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

BACKGROUND: Africa experiences a high burden of Streptococcus pyogenes disease but has limited epidemiological data. We characterized emm-types and emm-clusters associated with carriage and disease in The Gambia, a setting with high rheumatic heart disease burden. METHODS: A one-year household cohort study (2021-2022) recruited 442 participants from 44 households to assess S pyogenes carriage and non-invasive infection. Pharyngeal and skin swabs were collected to detect carriage, pharyngitis and pyoderma swabs were taken tp assess infection. Cultured isolates underwent emm-typing and were compared with previous collection from the same region. RESULTS: 221 cultured isolates showed 52 different emm-types and 16 emm-clusters. Strain diversity was high (Simpson's reciprocal index 29.3, 95% CI: 24.8-36.0), with highest diversity seen in pyoderma and lowest in pharyngitis. Based on available cross-opsonisation data, the 30-valent M-protein vaccine candidate would cover 50.3% of the isolates but cross-opsonisation data are unknown for 38.5% of them. emm-clusters showed lower diversity and were stable over time, with 4 clusters defining 65.2% of the isolates. 68% of isolates were collected from skin sites (carriage and pyoderma), with evidence of skin-to-throat transmission in the same host. CONCLUSION: This study provides a unique molecular analysis of skin and throat isolates prospectively collected from carriage and non-invasive infection in Africa. Despite high strain diversity, 4 clusters gathered two-thirds of the isolates, representing antigen priorities for broad vaccine coverage. In this rheumatic fever-endemic setting, pyoderma and skin carriage represent an important S pyogenes reservoir and should be included in further surveillance studies and public health interventions.