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Two lineages of  Salmonella enterica  serovar Typhimurium ( S . Typhimurium) of multi-locus sequence type ST313 have been linked with the emergence of invasive  Salmonella  disease across sub-Saharan Africa. The expansion of these lineages has a temporal association with the HIV pandemic and antibiotic usage. We analysed the whole genome sequence of 129 ST313 isolates representative of the two lineages and found evidence of lineage-specific genome degradation, with some similarities to that observed in  S . Typhi. Individual ST313  S . Typhimurium isolates exhibit a distinct metabolic signature and modified enteropathogenesis in both a murine and cattle model of colitis, compared to  S . Typhimurium outside of the ST313 lineages. These data define phenotypes that distinguish ST313 isolates from other  S . Typhimurium and may represent adaptation to a distinct pathogenesis and lifestyle linked to an-immuno-compromised human population.

Signatures of Adaptation in Human Invasive Salmonella Typhimurium ST313 Populations from Sub-Saharan Africa