Genetic analysis of Streptococcus pyogenes isolated in Akita Prefecture, Japan, between 2017 and 2025, revealing the spread of M113SNPs possessing prophage-associated virulence genes and sic with unique mutations.

In recent years, the number of Group A Streptococcus-associated infections has increased significantly in Akita Prefecture. An analysis of isolates collected between 2017 and 2025 revealed that the intermediate M113SNPs lineage has gained predominance as the cause, surpassing both the ancestral M1global and globally prevalent hypervirulent M1UK lineages. M113SNPs specifically harbored speC, spd1, and sdaD2; the latter was also present in most of M1UK. Furthermore, M113SNPs possessed unique mutations in sic, with the majority of the identified sic genotypes being novel variants. In the southern region of Akita, where the outbreak was particularly intense, region-specific subvariants characterized by aspartic acid substitutions were identified. These findings suggest that the surge in Group A Streptococcus-associated infections in Akita Prefecture was not merely caused by the introduction of a widespread global clone but was driven in part by the dissemination of the M113SNPs lineage, which possesses distinctive genetic features and may have undergone localized evolutionary adaptation.