{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T15:22:09Z","timestamp":1789572129305,"version":"build-2803163510"},"reference-count":45,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,5,15]],"date-time":"2025-05-15T00:00:00Z","timestamp":1747267200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100009947","name":"Merck Sharp & Dohme Ltd","doi-asserted-by":"publisher","award":["IIS 61354"],"award-info":[{"award-number":["IIS 61354"]}],"id":[{"id":"10.13039\/100009947","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009633","name":"National Institute of Child Health and Human Development","doi-asserted-by":"publisher","award":["5T32HD040128-20"],"award-info":[{"award-number":["5T32HD040128-20"]}],"id":[{"id":"10.13039\/100009633","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000071","name":"National Institute of Child Health and Human Development","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000071","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004319","name":"Pfizer","doi-asserted-by":"publisher","award":["5T32HD040128-20"],"award-info":[{"award-number":["5T32HD040128-20"]}],"id":[{"id":"10.13039\/100004319","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["thelancet.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["eBioMedicine"],"published-print":{"date-parts":[[2025,7]]},"DOI":"10.1016\/j.ebiom.2025.105781","type":"journal-article","created":{"date-parts":[[2025,6,3]],"date-time":"2025-06-03T19:58:15Z","timestamp":1748980695000},"page":"105781","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":6,"special_numbering":"C","title":["CC180 clade dynamics do not universally explain Streptococcus pneumoniae serotype 3 persistence post-vaccine: a global comparative population genomics study"],"prefix":"10.1016","volume":"117","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6386-2415","authenticated-orcid":false,"given":"Sydney","family":"Stanley","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catarina","family":"Silva-Costa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3658-1102","authenticated-orcid":false,"given":"Joana","family":"Gomes-Silva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jose","family":"Melo-Cristino","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8688-3398","authenticated-orcid":false,"given":"Richard","family":"Malley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4084-6233","authenticated-orcid":false,"given":"Mario","family":"Ramirez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"11","key":"10.1016\/j.ebiom.2025.105781_bib1","doi-asserted-by":"crossref","first-page":"1191","DOI":"10.1016\/S1473-3099(18)30310-4","article-title":"Estimates of the global, regional, and national morbidity, mortality, and aetiologies of lower respiratory infections in 195 countries, 1990\u20132016: a systematic analysis for the Global Burden of Disease Study 2016","volume":"18","author":"Troeger","year":"2018","journal-title":"Lancet Infect Dis"},{"issue":"7","key":"10.1016\/j.ebiom.2025.105781_bib2","doi-asserted-by":"crossref","first-page":"e744","DOI":"10.1016\/S2214-109X(18)30247-X","article-title":"Burden of Streptococcus pneumoniae and Haemophilus influenzae type b disease in children in the era of conjugate vaccines: global, regional, and national estimates for 2000\u201315","volume":"6","author":"Wahl","year":"2018","journal-title":"Lancet Global Health"},{"issue":"1","key":"10.1016\/j.ebiom.2025.105781_bib3","article-title":"Prognostic factors for mortality in invasive pneumococcal disease in adult: a system review and meta-analysis","volume":"11","author":"Chen","year":"2021","journal-title":"Sci Rep"},{"issue":"3","key":"10.1016\/j.ebiom.2025.105781_bib4","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1016\/S1473-3099(14)71081-3","article-title":"Effect of use of 13-valent pneumococcal conjugate vaccine in children on invasive pneumococcal disease in children and adults in the USA: analysis of multisite, population-based surveillance","volume":"15","author":"Moore","year":"2015","journal-title":"Lancet Infect Dis"},{"key":"10.1016\/j.ebiom.2025.105781_bib5","doi-asserted-by":"crossref","first-page":"100913","DOI":"10.1016\/j.lanepe.2024.100913","article-title":"Evolution of invasive pneumococcal disease by serotype 3 in adults: a Spanish three-decade retrospective study","volume":"41","author":"Calvo-Silveria","year":"2024","journal-title":"Lancet