The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa.
There is paucity of data regarding the geographical distribution, incidence, and phylogenetics of multi-drug resistant (MDR) Salmonella Typhi in sub-Saharan Africa. Here we present a phylogenetic reconstruction of whole genome sequenced 249 contemporaneous S. Typhi isolated between 2008-2015 in 11 sub-Saharan African countries, in context of the 2,057 global S. Typhi genomic framework. Despite the broad genetic diversity, the majority of organisms (225/249; 90%) belong to only three genotypes, 4.3.1 (H58) (99/249; 40%), 3.1.1 (97/249; 39%), and 2.3.2 (29/249; 12%). Genotypes 4.3.1 and 3.1.1 are confined within East and West Africa, respectively. MDR phenotype is found in over 50% of organisms restricted within these dominant genotypes. High incidences of MDR S. Typhi are calculated in locations with a high burden of typhoid, specifically in children aged <15 years. Antimicrobial stewardship, MDR surveillance, and the introduction of typhoid conjugate vaccines will be critical for the control of MDR typhoid in Africa.
Park, SE; Pham, DT; Boinett, C; Wong, VK; Pak, GD; Panzner, U; Espinoza, LMC; von Kalckreuth, V; Im, J; Schütt-Gerowitt, H; Crump, JA; Breiman, RF; Adu-Sarkodie, Y; Owusu-Dabo, E; Rakotozandrindrainy, R; Soura, AB; Aseffa, A; Gasmelseed, N; Keddy, KH; May, J; Sow, AG; Aaby, P; Biggs, HM; Hertz, JT; Montgomery, JM; Cosmas, L; Olack, B; Fields, B; Sarpong, N; Razafindrabe, TJL; Raminosoa, TM; Kabore, LP; Sampo, E; Teferi, M; Yeshitela, B; El Tayeb, MA; Sooka, A; Meyer, CG; Krumkamp, R; Dekker, DM; Jaeger, A; Poppert, S; Tall, A; Niang, A; Bjerregaard-Andersen, M; Løfberg, SV; Seo, HJ; Jeon, HJ; Deerin, JF; Park, J; Konings, F; Ali, M; Clemens, JD; Hughes, P; Sendagala, JN; Vudriko, T; Downing, R; Ikumapayi, UN; Mackenzie, GA; Obaro, S; Argimon, S; Aanensen, DM; Page, A; Keane, JA; Duchene, S; Dyson, Z; Holt, KE; Dougan, G; Marks, F; Baker, S
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