RT Journal Article SR Electronic T1 The genomic epidemiology of multi-drug resistant invasive non-typhoidal Salmonella in selected sub-Saharan African countries JF BMJ Global Health JO BMJ Global Health FD BMJ Publishing Group Ltd SP e005659 DO 10.1136/bmjgh-2021-005659 VO 6 IS 8 A1 Se Eun Park A1 Duy Thanh Pham A1 Gi Deok Pak A1 Ursula Panzner A1 Ligia Maria Cruz Espinoza A1 Vera von Kalckreuth A1 Justin Im A1 Ondari D. Mogeni A1 Heidi Schütt-Gerowitt A1 John A Crump A1 Robert F Breiman A1 Yaw Adu-Sarkodie A1 Ellis Owusu-Dabo A1 Raphaël Rakotozandrindrainy A1 Abdramane Bassiahi Soura A1 Abraham Aseffa A1 Nagla Gasmelseed A1 Arvinda Sooka A1 Karen H Keddy A1 Jürgen May A1 Peter Aaby A1 Holly M Biggs A1 Julian T Hertz A1 Joel M Montgomery A1 Leonard Cosmas A1 Beatrice Olack A1 Barry Fields A1 Nimako Sarpong A1 Tsiriniaina Jean Luco Razafindrabe A1 Tiana Mirana Raminosoa A1 Leon Parfait Kabore A1 Emmanuel Sampo A1 Mekonnen Teferi A1 Biruk Yeshitela A1 Muna Ahmed El Tayeb A1 Ralf Krumkamp A1 Denise Myriam Dekker A1 Anna Jaeger A1 Adama Tall A1 Amy Gassama A1 Aissatou Niang A1 Morten Bjerregaard-Andersen A1 Sandra Valborg Løfberg A1 Jessica Fung Deerin A1 Jin Kyung Park A1 Frank Konings A1 Megan E Carey A1 Sandra Van Puyvelde A1 Mohammad Ali A1 John Clemens A1 Gordon Dougan A1 Stephen Baker A1 Florian Marks YR 2021 UL http://gh.bmj.com/content/6/8/e005659.abstract AB Background Invasive non-typhoidal Salmonella (iNTS) is one of the leading causes of bacteraemia in sub-Saharan Africa. We aimed to provide a better understanding of the genetic characteristics and transmission patterns associated with multi-drug resistant (MDR) iNTS serovars across the continent.Methods A total of 166 iNTS isolates collected from a multi-centre surveillance in 10 African countries (2010–2014) and a fever study in Ghana (2007–2009) were genome sequenced to investigate the geographical distribution, antimicrobial genetic determinants and population structure of iNTS serotypes–genotypes. Phylogenetic analyses were conducted in the context of the existing genomic frameworks for various iNTS serovars. Population-based incidence of MDR-iNTS disease was estimated in each study site.Results Salmonella Typhimurium sequence-type (ST) 313 and Salmonella Enteritidis ST11 were predominant, and both exhibited high frequencies of MDR; Salmonella Dublin ST10 was identified in West Africa only. Mutations in the gyrA gene (fluoroquinolone resistance) were identified in S. Enteritidis and S. Typhimurium in Ghana; an ST313 isolate carrying blaCTX-M-15 was found in Kenya. International transmission of MDR ST313 (lineage II) and MDR ST11 (West African clade) was observed between Ghana and neighbouring West African countries. The incidence of MDR-iNTS disease exceeded 100/100 000 person-years-of-observation in children aged <5 years in several West African countries.Conclusions We identified the circulation of multiple MDR iNTS serovar STs in the sampled sub-Saharan African countries. Investment in the development and deployment of iNTS vaccines coupled with intensified antimicrobial resistance surveillance are essential to limit the impact of these pathogens in Africa.Data are available in a public, open access repository. Raw sequence data are available in the European Nucleotide Archive (Project number: ERP009684, ERP010763, ERP013866).