The genomic data of emm1 and emm12 Streptococcus pyogenes circulating in China between 1993-2024

Streptococcus pyogenes infections such as scarlet fever have increased in China since 2011. Based on a large longitudinal strain collection, we aimed to investigate the molecular epidemiological characteristics and population structure of dominant S. pyogenes emm types circulating in China between 1993-2024. Here, we analyzed genomes of 1029 China emm12 and emm1 isolates encompassing 1993-2024. The genomic data was integrated with national data on notifications of scarlet fever from 1993-2023. We found there are five incidence peaks during 1993-2023 with S. pyogenes emm12 and emm1 being the dominant genotypes. The two genotypes driving scarlet fever in China have evolved independently of the global epidemic lineages. Four emm12 clades were evident prior to 2011, with a single clade replacing other emm12 populations by 2020. One dominant emm1 clade (termed M1china) represents >98% of clinical cases in China since the 1980s, and diverged into endemic subclades that are evolutionary distinct from global epidemic lineages. Compared to clinical strains from the 1990s, expansion of emm12 and emm1 sub-clades coincides with high carriage of integrative conjugative elements containing macrolide and tetracycline resistance genes and virulence gene-encoding prophage. M1china virulence was comparable to M1global lineages within in vitro virulence assays. The ongoing maintenance of multidrug resistant mobile elements and prophage in both emm1 and emm12 populations underlie the resurgence of scarlet fever since 2011 in China.