Reg Health Eur"},{"issue":"4","key":"10.1016\/j.ebiom.2025.105781_bib6","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1016\/S1473-3099(18)30052-5","article-title":"Rapid increase in non-vaccine serotypes causing invasive pneumococcal disease in England and Wales, 2000\u201317: a prospective national observational cohort study","volume":"18","author":"Ladhani","year":"2018","journal-title":"Lancet Infect Dis"},{"issue":"3","key":"10.1016\/j.ebiom.2025.105781_bib7","doi-asserted-by":"crossref","first-page":"e1062","DOI":"10.1093\/cid\/ciac475","article-title":"Distribution of serotypes causing invasive pneumococcal disease in children from high- income countries and the impact of pediatric pneumococcal vaccination","volume":"76","author":"Grant","year":"2023","journal-title":"Clin Infect Dis"},{"key":"10.1016\/j.ebiom.2025.105781_bib8","doi-asserted-by":"crossref","first-page":"1616","DOI":"10.3389\/fmicb.2016.01616","article-title":"Portuguese group for the study of Streptococcal Infections. Serotype 3 remains the leading cause of invasive pneumococcal disease in adults in Portugal (2012\u20132014) despite continued reductions in other 13-valent conjugate vaccine serotypes","volume":"7","author":"Hor\u00e1cio","year":"2016","journal-title":"Front Microbiol"},{"key":"10.1016\/j.ebiom.2025.105781_bib9","doi-asserted-by":"crossref","DOI":"10.3389\/fpubh.2023.1279656","article-title":"Adult non-invasive pneumococcal pneumonia in Portugal is dominated by serotype 3 and non-PCV13 serotypes 3-years after near universal PCV13 use in children","volume":"11","author":"Silva-Costa","year":"2023","journal-title":"Front Public Health"},{"key":"10.1016\/j.ebiom.2025.105781_bib10","doi-asserted-by":"crossref","DOI":"10.1016\/j.jinf.2024.106242","article-title":"Rebound of pediatric invasive pneumococcal disease in Portugal after the COVID-19 pandemic was not associated with significant serotype changes","volume":"89","author":"Silva-Costa","year":"2024","journal-title":"J Infect"},{"issue":"4","key":"10.1016\/j.ebiom.2025.105781_bib11","doi-asserted-by":"crossref","DOI":"10.1128\/spectrum.01077-22","article-title":"Continued vaccine breakthrough cases of serotype 3 complicated pneumonia in vaccinated children, Portugal (2016\u20132019)","volume":"10","author":"Silva-Costa","year":"2022","journal-title":"Microbiol Spectr"},{"key":"10.1016\/j.ebiom.2025.105781_bib12","doi-asserted-by":"crossref","DOI":"10.3389\/fcimb.2020.613287","article-title":"Sugar-coated killer: serotype 3 pneumococcal disease","volume":"10","author":"Luck","year":"2020","journal-title":"Front Cell Infect Microbiol"},{"issue":"11","key":"10.1016\/j.ebiom.2025.105781_bib13","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1007438","article-title":"Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci","volume":"14","author":"Azarian","year":"2018","journal-title":"PLoS Pathog"},{"issue":"11","key":"10.1016\/j.ebiom.2025.105781_bib14","doi-asserted-by":"crossref","first-page":"845","DOI":"10.3390\/genes10110845","article-title":"Evolution of Streptococcus pneumoniae serotype 3 in England and Wales: a major vaccine evader","volume":"10","author":"Groves","year":"2019","journal-title":"Genes"},{"issue":"5","key":"10.1016\/j.ebiom.2025.105781_bib15","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1016\/S1473-3099(23)00706-5","article-title":"Invasive pneumococcal disease 3 years after introduction of a reduced 1+ 1 infant 13-valent pneumococcal conjugate vaccine immunisation schedule in England: a prospective national observational surveillance study","volume":"24","author":"Bertran","year":"2024","journal-title":"Lancet Infect Dis"},{"issue":"1","key":"10.1016\/j.ebiom.2025.105781_bib16","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1186\/s13073-022-01147-2","article-title":"Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA","volume":"14","author":"Kwun","year":"2022","journal-title":"Genome Med"},{"key":"10.1016\/j.ebiom.2025.105781_bib17","series-title":"The European committee on antimicrobial susceptibility testing. Breakpoint tables for interpretation of MICs and zone diameters","year":"2020"},{"key":"10.1016\/j.ebiom.2025.105781_bib18","series-title":"Performance standards for antimicrobial susceptibility