The genomic epidemiology of multi-drug resistant nontyphoidalSalmonellacausing invasive disease in sub-Saharan Africa
Authors: Park Se Eun , Pham Duy Thanh , Pak Gi Deok , Panzner Ursula , Espinoza Ligia Maria Cruz , von Kalckreuth Vera , Im Justin , Mogeni Ondari D. , Schütt-Gerowitt Heidi , Crump John A. , Breiman Robert F. , Adu-Sarkodie Yaw , Owusu-Dabo Ellis , Rakotozandrindrainy Raphaёl , Soura Abdramane Bassiahi , Aseffa Abraham , Gasmelseed Nagla , Sooka Arvinda , Keddy Karen H. , May Jürgen , Aaby Peter , Biggs Holly M. , Hertz Julian T. , Montgomery Joel M. , Cosmas Leonard , Olack Beatrice , Fields Barry , Sarpong Nimako , Razafindrabe Tsiriniaina Jean Luco , Raminosoa Tiana Mirana , Kabore Leon Parfait , Sampo Emmanuel , Teferi Mekonnen , Yeshitela Biruk , Tayeb Muna Ahmed El , Krumkamp Ralf , Dekker Denise Myriam , Jaeger Anna , Tall Adama , Niang Aissatou , Bjerregaard-Andersen Morten , Løfberg Sandra Valborg , Deerin Jessica Fung , Park Jin Kyung , Konings Frank , Van Puyvelde Sandra , Ali Mohammad , Clemens John D. , Dougan Gordon , Baker Stephen , Marks Florian 
Published: December 2020

Background

Invasive nontyphoidalSalmonella(iNTS) is one of the leading causes of bacteraemia in sub-Saharan Africa. Multi-drug resistance (MDR) and further resistance to third generation cephalosporins and fluoroquinolones have emerged in multiple iNTS serotypes. Molecular epidemiological investigations of nontyphoidalSalmonellaare needed to better understand the genetic characteristics and transmission dynamics associated with major MDR iNTS serotypes across the continent.

Methods

A total of 166 nontyphoidalSalmonellaisolates causing invasive disease were collected from a multi-centre study in eight African countries between 2010 and 2014, and whole-genome sequenced to investigate the geographical distribution, antimicrobial genetic determinants and population structure of iNTS serotypes-genotypes. Phylogeographical reconstruction was further conducted in context of the existing genomic framework of iNTS serotypes Typhimurium and Enteritidis. Population-based incidence of MDR-iNTS disease was also estimated.

Results

Salmonella entericasubsp.Entericaserotype Typhimurium (S. Typhimurium) sequence-type (ST) 313 andSalmonella entericasubsp.Entericaserotype Enteritidis (S. Enteritidis) ST11 were predominant, and both exhibited high frequencies of MDR.Salmonella entericasubsp.Entericaserotype Dublin (S. Dublin) ST10 emerged in West Africa. Mutations in thegyrAgene were identified inS. Enteritidis andS. Typhimurium in Ghana; and ST313 carryingblaCTX-M-15was found in Kenya. Inter-country transmission of MDR ST313 lineage II and the West African Clade of MDR ST11 between Ghana and neighbouring countries including Mali, Burkina Faso, and Nigeria were evident. The incidence of MDR-iNTS disease exceeded 100/100,000-person years-of-observation (PYO) in children aged <5 years in several West African countries.

Conclusions

Multiple MDR iNTS serotypes-sequence types, predominantlyS. Typhimurium ST313 andS. Enteritidis ST11, are co-circulating in sub-Saharan Africa with evidence of transmission between West African countries. The development of safe and effective iNTS vaccines coupled with appropriate antimicrobial stewardship and adequate epidemiological monitoring are essential to limit the impact of these pathogens in Africa.