Household molecular epidemiology ofStreptococcus pyogenescarriage and infection in The Gambia

• DOI: 10.1101/2025.03.28.25324710
• Publication Date: 2025-03-30T17:30:44Z
• Authors: Gabrielle de Crom...; Edwin P. Armitage; Alexander J. Keeley; Elina Senghore; Fatoumata Camara; Musukoi Jammeh; Amat Bittaye; Haddy Ceesay; Isatou Ceesay; Bunja Samateh; Muhammed Manneh; Gwenaëlle Botquin; Dalila Lakhloufi; Valerie Delforge; Saikou Y Bah; Jennifer N. Hall; Lionel Schiavolin; Claire E. Turner; Michael Marks; Thushan I. de Silva; Anne Botteaux; Pierre R. Smeesters

AbstractBackgroundHigh burden ofStreptococcus 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 characteriseemm-types andemm-clusters associated with carriage and disease in a setting with high rheumatic heart disease (RHD) burden, a peri-urban area in The Gambia.MethodsA one-year household cohort study was conducted in 2021-2022, recruiting 442 healthy participants from 44 households, looking forS pyogenescarriage 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 underwentemm-typing and were compared with a similar collection from 2018. Simpson’s reciprocal index (SRI) was used to measure diversity.Results221 isolates showed a positive culture forS pyogenes, representing 52emm-types and 16emm-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 atemm-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 circulatingemm-clusters.ConclusionThis 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 importantS pyogenesreservoir and should be included in further surveillance studies and public health interventions.FundingWellcome Trust, FNRS (Belgium), ESPIDKeypoints summaryFirst molecular analysis ofS pyogenesskin carriage in Africa. Skin carriage may be an important reservoir in RHD-endemic settings.Highest strain diversity is seen in pyoderma and lowest in pharyngitis.Fouremm-clusters are dominant and stable over time.