title: Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa.
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.
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Chinyere K
authors.initials: CK
authors.lastname: Okoro
authors.forename: Robert A
authors.initials: RA
authors.lastname: Kingsley
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Connor
authors.forename: Simon R
authors.initials: SR
authors.lastname: Harris
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Parry
authors.forename: Manar N
authors.initials: MN
authors.lastname: Al-Mashhadani
authors.forename: Samuel
authors.initials: S
authors.lastname: Kariuki
authors.forename: Chisomo L
authors.initials: CL
authors.lastname: Msefula
authors.forename: Melita A
authors.initials: MA
authors.lastname: Gordon
authors.forename: Elizabeth
authors.initials: E
authors.lastname: de Pinna
authors.forename: John
authors.initials: J
authors.lastname: Wain
authors.forename: Robert S
authors.initials: RS
authors.lastname: Heyderman
authors.forename: Stephen
authors.initials: S
authors.lastname: Obaro
authors.forename: Pedro L
authors.initials: PL
authors.lastname: Alonso
authors.forename: Inacio
authors.initials: I
authors.lastname: Mandomando
authors.forename: Calman A
authors.initials: CA
authors.lastname: MacLennan
authors.forename: Milagritos D
authors.initials: MD
authors.lastname: Tapia
authors.forename: Myron M
authors.initials: MM
authors.lastname: Levine
authors.forename: Sharon M
authors.initials: SM
authors.lastname: Tennant
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.forename: Gordon
authors.initials: G
authors.lastname: Dougan
mesh_terms: D017954:Africa South of the Sahara / Q000453:epidemiology; D000900:Anti-Bacterial Agents / Q000009:adverse effects / Q000627:therapeutic use; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics*; D019143:Evolution, Molecular; D015658:HIV Infections / Q000453:epidemiology; D006801:Humans; D010802:Phylogeny; D058974:Phylogeography; D020641:Polymorphism, Single Nucleotide; D012480:Salmonella Infections / Q000453:epidemiology / Q000235:genetics; D012486:Salmonella typhimurium / Q000145:classification / Q000235:genetics / Q000472:pathogenicity
chemical_list: D000900:Anti-Bacterial Agents