A highly invasive form of non-typhoidal Salmonella (iNTS) disease has recently been documented in many countries in sub-Saharan Africa. The most common Salmonella enterica serovar causing this disease is Typhimurium (Salmonella Typhimurium). We applied whole-genome sequence-based phylogenetic methods to define the population structure of sub-Saharan African invasive Salmonella Typhimurium isolates and compared these to global Salmonella Typhimurium populations. Notably, the vast majority of sub-Saharan invasive Salmonella Typhimurium isolates fell within two closely related, highly clustered phylogenetic lineages that we estimate emerged independently ∼52 and ∼35 years ago in close temporal association with the current HIV pandemic. Clonal replacement of isolates from lineage I by those from lineage II was potentially influenced by the use of chloramphenicol for the treatment of iNTS disease. Our analysis suggests that iNTS disease is in part an epidemic in sub-Saharan Africa caused by highly related Salmonella Typhimurium lineages that may have occupied new niches associated with a compromised human population and antibiotic treatment.
Bibliographical noteFunding Information:
We thank J. Cheesborough for providing the DRC isolates, M. Okong, N. French and the Medical Research Council, Uganda, for providing the Uganda isolates, S. Nair for providing the Health Protection Agency (HPA) isolates, L. Barquist for modeling the pre-1990 HIV prevalence data and the Sequencing team at the Wellcome Trust Sanger Institute. This work was funded by a Wellcome Trust grant (098051). C.A.M. was supported by a Tropical Research Fellowship from the Wellcome Trust and a Clinical Research Fellowship from GlaxoSmithKline.