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 journalArticle

209 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 (US)
Pages (from-to)1215-1221
Number of pages7
JournalNature Genetics
Volume44
Issue number11
DOIs
StatePublished - Nov 1 2012

Fingerprint

Africa South of the Sahara
Salmonella typhimurium
Salmonella
Population
Salmonella enterica
Pandemics
Chloramphenicol
HIV
Genome
Anti-Bacterial Agents

ASJC Scopus subject areas

  • Genetics

Cite this

Okoro, C. K., Kingsley, R. A., Connor, T. R., Harris, S. R., Parry, C. M., Al-Mashhadani, M. N., ... Dougan, G. (2012). Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa. Nature Genetics, 44(11), 1215-1221. https://doi.org/10.1038/ng.2423

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

In: Nature Genetics, Vol. 44, No. 11, 01.11.2012, p. 1215-1221.

Research output: Contribution to journalArticle

Okoro, CK, Kingsley, RA, Connor, TR, Harris, SR, Parry, CM, Al-Mashhadani, MN, Kariuki, S, Msefula, CL, Gordon, MA, De Pinna, E, Wain, J, Heyderman, RS, Obaro, S, Alonso, PL, Mandomando, I, MacLennan, CA, Tapia, MD, Levine, MM, Tennant, SM, Parkhill, J & Dougan, G 2012, 'Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa', Nature Genetics, vol. 44, no. 11, pp. 1215-1221. https://doi.org/10.1038/ng.2423
Okoro CK, Kingsley RA, Connor TR, Harris SR, Parry CM, Al-Mashhadani MN et al. Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa. Nature Genetics. 2012 Nov 1;44(11):1215-1221. https://doi.org/10.1038/ng.2423
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. / Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa. In: Nature Genetics. 2012 ; Vol. 44, No. 11. pp. 1215-1221.
@article{5b75feb4c7ad40229b02ebae9b398ce9,
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.",
author = "Okoro, {Chinyere K.} and Kingsley, {Robert A.} and Connor, {Thomas R.} and Harris, {Simon R.} and Parry, {Christopher M.} and Al-Mashhadani, {Manar N.} and Samuel Kariuki and Msefula, {Chisomo L.} and Gordon, {Melita A.} and {De Pinna}, Elizabeth and John Wain and Heyderman, {Robert S.} and Stephen Obaro and Alonso, {Pedro L.} and Inacio Mandomando and MacLennan, {Calman A.} and Tapia, {Milagritos D.} and Levine, {Myron M.} and Tennant, {Sharon M.} and Julian Parkhill and Gordon Dougan",
year = "2012",
month = "11",
day = "1",
doi = "10.1038/ng.2423",
language = "English (US)",
volume = "44",
pages = "1215--1221",
journal = "Nature Genetics",
issn = "1061-4036",
publisher = "Nature Publishing Group",
number = "11",

}

TY - JOUR

T1 - Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa

AU - Okoro, Chinyere K.

AU - Kingsley, Robert A.

AU - Connor, Thomas R.

AU - Harris, Simon R.

AU - Parry, Christopher M.

AU - Al-Mashhadani, Manar N.

AU - Kariuki, Samuel

AU - Msefula, Chisomo L.

AU - Gordon, Melita A.

AU - De Pinna, Elizabeth

AU - Wain, John

AU - Heyderman, Robert S.

AU - Obaro, Stephen

AU - Alonso, Pedro L.

AU - Mandomando, Inacio

AU - MacLennan, Calman A.

AU - Tapia, Milagritos D.

AU - Levine, Myron M.

AU - Tennant, Sharon M.

AU - Parkhill, Julian

AU - Dougan, Gordon

PY - 2012/11/1

Y1 - 2012/11/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84868201561&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84868201561&partnerID=8YFLogxK

U2 - 10.1038/ng.2423

DO - 10.1038/ng.2423

M3 - Article

C2 - 23023330

AN - SCOPUS:84868201561

VL - 44

SP - 1215

EP - 1221

JO - Nature Genetics

JF - Nature Genetics

SN - 1061-4036

IS - 11

ER -