasites and Microbes, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-3857-5242","authenticated-orcid":false,"given":"Harry C. H.","family":"Hung","sequence":"additional","affiliation":[{"name":"Parasites and Microbes, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1250-4604","authenticated-orcid":false,"given":"Feroze A.","family":"Ganaie","sequence":"additional","affiliation":[{"name":"Division of Pulmonary\/Allergy\/Critical Care, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6015-0279","authenticated-orcid":false,"given":"Anne L.","family":"Wyllie","sequence":"additional","affiliation":[{"name":"Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7694-9605","authenticated-orcid":false,"given":"Sam","family":"Manna","sequence":"additional","affiliation":[{"name":"Department of Paediatrics, The University of Melbourne, Melbourne, Australia"},{"name":"Infection, Immunity, and Global Health, Murdoch Children\u2019s Research Institute, Melbourne, Australia"},{"name":"Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3164-8849","authenticated-orcid":false,"given":"Catherine","family":"Satzke","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia"},{"name":"Infection, Immunity, and Global Health, 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