Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa

Chinyere K. Okoro, Robert A Kingsley, Thomas R Connor, Simon R. Harris, Christopher M. Parry, Manar N. Al-Mashhadani, Samuel Kariuki, Chisomo L. Msefula, Melita A Gordon, Elizabeth De Pinna, John Wain, Robert S. Heyderman, Stephen Obaro, Pedro L. Alonso, Inacio Mandomando, Calman A MacLennan, Milagritos D. Tapia, Myron M. Levine, Sharon M Tennant, Julian ParkhillGordon Dougan

Research output: Contribution to journalArticleResearchpeer-review

230 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)1215-1221
Number of pages7
JournalNature Genetics
Volume44
Issue number11
DOIs
Publication statusPublished - Nov 2012
Externally publishedYes

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