Elucidating the role of group A Streptococcus genomics and pharyngeal microbiota in acute paediatric pharyngitis

The post pandemic period has witnessed a notable increase in invasive Streptococcus pyogenes (GAS) infections across several countries. This surge has been partly attributed to the emergence of more virulent strains, and factors like the non-pharmaceutical interventions or the immunity debt. Despite its dual role as both a commensal and pathogen, our understanding of GAS carriage and the dynamics influencing the transition to invasive disease remains limited. In particular, the role of the pharyngeal microbiota in modulating GAS colonization and infection warrants further investigation. We performed a comprehensive analysis of a pediatric cohort in the post pandemic period collecting clinical data alongside diagnostic evaluations by using pharyngeal swabs and Rapid Antigen Detection Tests (RADTs) to differentiate GAS-positive from GAS-negative cases. Comparative genomic analyses were performed on clinical isolates to identify the prevalence of specific clones or virulence determinants. Additionally, the pharyngeal microbiota was characterized using 16 S rRNA targeted sequencing to assess differences in microbial community composition between the two groups. The overall composition of the pharyngeal microbiota appeared comparable between GAS-positive and GAS-negative children. Alpha diversity metrics (Observed Species, Shannon diversity and Pielou's Evenness) were not significantly different (p = 0.820, p = 0.280 and p = 0.240, respectively), while Bray-Curtis defined two distinct groups (PERMANOVA, p = 0.01, R² = 0.523). The relative abundance of S. pyogenes within the Streptococcus genus emerged as a key differentiator. Genomic analysis revealed a mosaic representation of GAS clones, with the emm12.0 that was the most represented type, suggesting genomic characteristics did not directly correlate with the upsurge of respiratory GAS infections in our cohort. Our study underscores the complexity of GAS pathogenesis, highlighting that the transition from colonization to infection (acute pharyngitis) remains largely elusive and pharyngeal microbiota may contribute to a multifaceted interplay between host immunity and S. pyogenes.