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

• Published in: Nature genetics Vol. 44; no. 11; pp. 1215 - 1221
• Main Authors: Okoro, Chinyere K, Kingsley, Robert A, Connor, Thomas R, Harris, Simon R, Parry, Christopher M, Al-Mashhadani, Manar N, Kariuki, Samuel, Msefula, Chisomo L, Gordon, Melita A, de Pinna, Elizabeth, Wain, John, Heyderman, Robert S, Obaro, Stephen, Alonso, Pedro L, Mandomando, Inacio, MacLennan, Calman A, Tapia, Milagritos D, Levine, Myron M, Tennant, Sharon M, Parkhill, Julian, Dougan, Gordon
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.11.2012; Nature Publishing Group
• Subjects: 631/181/757; 631/208/325/2482; 692/700/478/174; Acquired immune deficiency syndrome; Adults; Africa South of the Sahara - epidemiology; Agriculture; AIDS; Analysis; Animal Genetics and Genomics; Anti-Bacterial Agents - adverse effects; Anti-Bacterial Agents - therapeutic use; Antibacterial agents; Biological and medical sciences; Biomedicine; Cancer Research; Causes of; Chloramphenicol; Diseases; DNA sequencing; Drug Resistance, Multiple, Bacterial - genetics; Drug therapy; Evolution, Molecular; Fundamental and applied biological sciences. Psychology; Gene Function; Genetics of eukaryotes. Biological and molecular evolution; Genomes; Genomics; Health aspects; HIV; HIV Infections - epidemiology; Hogs; Human Genetics; Human immunodeficiency virus; Human populations; Humans; Invasive fish; Medical schools; Microbiology; Phylogenetics; Phylogeny; Phylogeography; Polymorphism, Single Nucleotide; Population structure; Risk factors; Salmonella; Salmonella enterica; Salmonella Infections - epidemiology; Salmonella Infections - genetics; Salmonella typhimurium; Salmonella typhimurium - classification; Salmonella typhimurium - genetics; Salmonella typhimurium - pathogenicity; Salmonellosis; Studies; Tropical diseases; Sub-Saharan Africa; Africa; Africa South of the Sahara; Mozambique; Malawi; Mali; United Kingdom; Uganda; Kenya; Nigeria; Human; Bacteria; Salmonella typhimurium; Enterobacteriaceae
• ISSN: 1061-4036; 1546-1718
• DOI: 10.1038/ng.2423

Gordon Dougan and colleagues report whole-genome sequencing of a global collection of 179 Salmonella Typhimurium isolates, including 129 diverse sub-Saharan African isolates associated with invasive disease. They determine the phylogenetic structure of invasive Salmonella Typhimurium in sub-Saharan Africa and find that the majority are from two closely related highly conserved lineages, which emerged in the last 60 years in close temporal association with the current HIV epidemic. 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.