testing","year":"2022"},{"issue":"4","key":"10.1016\/j.ebiom.2025.105781_bib19","doi-asserted-by":"crossref","first-page":"502","DOI":"10.1093\/bioinformatics\/btq696","article-title":"Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq","volume":"27","author":"Wu","year":"2011","journal-title":"Bioinformatics"},{"issue":"3","key":"10.1016\/j.ebiom.2025.105781_bib20","doi-asserted-by":"crossref","first-page":"e15","DOI":"10.1093\/nar\/gku1196","article-title":"Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins","volume":"43","author":"Croucher","year":"2015","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"10.1016\/j.ebiom.2025.105781_bib21","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol Biol Evol"},{"issue":"3","key":"10.1016\/j.ebiom.2025.105781_bib22","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2\u2013approximately maximum-likelihood trees for large alignments","volume":"5","author":"Price","year":"2010","journal-title":"PLoS One"},{"key":"10.1016\/j.ebiom.2025.105781_bib23","article-title":"Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool","volume":"13","author":"Letunic","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"10.1016\/j.ebiom.2025.105781_bib24","doi-asserted-by":"crossref","first-page":"124","DOI":"10.12688\/wellcomeopenres.14826.1","article-title":"Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications","volume":"3","author":"Jolley","year":"2018","journal-title":"Wellcome Open Res"},{"issue":"9","key":"10.1016\/j.ebiom.2025.105781_bib25","doi-asserted-by":"crossref","first-page":"1395","DOI":"10.1101\/gr.232397.117","article-title":"GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens","volume":"28","author":"Zhou","year":"2018","journal-title":"Genome Res"},{"issue":"2","key":"10.1016\/j.ebiom.2025.105781_bib26","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1101\/gr.241455.118","article-title":"Fast and flexible bacterial genomic epidemiology with PopPUNK","volume":"29","author":"Lees","year":"2019","journal-title":"Genome Res"},{"issue":"10","key":"10.1016\/j.ebiom.2025.105781_bib27","article-title":"ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads","volume":"3","author":"Hunt","year":"2017","journal-title":"Microbial Genom"},{"issue":"1","key":"10.1016\/j.ebiom.2025.105781_bib28","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1128\/AAC.01310-13","article-title":"ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes","volume":"58","author":"Gupta","year":"2014","journal-title":"Antimicrob Agents Chemother"},{"issue":"D1","key":"10.1016\/j.ebiom.2025.105781_bib29","doi-asserted-by":"crossref","first-page":"D690","DOI":"10.1093\/nar\/gkac920","article-title":"CARD 2023: expanded curation, support for machine learning, and resistome prediction at the comprehensive antibiotic resistance database","volume":"51","author":"Alcock","year":"2023","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"10.1016\/j.ebiom.2025.105781_bib30","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1128\/mBio.00756-16","article-title":"Penicillin-binding protein transpeptidase signatures for tracking and predicting \u03b2-lactam resistance levels in Streptococcus pneumoniae","volume":"7","author":"Li","year":"2016","journal-title":"mBio"},{"key":"10.1016\/j.ebiom.2025.105781_bib31","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2021.649969","article-title":"BacAnt: a combination annotation server for bacterial DNA sequences to identify antibiotic resistance genes, integrons, and transposable elements","volume":"12","author":"Hua","year":"2021","journal-title":"Front Microbiol"},{"issue":"1","key":"10.1016\/j.ebiom.2025.105781_bib32","article-title":"PhaBOX: a web server for identifying and characterizing phage contigs in metagenomic data","volume":"3","author":"Shang","year":"2023","journal-title":"Bioinform Adv"},{"issue":"14","key":"10.1016\/j.ebiom.2025.105781_bib33","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ebiom.2025.105781_bib34","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-020-02090-4","article-title":"Producing polished prokaryotic pangenomes with the Panaroo pipeline","volume":"21","author":"Tonkin-Hill","year":"2020","journal-title":"Genome Biol"},{"issue":"24","key":"10.1016\/j.ebiom.2025.105781_bib35","doi-asserted-by":"crossref","first-page":"4310","DOI":"10.1093\/bioinformatics\/bty539","article-title":"Pyseer: a comprehensive tool for microbial pangenome-wide association