Original research BMJ Glob Health: first published as 10.1136/bmjgh-2021-005659 on 2 August 2021. Downloaded from The genomic epidemiology of multi- drug resistant invasive non- typhoidal Salmonella in selected sub-Saharan African countries 1,2 3,4 1 1 Se Eun Park , Duy Thanh Pham, Gi Deok Pak, Ursula Panzner, Ligia Maria Cruz Espinoza,1 Vera von Kalckreuth,1 Justin Im,1 Ondari D. Mogeni,1 1,5 6,7,8,9 10,11 Heidi Schütt- Gerowitt, John A Crump , Robert F Breiman, Yaw Adu- Sarkodie,12,13 Ellis Owusu- Dabo,12,13 Raphaël Rakotozandrindrainy,14 Abdramane Bassiahi Soura,15 Abraham Aseffa,16 Nagla Gasmelseed,17,18 Arvinda Sooka,19 Karen H Keddy,20 Jürgen May,21,22 Peter Aaby,23,24 Holly M Biggs,7,9 Julian T Hertz,7,9 Joel M Montgomery,10 Leonard Cosmas,10 Beatrice Olack,25 Barry Fields,10 Nimako Sarpong,12,22 Tsiriniaina Jean Luco Razafindrabe,14 Tiana Mirana Raminosoa,14 Leon Parfait Kabore,26 Emmanuel Sampo,26 Mekonnen Teferi,16 Biruk Yeshitela,16 Muna Ahmed El Tayeb,17 Ralf Krumkamp,21,22 Denise Myriam Dekker,21,22 Anna Jaeger,21,22 Adama Tall,27 Amy Gassama,27,28 Aissatou Niang,27 Morten Bjerregaard- Andersen,23,24 Sandra Valborg Løfberg,23,24 Jessica Fung Deerin,1 Jin Kyung Park,1 Frank Konings,1 Megan E Carey,29 To cite: Park SE, Pham DT, 30,31,32 1,33 1,34,35 Pak GD, . The genomic Sandra Van Puyvelde, Mohammad Ali, John Clemens, et al 29 29 1 epidemiology of multi- drug Gordon Dougan, Stephen Baker, Florian Marks resistant invasive non- typhoidal Salmonella in selected sub- Saharan African countries. BMJ Global Health ABSTRACT 2021;6:e005659. doi:10.1136/ Key questions bmjgh-2021-005659 Background Invasive non- typhoidal Salmonella (iNTS) is one of the leading causes of bacteraemia in sub- Saharan http://gh.bmj.com/ What is already known? Africa. We aimed to provide a better understanding of Handling editor Seye Abimbola Invasive non- typhoidal Salmonella (iNTS) disease is the genetic characteristics and transmission patterns ► an emerging pathogen in sub- Saharan Africa. ► Additional supplemental associated with multi- drug resistant (MDR) iNTS serovars iNTS is now a leading cause of bacteraemia in sub- material is published online only. across the continent. ► To view, please visit the journal Saharan Africa. Methods A total of 166 iNTS isolates collected from online (http:// dx. doi. org/ 10. The disease is associated with specific sequence a multi- centre surveillance in 10 African countries ► 1136/ bmjgh- 2021- 005659). types of S. Enteritidis and S. Typhimurium. on September 24, 2021 by guest. Protected copyright. (2010–2014) and a fever study in Ghana (2007–2009) were genome sequenced to investigate the geographical SEP and DTP contributed distribution, antimicrobial genetic determinants and equally. population structure of iNTS serotypes–genotypes. Conclusions We identified the circulation of multiple MDR iNTS serovar STs in the sampled sub-Saharan African Phylogenetic analyses were conducted in the context of the countries. Investment in the development and deployment Received 12 March 2021 existing genomic frameworks for various iNTS serovars. Accepted 6 July 2021 of iNTS vaccines coupled with intensified antimicrobial Population- based incidence of MDR- iNTS disease was resistance surveillance are essential to limit the impact of estimated in each study site. these pathogens in Africa. Results Salmonella Typhimurium sequence-type (ST) 313 © Author(s) (or their and Salmonella Enteritidis ST11 were predominant, and both employer(s)) 2021. Re- use exhibited high frequencies of MDR; Salmonella Dublin ST10 permitted under CC BY-NC. No was identified in West Africa only. Mutations in thegyrA gene BACKGROUND commercial re- use. See rights (fluoroquinolone resistance) were identified inS . Enteritidis and permissions. Published by The non- typhoidal members of Salmonella and S. Typhimurium in Ghana; an ST313 isolate carrying BMJ. enterica are archetypal zoonotic pathogens typi- blaCTX- M-15 was found in Kenya. International transmission For numbered affiliations see of MDR ST313 (lineage II) and MDR ST11 (West African cally associated with self- limiting diarrhoea in end of article. clade) was observed between Ghana and neighbouring humans. However, certain non- typhoidal Salmo- Correspondence to West African countries. The incidence of MDR-iNTS disease nella serovars are also a recognised cause of Professor Stephen Baker; exceeded 100/100 000 person- years- of- observation in invasive disease in specific geographical regions. sgb47@ medschl. cam. ac. uk children aged <5 years in several West African countries. Invasive non- typhoidal Salmonella (iNTS) is Park SE, et al. BMJ Global Health 2021;6:e005659. doi:10.1136/bmjgh-2021-005659 1 BMJ Global Health BMJ Glob Health: first published as 10.1136/bmjgh-2021-005659 on 2 August 2021. Downloaded from extensively drug-resistant (XDR) (MDR plus resistance to Key questions fluoroquinolones and third- generation cephalosporins) S. Typhimurium ST313 organisms have been reported What are the new findings? 