Supporting evidence for a human reservoir of invasive non-Typhoidal Salmonella from household samples in Burkina Faso

Abstract

BackgroundSalmonella Typhimurium and Enteritidis are major causes of bloodstream infection in children in sub-Saharan Africa. This study assessed evidence for their zoonotic versus human reservoir.MethodsIndex patients were children with blood culture confirmed Salmonella infection recruited during a microbiological surveillance study in Nanoro, rural Burkina between May 2013 and August 2014. After consent, their households were visited. Stool from household members and livestock (pooled samples per species) as well as drinking water were cultured for Salmonella. Isolates with identical serotype obtained from index patient and any household sample were defined as “paired isolates” and assessed for genetic relatedness by multilocus variable number tandem-repeat analysis (MLVA) and whole-genome sequencing (WGS).ResultsTwenty-nine households were visited for 32/42 (76.2%) eligible index patients: two households comprised two index patients each, and in a third household the index patient had a recurrent infection. Among the 32 index patients, serotypes were Salmonella Typhimurium (n = 26), Salmonella Enteritidis (n = 5) and Salmonella Freetown (n = 1). All Typhimurium isolates were sequence type (ST)313. Median delay between blood culture sampling and household visits was 13 days (range 6–26). Salmonella was obtained from 16/186 (8.6%) livestock samples (13 serotypes) and 18/290 (6.2%) household members (9 serotypes). None of the water samples yielded Salmonella. Paired Salmonella Typhimurium isolates were obtained from three households representing four index patients. MLVA types were identical in two pairs and similar in the third (consisting of two index patients and one household member). WGS showed a strong genetic relatedness with 0 to 2 core genome SNPs difference between pairs on a household level. Livestock samples did not yield any Salmonella Typhimurium or Salmonella Enteritidis, and the latter was exclusively obtained from blood culture. Other serotypes shared by human and/or livestock carriers in the same household were Salmonella Derby, Drac, Tennessee and Muenster.Conclusions/SignificanceThe current study provides further evidence of a human reservoir for invasive non-Typhoidal Salmonella (iNTS) in sub-Saharan Africa.

High genetic similarity between non-typhoidal Salmonella isolated from paired blood and stool samples of children in the Democratic Republic of the Congo

“…The high rate of NTS pairs (29.1% but probably higher given the single stool sampling under antibiotic coverage) provides incremental evidence for a human reservoir of invasive NTS. It complements studies showing NTS stool excretion among household members of index patients with NTS BSI [12,40]. In addition, MLVA types of stool isolates from the control group were similar to those of the NTS pairs from the NTS BSI group, which is in line with previous findings from the same area in DR Congo [39].…”

Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa

“…This study provides a snapshot of the large repertoire of genomic changes that shaped the emergence of successful ST313 lineages. The stepwise pseudogenization of genes reported here is consistent with the host adaptation of S. Typhimurium ST313 lineages over evolutionary history 6,40 and 14 ).…”

“…ST313 L3 has a functional bcsG gene and had the same csgD-associated −189 promoter mutation as ST313 L1 and L2 39 . Our finding that ST313 L3 has lost traits required for stress resistance and biofilm formation is consistent with a reduced requirement for environmental survival and the mounting evidence for human-to-human transmission of ST313 40,41 .…”

Pathogenic signature of invasive non-typhoidal Salmonella in Africa: implications for vaccine development

“…10,14,15 To date, an animal reservoir for iNTS has not been identified, 16 whereas asymptomatic carriage has recently been described in humans. 17,18 These observations corroborate the hypothesis that African NTS serovars are increasing their potential for systemic dissemination in humans and can be spread from person to person, in addition to the classic zoonotic transmission.…”