Synchronous emergence of Streptococcus pyogenes emm type 3.93 with unique genomic inversion among invasive infections in the Netherlands and England

A global increase in the incidence of invasive group A streptococcal (iGAS) infections was observed after lifting COVID-19-related restrictions in 2022 with dominance of M1 UK in many countries. After seasonal declines in iGAS incidence during the summer of 2023, simultaneous, rapid expansion of a previously rare emm type 3.93 was seen in both England and the Netherlands from November 2023, causing 20% and 60% of all iGAS cases, respectively, within 4 months. Emm 3.93 was associated with iGAS in children 6-17 years of age and with increased risk of pneumonia/pleural empyema and meningitis in both countries. No significant excess risk of death was identified for emm 3.93 compared to other types. Genomic analysis of historic and contemporary emm 3.93 isolates revealed the emergence of three new clades with a previously undescribed genomic inversion. Our findings underscore the value of molecular surveillance, including long-read sequencing, in identifying clinical and public health threats.