Prevalence of Salmonella in Stool during the Vaccine Impact on Diarrhea in Africa (VIDA) Study, 2015-2018

Background: Non-Typhoidal Salmonella (NTS) is a common cause of gastroenteritis in young children, with limited data on NTS serovars and antimicrobial resistance in Africa. Methods: We determined the prevalence of Salmonella spp. and frequency of antimicrobial resistance among serovars identified in stools of 0-59 month-old children with moderate-To-severe diarrhea (MSD) and controls enrolled in the Vaccine Impact on Diarrhea in Africa (VIDA) Study in The Gambia, Mali, and Kenya in 2015-2018, and compared with data from the Global Enteric Multicenter Study (GEMS; 2007-2010) and the GEMS-1A study (2011). Salmonella spp. was detected by quantitative real-Time PCR (qPCR) and culture-based methods. Identification of serovars was determined by microbiological methods. Results: By qPCR, the prevalence of Salmonella spp. among MSD cases was 4.0%, 1.6%, and 1.9% and among controls was 4.6%, 2.4%, and 1.6% in The Gambia, Mali, and Kenya, respectively, during VIDA. We observed year-To-year variation in serovar distribution and variation between sites. In Kenya, Salmonella enterica serovar Typhimurium decreased (78.1% to 23.1%; P <. 001) among cases and controls from 2007 to 2018, whereas serogroup O:8 increased (8.7% to 38.5%; P =. 04). In The Gambia, serogroup O:7 decreased from 2007 to 2018 (36.3% to 0%; P =. 001) but S. enterica serovar Enteritidis increased during VIDA (2015 to 2018; 5.9% to 50%; P =. 002). Only 4 Salmonella spp. were isolated in Mali during all 3 studies. Multidrug resistance was 33.9% in Kenya and 0.8% in The Gambia across all 3 studies. Ceftriaxone resistance was only observed in Kenya (2.3%); NTS isolates were susceptible to ciprofloxacin at all sites. Conclusions: Understanding variability in serovar distribution will be important for the future deployment of vaccines against salmonellosis in Africa.