Chinyere K. Okoro 1 , Robert A. Kingsley 1 , Thomas R. Connor 1 , Simon R. Harris 1 , Christopher M. Parry 2 , 3 , Manar N Al-Mashhadani 3 , Samuel Kariuki 4 , Chisomo L. Msefula 5 , 6 , Melita A. Gordon 7 , Elizabeth de Pinna 8 , John Wain 8 , 9 , Robert S. Heyderman 5 , 10 , Stephen Obaro 11 , 12 , Pedro L. Alonso 13 , 14 , Inacio Mandomando 14 , 15 , Calman A. MacLennan 16 , 17 , Milagritos D. Tapia 18 , Myron M. Levine 18 , 19 , Sharon M Tennant 19 , Julian Parkhill 1 , Gordon Dougan § , 1
30 September 2012
A highly invasive form of non-typhoidal Salmonella (iNTS) disease has been recently documented in many countries in sub-Saharan Africa. The most common Salmonella enterica serovar causing this disease is Typhimurium. We applied whole-genome sequence-based phylogenetic methods to define the population structure of sub-Saharan African invasive Salmonella Typhimurium and compared these to global Salmonella Typhimurium isolates. Notably, the vast majority of sub-Saharan invasive Salmonella Typhimurium 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 of lineage I by 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.