Streptococcus pyogenes carriage is associated with distinct in vivo transcriptional states but not carrier-specific genotypes

Group A Streptococcus (GAS) is a major human pathogen causing extensive global morbidity. While the asymptomatic carrier state challenges clinical management and contributes to community transmission, genomic, and transcriptomic analyses of naturally acquired human GAS carriage have been lacking. In this study, samples are collected from individuals before and after treatment for acute GAS pharyngitis. Selected isolates undergo whole-genome sequencing and RNA sequencing, providing transcriptional profiling of GAS directly from human-derived oropharyngeal swabs. Genomic analysis reveals no consistent carrier-specific genotypes, and in vitro assays show no major differences in biofilm formation or antibiotic susceptibility between carrier and non-carrier isolates. However, in vivo transcriptional profiling identifies distinct gene expression patterns when comparing acute infection and post-treatment carriage phases, though acute-phase profiles do not predict treatment failure. These findings suggest GAS carriage is influenced by both bacterial traits and host factors, advancing our understanding of persistence and transmission.