Whole genome sequencing of Salmonella enterica serovars isolated from humans, animals and environment in Nigeria

In the current study, the serotyping of non-typhoidal Salmonella (NTS) isolates from different sources in Lagos, Nigeria, was carried out, and their virulence and antimicrobial resistance genes were investigated using WGS data. In total, 2,522 samples were collected from patients, animals, and environmental sources between December 2017 and May 2019. Forty eight (48) NTS isolates (1.9%) were obtained. The prevalence of NTS from clinical sources was 0.9%, while 4% was recorded for animal sources. The serovars identified were S. Cotham (n=17), S. Give (n=16), S. Mokola (n=6), S. Abony (n=4), S. Typhimurium (n=4), and S. Senftenberg (n=1). WGS revealed that strains of each Salmonella serovar could be assigned to a single MLST cluster and strains within the clusters were closely related and likely shared a common ancestor. The dominant sequence types were S. Give ST516 and S. Cotham ST617. All the 48 Salmonella isolates carried multiple intrinsic and acquired genes which had been described to confer resistance to antibiotics, heavy metals and transporters. Between 100 and 118 virulence gene markers distributed across several Salmonella pathogenicity islands (SPIs), clusters, prophages, and plasmid operons were found in each isolate. However, phenotypic resistance testing could not confirm the predicted resistance in all cases. We found almost identical strains in human, animal, and environmental samples in the same locality, which demonstrates the great potential of the applied tools to trace back outbreak-strains. Strategies to control and prevent the evolution of NTS in the context of one health are essential to prevent further outbreaks.