14 27 28 29 ► iNTS disease is widespread across the sampled locations. in Kenya, Malawi and DRC. These new resistance ► Salmonella Typhimurium sequence- type (ST) 313 and Salmonella phenotypes pose a significant challenge for the control 14 Enteritidis ST11 are the predominant pathogens. of iNTS disease. ► There is a high frequency of multi- drug resistant (MDR) phenotypes. Here, we subjected a contemporaneous collection of iNTS ► The incidence of MDR- iNTS disease exceeded 100/100 000 organisms from multiple sites in sub- Saharan Africa to whole person- years- of- observation in children aged <5 years in several genome sequencing to investigate the phylogenetic distribu- West African countries. tion of these organisms and their corresponding sequence What do the new findings imply? types (STs) and antimicrobial resistance (AMR) determi- ► Sustained disease surveillance of MDR- iNTS organisms is essential. nants. We also estimated the incidence rates of MDR iNTS ► There is a need for acceleration of iNTS vaccines. disease in the sampling locations and performed phyloge- ► We need a better understanding of the disease reservoir and netic analyses of S. Typhimurium ST313 and S. Enteritidis human- to- human transmission. ST11 in a global context. METHODS most commonly observed in infants and young adults with Ethics approval and consent to participate HIV, malaria and malnutrition.1 Annually, there are an esti- This research was conducted under the ethical prin- mated 3.4 million cases of iNTS globally, 20% of which are ciples of the Declaration of Helsinki. The IVI Institu- fatal.2 3 The vast majority of iNTS disease is reported in sub- tional Review Board (IRB), the national ethical review Saharan Africa, where annual incidence rates of 175–388 committees in each participating country, and local cases per 100 000 person- years and case fatality rates as high research ethics committees approved the study protocol. as 25% have been reported in young children.4–6 A recent All eligible patients meeting the study inclusion criteria multi- centre study across 10 countries in sub- Saharan Africa were provided with a detailed explanation of the study identified iNTS as a major cause of bacteraemia in febrile purpose, and written informed consent was obtained patients, with incidence rates exceeding 100 cases per 100 prior to study enrolment. For children, written informed 000 person- years recorded in multiple sampling locations.7 consent was obtained from parent or guardian.30 Various Salmonella serovars have been associated with 8 9 iNTS disease, including S. Isangi, S. Concord, S. Stan- Study design and inclusion criteria 10 leyville and S. Dublin. However, the majority of iNTS The majority of iNTS isolates (117/166) in this study infections in sub- Saharan Africa can be attributed to S. originated from the Typhoid Fever Surveillance in Africa 11 12 Typhimurium and S. Enteritidis. Salmonella Typh- Program (TSAP),30 conducted in 13 sites in 10 countries imurium iNTS in sub- Saharan Africa is largely asso- between 2010 and 2014. Febrile patients from all age http://gh.bmj.com/ ciated with a multi-drug resistant (MDR; resistant to groups (except in Ghana, where only children aged <15 ampicillin, chloramphenicol and trimethoprim–sulfa- years were enrolled) with a tympanic or axillary temper- methoxazole) variant of ST313, which comprised two ature of ≥38.0 or ≥37.5 , respectively, living in a 11 ℃ ℃ major lineages (I and II). Salmonella Enteritidis account defined study catchment area were eligible for recruit- for approximately one- third of the iNTS cases reported ment. For inpatients, reported fever within 72 hours in sub- Saharan Africa and are primarily associated with of admission was also necessary for inclusion. Written on September 24, 2021 by guest. Protected copyright. genotype ST11. There are three major clades of S. Enter- informed consent/assent was obtained. Clinical assess- itidis ST11 (Global epidemic, West African and Central/ ments of patients included history of illness, physical East African clades) co- circulating in this region, in which examination and clinical appraisal. Blood samples (5–10 13 MDR phenotypes are common. mL for adults; 1–3 mL for children) were collected for Ampicillin, chloramphenicol and trimethoprim–sulfa- microbiological testing and diagnosis. An additional 49 methoxazole (co- trimoxazole) have traditionally served as iNTS isolates were obtained from a febrile surveillance 14 first- line treatment for iNTS and typhoid fever in Africa. study