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To support a new controlled human infection (\u2018challenge\u2019) model seeking to accelerate<jats:italic>S. pyogenes<\/jats:italic>vaccine development, we aimed to develop an accurate and reliable molecular method for quantifying bacterial load from pharyngeal swabs collected during experimental human pharyngitis.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Combined sequential RNA\u2009+\u2009DNA extraction from throat swabs was compared to traditional separate RNA-only and DNA-only extractions. An<jats:italic>emm<\/jats:italic>-type specific qPCR was developed to detect the<jats:italic>emm<\/jats:italic>75 challenge strain. Results from the qPCR were compared to culture, using throat swab samples collected in a human challenge study.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The qPCR was 100% specific for the<jats:italic>emm<\/jats:italic>75 challenge strain when tested against a panel of<jats:italic>S. pyogenes emm<\/jats:italic>-types and other respiratory pathogens. Combined RNA\u00a0+ DNA extraction had similar yield to traditional separate extractions. The combined extraction method and<jats:italic>emm<\/jats:italic>75 qPCR had 98.8% sensitivity compared to culture for throat swabs collected from challenge study participants.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>We have developed a reliable molecular method for measuring<jats:italic>S. pyogenes<\/jats:italic>bacterial load from throat swabs collected in a controlled human infection model of<jats:italic>S. pyogenes<\/jats:italic>pharyngitis.<\/jats:p><\/jats:sec><jats:sec><jats:title>Trial registration<\/jats:title><jats:p><jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/clinicaltrials.gov\/ct2\/show\/NCT03361163\">NCT03361163<\/jats:ext-link>on 4th December 2017.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12879-021-06173-w","type":"journal-article","created":{"date-parts":[[2021,5,21]],"date-time":"2021-05-21T08:03:04Z","timestamp":1621584184000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["An emm-type specific qPCR to track bacterial load during experimental human Streptococcus pyogenes pharyngitis"],"prefix":"10.1186","volume":"21","author":[{"given":"Loraine V.","family":"Fabri","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristy I.","family":"Azzopardi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9432-6700","authenticated-orcid":false,"given":"Joshua","family":"Osowicki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hannah R.","family":"Frost","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pierre R.","family":"Smeesters","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew C.","family":"Steer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,5,21]]},"reference":[{"issue":"11","key":"6173_CR1","doi-asserted-by":"publisher","first-page":"685","DOI":"10.1016\/S1473-3099(05)70267-X","volume":"5","author":"JR Carapetis","year":"2005","unstructured":"Carapetis JR, Steer AC, Mulholland EK, Weber M. 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