{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,27]],"date-time":"2026-04-27T10:50:10Z","timestamp":1777287010047,"version":"3.51.4"},"reference-count":45,"publisher":"Public Library of Science (PLoS)","issue":"6","license":[{"start":{"date-parts":[[2021,6,14]],"date-time":"2021-06-14T00:00:00Z","timestamp":1623628800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Link Equine Research Endowment"},{"name":"Department of Large Animal Clinical Sciences, Texas A&M University"},{"DOI":"10.13039\/501100001862","name":"Svenska Forskningsr\u00e5det Formas","doi-asserted-by":"publisher","award":["221-2013-606"],"award-info":[{"award-number":["221-2013-606"]}],"id":[{"id":"10.13039\/501100001862","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Patsy Link Chair"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p><jats:italic>Streptococcus equi<\/jats:italic> subsp. <jats:italic>equi<\/jats:italic> (SEE) is a host-restricted bacterium that causes the common infectious upper respiratory disease known as strangles in horses. Perpetuation of SEE infection appears attributable to inapparent carrier horses because it neither persists long-term in the environment nor infects other host mammals or vectors, and infection results in short-lived immunity. Whether pathogen factors enable SEE to remain in horses without causing clinical signs remains poorly understood. Thus, our objective was to use next-generation sequencing technologies to characterize the genome, methylome, and transcriptome of isolates of SEE from horses with acute clinical strangles and inapparent carrier horses\u2014including isolates recovered from individual horses sampled repeatedly\u2014to assess pathogen-associated changes that might reflect specific adaptions of SEE to the host that contribute to inapparent carriage. The accessory genome elements and methylome of SEE isolates from Sweden and Pennsylvania revealed no significant or consistent differences between acute clinical and inapparent carrier isolates of SEE. RNA sequencing of SEE isolates from Pennsylvania demonstrated no genes that were differentially expressed between acute clinical and inapparent carrier isolates of SEE. The absence of specific, consistent changes in the accessory genomes, methylomes, and transcriptomes of acute clinical and inapparent carrier isolates of SEE indicates that adaptations of SEE to the host are unlikely to explain the carrier state of SEE. Efforts to understand the carrier state of SEE should instead focus on host factors.<\/jats:p>","DOI":"10.1371\/journal.pone.0252804","type":"journal-article","created":{"date-parts":[[2021,6,14]],"date-time":"2021-06-14T17:24:34Z","timestamp":1623691474000},"page":"e0252804","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":6,"title":["Differences in the genome, methylome, and transcriptome do not differentiate isolates of Streptococcus equi subsp. equi from horses with acute clinical signs from isolates of inapparent carriers"],"prefix":"10.1371","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7957-4642","authenticated-orcid":true,"given":"Ellen Ruth A.","family":"Morris","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ashley 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Riihimaki","year":"2018","journal-title":"Vet Microbiol"},{"key":"pone.0252804.ref014","doi-asserted-by":"crossref","first-page":"108638","DOI":"10.1016\/j.vetmic.2020.108638","article-title":"Comparison of whole genome sequences of Streptococcus equi subsp. equi from an outbreak in Texas with isolates from within the region, Kentucky, USA, and other countries","volume":"243","author":"ERA Morris","year":"2020","journal-title":"Vet Microbiol"},{"issue":"Pt 6","key":"pone.0252804.ref015","doi-asserted-by":"crossref","first-page":"1361","DOI":"10.1099\/00221287-146-6-1361","article-title":"Streptococcus equi with truncated M-proteins isolated from outwardly healthy horses","volume":"146","author":"N Chanter","year":"2000","journal-title":"Microbiology (Reading)"},{"issue":"5","key":"pone.0252804.ref016","doi-asserted-by":"crossref","first-page":"1274","DOI":"10.1111\/j.1365-2958.2008.06481.x","article-title":"A novel streptococcal integrative conjugative element involved in iron 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Brettin","year":"2015","journal-title":"Sci Rep"},{"issue":"1","key":"pone.0252804.ref032","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1186\/s12859-018-2154-x","article-title":"ClustAGE: a tool for clustering and distribution analysis of bacterial accessory genomic elements","volume":"19","author":"EA Ozer","year":"2018","journal-title":"BMC Bioinformatics"},{"key":"pone.0252804.ref033","article-title":"The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities","author":"JJ Davis","year":"2019","journal-title":"Nucleic acids research"},{"issue":"1","key":"pone.0252804.ref034","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1038\/msb.2011.75","article-title":"Fast, scalable generation of high\u2010quality protein multiple sequence alignments using Clustal Omega","volume":"7","author":"F Sievers","year":"2011","journal-title":"Mol Syst Biol"},{"issue":"Web 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