Full genomic dissection of the emerging clone of Salmonella serovar Typhimurium ST313 from several African countries - real virulence or just opportunism?

Background; Salmonella Typhimurium ST313 is a invasive and phylogenetically distinct lineage in sub-Saharan Africa. We report the presence S. Typhimurium ST313 from patients in Democratic Republic of Congo and Nigeria. Methods; Eighteen ST313 isolates were characterized by antimicrobial susceptibility testing, pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST). Six isolates were also characterized by whole genome sequence typing (WGST). The presence of a putative virulence determinant was examined in 177 Salmonella isolates belonging to 57 different serovars. Results; All ST313 isolates contained resistant phenotype encoded by blaTEM1b, catA1, strA/B, sul1, and dfrA1. Additionally, aac(6’)1aa was detected. Phylogenetic analyses revealed close genetic relationships among Congolese and Nigerian isolates from both blood and stool. Comparative genomic analyses identified a putative virulence fragment (ST313-TD) unique to S. Typhimurium ST313 and S. Dublin. Conclusion; Our data suggest that S. Typhimurium ST313 is a recently emerged lineage capable of gastrointestinal and invasive disease. The genetic similarity of isolates across sub-Saharan Africa and the absence of a food-animal reservoir suggest a recent dissemination due to human or wild animal migration.