The genomic epidemiology of multi-drug resistant invasive non-typhoidal Salmonella in selected sub-Saharan African countries

Se Eun Park, Duy Thanh Pham, Gi Deok Pak, Ursula Panzner, Ligia Maria Cruz Espinoza, Vera von Kalckreuth, Justin Im, Ondari D Mogeni, Heidi Schütt-Gerowitt, John A Crump, Robert F Breiman, Yaw Adu-Sarkodie, Ellis Owusu-Dabo, Raphaël Rakotozandrindrainy, Abdramane Bassiahi Soura, Abraham Aseffa, Nagla Gasmelseed, Arvinda Sooka, Karen H Keddy, Jürgen MayPeter Aaby, Holly M Biggs, Julian T Hertz, Joel M Montgomery, Leonard Cosmas, Beatrice Olack, Barry Fields, Nimako Sarpong, Tsiriniaina Jean Luco Razafindrabe, Tiana Mirana Raminosoa, Leon Parfait Kabore, Emmanuel Sampo, Mekonnen Teferi, Biruk Yeshitela, Muna Ahmed El Tayeb, Ralf Krumkamp, Denise Myriam Dekker, Anna Jaeger, Adama Tall, Amy Gassama, Aissatou Niang, Morten Bjerregaard-Andersen, Sandra Valborg Løfberg, Jessica Fung Deerin, Jin Kyung Park, Frank Konings, Megan E Carey, Sandra Van Puyvelde, Mohammad Ali, John Clemens, Gordon Dougan, Stephen Baker, Florian Marks

    Research output: Contribution to journalA1: Web of Science-article

    Abstract

    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 bla CTX-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.

    Original languageEnglish
    Article numbere005659
    JournalBMJ Global Health
    Volume6
    Issue number8
    Number of pages27
    ISSN2059-7908
    DOIs
    Publication statusPublished - 2021

    Keywords

    • Child
    • Genomics
    • Humans
    • Kenya
    • Pharmaceutical Preparations
    • Phylogeny
    • Salmonella typhimurium/genetics

    Cite this