Non-Typhoidal Salmonella (NTS) mainly causes gastroenteritis; however, the NTS strains prevalent in Africa are a leading cause of bloodstream or invasive infections in children and immunocompromised adults, with a fatality rate of 20–25% [1-3]. Two-thirds of the invasive NTS (iNTS) cases were caused by Salmonella Typhimurium. The mechanisms by which the prevalent African NTS strains cause bloodstream infections remain unclear.
This study included an analysis of 2002 Salmonella Typhimurium genomes, encompassing both iNTS and gastroenteritis-causing strains, to identify putative genetic factors associated with iNTS. Genetic variations were identified and categorized into different types: synonymous and non-synonymous variations, pseudogenization, and gene upstream variations. The 2002 genomes were grouped into 9 lineages, 3 of which were prevalent in Africa and were associated with bloodstream infections. Genetic variations that were specifically present in Africa prevalent lineages may play a role in iNTS. SalcomSNP, an interactive visualization dashboard, was developed to shortlist the genetic variations present in iNTS lineages but absent in gastroenteritis lineages. To further assess the functions of these iNTS lineage-specific genetic variations, transcriptomics and mutagenesis data were incorporated. Using this interactive multi-omics analysis method, previously published genes associated with iNTS were successfully shortlisted [4-5]. Additionally, a list of new genes potentially associated with iNTS was identified for further experimental assessment.
Overall, SalcomSNP is a robust multi-omics platform for elucidating the mechanisms of bloodstream infections caused by African non-Typhoidal Salmonella.