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

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Pham, Duy Thanh 
Pak, Gi Deok 
Panzner, Ursula 
Maria Cruz Espinoza, Ligia 


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.


Funder: Swedish International Development Cooperation Agency (SIDA)

Funder: Government of Republic of Korea

Funder: US Centers for Disease Control and Prevention


Original research, 1506, epidemiology, medical microbiology, typhoid and paratyphoid fevers, cross-sectional survey

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BMJ Global Health

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BMJ Publishing Group
Oak Foundation (215515/Z/19/Z, OCAY-15-547)
Biotechnology and Biological Sciences Research Council (BB/J010367)
Bill & Melinda Gates Foundation (OPPGH5231)
National Institutes of Health (P30 AI064518, PA-03-018, R01TW009237, R24 TW007988, U01 AI062563, U01 AI067854, U01 AI069484)