{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T14:23:44Z","timestamp":1785421424928,"version":"3.56.0"},"posted":{"date-parts":[[2025,10,22]]},"group-title":"Microbiology","reference-count":58,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T00:00:00Z","timestamp":1761091200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.biorxiv.org\/about\/FAQ#license"}],"funder":[{"award":["1R21AI147502"],"award-info":[{"award-number":["1R21AI147502"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["UL1TR002003"],"award-info":[{"award-number":["UL1TR002003"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,10,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  The carrier state of\n                  <jats:italic>Streptococcus pyogenes<\/jats:italic>\n                  (Group A Streptococcus, GAS), is defined by the presence of the organism without symptoms or an immune response. Carriage poses challenges for clinical management and contributes to transmission in the community. Prior studies suggest genetic and phenotypic differences between isolates from symptomatic (acute) infections and those from carriers, yet comprehensive genomic and transcriptomic analyses of naturally acquired human GAS carriage have been lacking. In this study, we collected longitudinal samples from individuals before and after antibiotic treatment for acute pharyngitis, performing whole genome sequencing and RNA-seq on selected isolates. This is the first report of transcriptional profiling of GAS directly from human derived oropharyngeal swabs. Genomic analysis revealed no consistent carrier-specific genotypes, and\n                  <jats:italic>in vitro<\/jats:italic>\n                  assays showed no major differences in biofilm formation or antibiotic susceptibility between carrier and acute isolates. Transcriptional profiling from oropharyngeal swabs identified distinct gene expression patterns when comparing the acute infection and post-treatment carriage phases, although early acute expression profiles did not predict treatment failure. These findings suggest that GAS carriage is likely influenced by conserved bacterial traits as well as host factors, advancing our understanding of GAS persistence and transmission.\n                <\/jats:p>\n                <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Longitudinal samples were collected from individuals before and after treatment for acute Group A Streptococcal pharyngitis. Whole genome sequencing and RNA-seq was performed on selected isolates. This is the first report of transcriptional profiling of GAS directly from human oropharyngeal swabs. Distinct gene expression patterns were observed when comparing the acute infection and post-treatment carriage.<\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/2025.10.22.683982","type":"posted-content","created":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T00:05:12Z","timestamp":1761177912000},"source":"Crossref","is-referenced-by-count":0,"title":["Unraveling\n                  <i>Streptococcus pyogenes<\/i>\n                  Carriage: Genomic and Transcriptomic Insights from Acute and Post-Treatment Phases"],"prefix":"10.64898","author":[{"given":"Nicholas","family":"Faiola","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason","family":"Woods","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"May","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kevin","family":"Quirk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher","family":"Thomas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eliza","family":"Klos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jordan","family":"Thesier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mitchell","family":"Waldran","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Mainschein-Cline","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael J.","family":"Federle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gregory P.","family":"Demuri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ellen R.","family":"Wald","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Cook","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2025102407451013000_2025.10.22.683982v1.1","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(05)70267-X"},{"key":"2025102407451013000_2025.10.22.683982v1.2","doi-asserted-by":"crossref","first-page":"2008","DOI":"10.3390\/jcm14062008","article-title":"Prevalence of Asymptomatic Group A Streptococcus Carriage Based on Rapid Antigen Detection Test in Healthy Adults in Poland","volume":"14","author":"Department of Infectious Diseases LDaAID, Wroclaw Medical University, 51-149 Wroclaw, Poland,","year":"2025","journal-title":"J Clin Med"},{"key":"2025102407451013000_2025.10.22.683982v1.3","doi-asserted-by":"crossref","first-page":"1526","DOI":"10.1099\/jmm.0.001054","article-title":"Prevalence and long-term persistence of beta-haemolytic streptococci throat carriage among children and young adults","volume":"68","year":"2019","journal-title":"Journal of medical microbiology"},{"key":"2025102407451013000_2025.10.22.683982v1.4","doi-asserted-by":"crossref","first-page":"127","DOI":"10.3961\/jpmph.15.073","article-title":"Throat Carriage Rate and Antimicrobial Resistance of Streptococcus pyogenes In Rural Children in Argentina","volume":"50","year":"2017","journal-title":"J Prev Med Public Health"},{"key":"2025102407451013000_2025.10.22.683982v1.5","first-page":"446","article-title":"The Prevalence of Group A Streptococci Carriers Among Asymptomatic School Children","volume":"7","year":"2013","journal-title":"J Clin Diagnostic Res"},{"key":"2025102407451013000_2025.10.22.683982v1.6","doi-asserted-by":"publisher","DOI":"10.1542\/peds.2009-2648"},{"key":"2025102407451013000_2025.10.22.683982v1.7","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1097\/QCO.0000000000001095","article-title":"The reemergence of Streptococcus pyogenes in skin and soft tissue infections: a review of epidemiology, pathogenesis, and management strategies","volume":"38","year":"2025","journal-title":"Curr Opin Infect Dis"},{"key":"2025102407451013000_2025.10.22.683982v1.8","doi-asserted-by":"crossref","first-page":"1778","DOI":"10.1007\/s44197-024-00316-3","article-title":"Reemergence of Streptococcus pyogenes Infections in a Large Italian Hospital: A d\u00e9j\u00e0 vu from past Years","volume":"14","year":"2024","journal-title":"J Epidemiol Glob Health"},{"key":"2025102407451013000_2025.10.22.683982v1.9","doi-asserted-by":"crossref","unstructured":"Di Pietro GM , Marchisio P , Bosi P , Castellazzi ML , Lemieux P . 2024. 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