Whole genome sequencing of Streptococcus pyogenes (Group A Streptococcus, GAS) M1 isolates associated with a 2022-23 surge in infections in Iceland and Scotland

Following the easing of infectious disease transmission prevention practices (hand washing, masking, social distancing, etc.) employed during the COVID-19 pandemic, many countries reported a surge in respiratory infectious diseases, including those caused by the bacterial pathogen Streptococcus pyogenes (Group A Streptococcus,GAS). Public health infectious disease surveillance in Iceland and Scotland observed an alarming increase in GAS invasive infections beginning in 2022 and extending into 2023. Emm1 strains were the most prevalent GAS molecular genotype causing infections and young children were disproportionately affected. Whole genome sequencing was used to genetically investigate and characterize the M1 strains causing the surge in infections. The genome of 295 clinical isolates from Scotland (n = 250) and Iceland (n =45) were Illumina PE short read sequenced as part of the investigation.50 of the isolates were also whole genome sequenced using Oxford Nanopore technology long read sequencing, and complete closed genomes were determined by hybrid assembly.