Genomic analysis of Streptococcus pyogenes emm1-type isolates reveals M1UK circulation and a genetically distinct Brazilian sublineage

Abstract Background Streptococcus pyogenes (GAS) causes diseases ranging from mild pharyngitis to severe invasive infections. The emm 1 type is the most prevalent worldwide, and a highly transmissible variant, M1 UK , characterized by increased speA expression, has recently emerged and spread globally. Objective To characterize the genomic diversity of invasive GAS isolates collected from severe cases and epidemiologically important outbreaks in Brazil. Methods Whole-genome sequencing was performed on 229 invasive GAS isolates collected in Brazil between January 2023 and November 2024. Genomes were analyzed for emm typing, lineage assignment, and virulence gene profiling. Comparative genomic analyses, including global M1 global and M1 UK genomes, were performed to contextualize the Brazilian isolates within the global population structure. Results Thirty-four distinct emm types were identified, with emm 1 accounting for 52.4%. Of these, 14% were confirmed as M1 UK clones, detected across multiple Brazilian regions. Comparative genomic analysis showed that the remaining emm 1 isolates clustered into a well-supported group representing a genetically distinct Brazilian sublineage (Br clade). Conclusion The detection of M1 UK isolates in multiple Brazilian states indicates that this lineage is circulating in the country. Most emm 1 isolates analyzed in this study belonged to the Br clade rather than the M1 UK lineage, suggesting that the distribution of emm 1 sublineages in this selected dataset differs from patterns reported in countries where M1 UK has become predominant. These findings highlight the importance of genomic and public health surveillance to monitor and control the spread of invasive GAS infections.