Genomic characterisation of skin and soft tissue Streptococcus pyogenes isolates from a low-income and a high-income setting

Streptococcus pyogenes is a leading cause of human morbidity and mortality, especially in resource limited settings. The development of a vaccine against S. pyogenes is a global health priority to reduce the burden of post-infection rheumatic heart disease. To support this, molecular characterisation of circulating S. pyogenes isolates is needed. We performed whole genome analyses of S. pyogenes isolates from skin and soft tissue infections in Sukuta, The Gambia, a low-income country (LIC) in West Africa where there is a high burden of such infections. To act as a comparator to these LIC isolates, skin infection isolates from Sheffield, UK (a high-income country, HIC) were also sequenced. The LIC isolates from The Gambia were genetically more diverse (46 emm-types in 107 isolates) compared to the HIC isolates from Sheffield (23 emm-types in 142 isolates), with only 7 overlapping emm-types. Other molecular markers were shared, including a high prevalence of the skin infection-associated emm-pattern D and the variable fibronectin-collagen-T antigen (FCT) types FCT-3 and FCT4. Fewer of the Gambian LIC isolates carried prophage-associated superantigens (64%) and DNAses (26%) compared to the Sheffield HIC isolates (99% and 95% respectively). We also identified streptococcin genes unique to 36% of the Gambian LIC isolates, and a higher prevalence (48%) of glucuronic acid utilisation pathway genes compared to the Sheffield HIC isolates (26%). Comparison to a wider collection of HIC and LIC isolate genomes supported our findings of differing emm-diversity and prevalence of bacterial factors. Our study provides insight into the genetics of LIC isolates, and how they compare to HIC isolates