Table 3_The invasive GAS puzzle in Italy: genomic insights from a hospital cohort in a fragmented surveillance landscape.docx

Streptococcus pyogenes (Group A Streptococcus, GAS) is a re-emerging human pathogen responsible for a wide spectrum of diseases, from mild pharyngitis to life-threatening invasive infections that have risen globally in recent years. We performed a retrospective genomic and epidemiological analysis of 61 invasive Group A Streptococcus (iGAS) isolates collected from 2016 to 2024 at a major tertiary Italian hospital. Whole-genome sequencing, emm typing, phylogenetic reconstruction, and mutational profiling were performed to assess clonal diversity, virulence determinants, antimicrobial resistance (AMR) genes, and mobile genetic elements. Our data revealed high genetic diversity, with multiple emm types identified, including emm1.0, emm28.0, emm89.0, emm22.21, and emm44.0 being the most prevalent. Notably, four isolates belonged to the hypervirulent M1UK sub-lineage, which has circulated in Italy since 2018 without a marked post-pandemic resurgence. Genome-wide analysis identified multiple genomic alterations. Regulatory gene mutations were widespread, particularly in rexB (97%), covS (82%), and rexA (80%) suggesting a complex modulation of virulence pathways. AMR genes were sporadic and largely absent in emm1.0 and M1UK strains, showing 12 or 26 core SNPs, reinforcing the hypothesis that virulence, rather than resistance underpins their clinical relevance. Our findings depict a genetically diverse and evolving S. pyogenes population in Italy, dominated by a few high-risk lineages. The persistence of M1UK strains without explosive spread underscores the influence of local epidemiological contexts and surveillance limitations. This study emphasizes the urgent need for a national genomic surveillance network to enable timely detection of emerging clones and guide public health responses.