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Background   Streptococcus pyogenes  causes a profound global burden of morbidity and mortality across its diverse clinical spectrum. To support a new controlled human infection (challenge) model seeking to accelerate  S. pyogenes  vaccine development, we aimed to develop an accurate and reliable molecular method for quantifying bacterial load from pharyngeal swabs collected during experimental human pharyngitis.    Methods  Combined sequential RNA+DNA extraction from throat swabs was compared to traditional separate RNA-only and DNA-only extractions. An  emm -type specific qPCR was developed to detect the  emm 75 challenge strain. Results from the qPCR were compared to culture, using throat swab samples collected in a human challenge study.    Results  The qPCR was 100% specific for the  emm 75 challenge strain when tested against a panel of  S. pyogenes emm -types and other respiratory pathogens. Combined RNA+ DNA extraction had similar yield to traditional separate extractions. The combined extraction method and  emm 75 qPCR had 98.8% sensitivity compared to culture for throat swabs collected from challenge study participants.    Conclusions  We have developed a reliable molecular method for measuring  S. pyogenes  bacterial load from throat swabs collected in a controlled human infection model of  S. pyogenes  pharyngitis.    Trial registration   NCT03361163  on 4th December 2017.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12879-021-06173-w.

An emm-type specific qPCR to track bacterial load during experimental human Streptococcus pyogenes pharyngitis