Local Genomic Surveillance of Invasive Streptococcus pyogenes in Eastern North Carolina (ENC) in 2022-2023.

The recent increase in Group A Streptococcus (GAS) incidences in several countries across Europe and some areas of the Unites States (U.S.) has raised concerns. To understand GAS diversity and prevalence, we conducted a local genomic surveillance in Eastern North Carolina (ENC) in 2022-2023 with 95 isolates and compared its results to those of the existing national genomic surveillance in the U.S. in 2015-2021 with 13,064 isolates. We observed their epidemiological changes before and during the COVID-19 pandemic and detected a unique sub-lineage in ENC among the most common invasive GAS strain, ST28/ emm1 . We further discovered a multiple-copy insertion sequence, IS Lgar5 , in ST399/ emm77 and its single-copy variants in some other GAS strains. We discovered IS Lgar5 was linked to a Tn 5801-like tet M-carrying integrative and conjugative element, and its copy number was associated with an erm T-carrying pRW35-like plasmid. The dynamic insertions of IS Lgar5 may play a vital role in genome fitness and adaptation, driving GAS evolution relevant to antimicrobial resistance and potentially GAS virulence.