Genomic insights of invasive M1_UK Group A Streptococci in Greece, 2019-2024

Increases in invasive group A Streptococcus (iGAS) disease during the late COVID-19 period have coincided with global expansion of the M1_UK lineage. We investigated genomic characteristics and evolutionary dynamics of emm1 iGAS isolates from three major Greek cities during 2019-2024.

Whole-genome sequencing data of 16 emm1 iGAS isolates were retrieved from the NCBI database and analyzed using in silico approaches. Predictions of antimicrobial resistance determinants, virulence factors, and prophage content, along with comparative genomics and phylogenomic analyses were performed.

All isolates harbored genes encoding antimicrobial efflux pumps (imrP, mef(A/E), mreA, patA/patB), and key virulence factors, including streptococcal exotoxins SpeA, SpeB, and SpeG. Prophages T12, P9, and 315.3 were predicted in most genomes. Of the 16 emm1 iGAS, 11 (68.7%) and five (31.3%) isolates were assigned to the M1_UK and M1_global lineages, respectively. Among iGAS, the proportion of M1_UK isolates increased markedly (percentage change: +131%) between the pre- (1/3) and the post- (10/13) COVID-19 periods. The Greek M1_UK iGAS strains showed high genomic similarity (<20 SNPs in some cases) to strains from Australia, Scotland, Iceland, and Italy and shared a mutation that has been previously associated with increased SpeA expression and invasiveness.

A single iGAS isolate of the M1_UK lineage was identified in 2019, while its circulation was documented across three different Greek regions in 2023, likely driven by multiple introductions. The detection of a virulence-associated marker previously linked to enhanced SpeA expression underscores the need for integrated genomic and epidemiological surveillance to guide public health responses.