Household molecular epidemiology of Streptococcus pyogenes carriage and infection in The Gambia

Background High burden of Streptococcus pyogenes (S pyogenes) disease is seen in Africa which is also the continent with the least epidemiological data on circulating strains. We aimed to better characterise emm-types and emm-clusters associated with carriage and disease in a setting with high rheumatic heart disease (RHD) burden, a peri-urban area in The Gambia. Methods A one-year household cohort study was conducted in 2021-2022, recruiting 442 healthy participants from 44 households, looking for S pyogenes carriage and non-invasive infection. Pharyngeal and normal skin swabs were collected to assess carriage, pharyngitis and pyoderma swabs were captured to assess infection. Cultured isolates underwent emm-typing and were compared with a similar collection from 2018. Simpson's reciprocal index (SRI) was used to measure diversity. Results 221 isolates showed a positive culture for S pyogenes, representing 52 emm-types and 16 emm-clusters, with 4 over-represented clusters comprising 65.2% of the isolates. emm-type diversity was high (SRI 29.3, 95% CI: 24.8-36.0). Looking at emm-type and intra-individual transmission, we found frequent transmission between pyoderma and intact skin, and evidence of bidirectional transmission between skin and pharynx in the same host. A comparison with pyoderma isolates collected in 2018 from the same region revealed no major changes in circulating emm-clusters. Conclusion This study provides the first molecular analysis of skin and throat isolates prospectively collected from carriage and non-invasive infection in Africa. In this RHD-endemic setting, pyoderma and skin carriage represent an important S pyogenes reservoir and should be included in further surveillance studies and public health interventions.