studies","volume":"34","author":"Lees","year":"2018","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ebiom.2025.105781_bib36","doi-asserted-by":"crossref","DOI":"10.3389\/fcimb.2022.824449","article-title":"Extensive\/multidrug-resistant pneumococci detected in clinical respiratory tract samples in Southern Sweden are closely related to international multidrug-resistant lineages","volume":"12","author":"Yamba Yamba","year":"2022","journal-title":"Front Cell Infect Microbiol"},{"issue":"7","key":"10.1016\/j.ebiom.2025.105781_bib37","doi-asserted-by":"crossref","first-page":"1428","DOI":"10.3390\/microorganisms9071428","volume":"9","author":"Silva-Costa","year":"2021","journal-title":"Microorganisms"},{"issue":"22","key":"10.1016\/j.ebiom.2025.105781_bib38","doi-asserted-by":"crossref","DOI":"10.1016\/j.vaccine.2024.126219","article-title":"Streptococcus pneumoniae carriage, serotypes, genotypes, and antimicrobial resistance trends among children in Portugal, after introduction of PCV13 in national immunization program: a cross-sectional study","volume":"42","author":"Candeias","year":"2024","journal-title":"Vaccine"},{"issue":"suppl_2","key":"10.1016\/j.ebiom.2025.105781_bib39","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1093\/jac\/dkf806","article-title":"Molecular characterization of macrolide resistance mechanisms among Streptococcus pneumoniae and Streptococcus pyogenes isolated from the PROTEKT 1999-2000 study","volume":"50","author":"Farrell","year":"2002","journal-title":"J Antimicrob Chemother"},{"key":"10.1016\/j.ebiom.2025.105781_bib40","doi-asserted-by":"crossref","DOI":"10.1016\/j.micres.2022.127221","article-title":"Epidemiological characteristics and antibiotic resistance mechanisms of Streptococcus pneumoniae: an updated review","volume":"266","author":"Li","year":"2023","journal-title":"Microbiol Res"},{"issue":"4","key":"10.1016\/j.ebiom.2025.105781_bib41","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1038\/s41579-021-00650-4","article-title":"Horizontal gene transfer and adaptive evolution in bacteria","volume":"20","author":"Arnold","year":"2022","journal-title":"Nat Rev Microbiol"},{"issue":"3","key":"10.1016\/j.ebiom.2025.105781_bib42","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1128\/mSphere.00145-21","article-title":"Competence- associated peptide BriC alters fatty acid biosynthesis in Streptococcus pneumoniae","volume":"6","author":"Aggarwal","year":"2021","journal-title":"mSphere"},{"issue":"4","key":"10.1016\/j.ebiom.2025.105781_bib43","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1128\/mBio.01304-21","article-title":"Inactivation of transcriptional regulator FabT influences colony phase variation of Streptococcus pneumoniae","volume":"12","author":"Zhang","year":"2021","journal-title":"mBio"},{"issue":"10","key":"10.1016\/j.ebiom.2025.105781_bib44","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1007328","article-title":"Function of BriC peptide in the pneumococcal competence and virulence portfolio","volume":"14","author":"Aggarwal","year":"2018","journal-title":"PLoS Pathog"},{"key":"10.1016\/j.ebiom.2025.105781_bib45","article-title":"Evidence of reduced virulence and increased colonization among pneumococcal isolates of serotype 3 clade II lineage in mice","volume":"29","author":"Sekulovic","year":"2024","journal-title":"J Infect Dis"}],"container-title":["eBioMedicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2352396425002257?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2352396425002257?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,7,15]],"date-time":"2025-07-15T21:14:58Z","timestamp":1752614098000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2352396425002257"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7]]},"references-count":45,"alternative-id":["S2352396425002257"],"URL":"https:\/\/doi.org\/10.1016\/j.ebiom.2025.105781","relation":{},"ISSN":["2352-3964"],"issn-type":[{"value":"2352-3964","type":"print"}],"subject":[],"published":{"date-parts":[[2025,7]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"CC180 clade dynamics do not universally explain Streptococcus pneumoniae serotype 3 persistence post-vaccine: a global comparative population genomics study","name":"articletitle","label":"Article Title"},{"value":"eBioMedicine","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.ebiom.2025.105781","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Authors. Published by Elsevier B.V.","name":"copyright","label":"Copyright"}],"article-number":"105781"}}