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Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa. / Pulford, Caisey V.; Perez-Sepulveda, Blanca M.; Canals, Rocío; Bevington, Jessica A.; Bengtsson, Rebecca J.; Wenner, Nicolas; Rodwell, Ella V.; Kumwenda, Benjamin; Zhu, Xiaojun; Bennett, Rebecca J.; Stenhouse, George E.; Malaka De Silva, P.; Webster, Hermione J.; Bengoechea, Jose A.; Dumigan, Amy; Tran-Dien, Alicia; Prakash, Reenesh; Banda, Happy C.; Alufandika, Lovemore; Mautanga, Mike P.; Bowers-Barnard, Arthur; Beliavskaia, Alexandra Y.; Predeus, Alexander V.; Rowe, Will P.M.; Darby, Alistair C.; Hall, Neil; Weill, François Xavier; Gordon, Melita A.; Feasey, Nicholas A.; Baker, Kate S.; Hinton, Jay C.D.

In: Nature Microbiology, Vol. 6, No. 3, 03.2021, p. 327-338.

Research output: Contribution to journal › Article › peer-review

Harvard

Pulford, CV, Perez-Sepulveda, BM, Canals, R, Bevington, JA, Bengtsson, RJ, Wenner, N, Rodwell, EV, Kumwenda, B, Zhu, X, Bennett, RJ, Stenhouse, GE, Malaka De Silva, P, Webster, HJ, Bengoechea, JA, Dumigan, A, Tran-Dien, A, Prakash, R, Banda, HC, Alufandika, L, Mautanga, MP, Bowers-Barnard, A, Beliavskaia, AY, Predeus, AV, Rowe, WPM, Darby, AC, Hall, N, Weill, FX, Gordon, MA, Feasey, NA, Baker, KS & Hinton, JCD 2021, 'Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa', Nature Microbiology, vol. 6, no. 3, pp. 327-338. https://doi.org/10.1038/s41564-020-00836-1

APA

Pulford, C. V., Perez-Sepulveda, B. M., Canals, R., Bevington, J. A., Bengtsson, R. J., Wenner, N., Rodwell, E. V., Kumwenda, B., Zhu, X., Bennett, R. J., Stenhouse, G. E., Malaka De Silva, P., Webster, H. J., Bengoechea, J. A., Dumigan, A., Tran-Dien, A., Prakash, R., Banda, H. C., Alufandika, L., ... Hinton, J. C. D. (2021). Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa. Nature Microbiology, 6(3), 327-338. https://doi.org/10.1038/s41564-020-00836-1

Vancouver

Pulford CV, Perez-Sepulveda BM, Canals R, Bevington JA, Bengtsson RJ, Wenner N et al. Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa. Nature Microbiology. 2021 Mar;6(3):327-338. https://doi.org/10.1038/s41564-020-00836-1

Author

Pulford, Caisey V. ; Perez-Sepulveda, Blanca M. ; Canals, Rocío ; Bevington, Jessica A. ; Bengtsson, Rebecca J. ; Wenner, Nicolas ; Rodwell, Ella V. ; Kumwenda, Benjamin ; Zhu, Xiaojun ; Bennett, Rebecca J. ; Stenhouse, George E. ; Malaka De Silva, P. ; Webster, Hermione J. ; Bengoechea, Jose A. ; Dumigan, Amy ; Tran-Dien, Alicia ; Prakash, Reenesh ; Banda, Happy C. ; Alufandika, Lovemore ; Mautanga, Mike P. ; Bowers-Barnard, Arthur ; Beliavskaia, Alexandra Y. ; Predeus, Alexander V. ; Rowe, Will P.M. ; Darby, Alistair C. ; Hall, Neil ; Weill, François Xavier ; Gordon, Melita A. ; Feasey, Nicholas A. ; Baker, Kate S. ; Hinton, Jay C.D. / Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa. In: Nature Microbiology. 2021 ; Vol. 6, No. 3. pp. 327-338.

BibTeX

@article{f05fcf31017d4249a055350475562440,
title = "Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa",
abstract = "Bloodstream infections caused by nontyphoidal Salmonella are a major public health concern in Africa, causing ~49,600 deaths every year. The most common Salmonella enterica pathovariant associated with invasive nontyphoidal Salmonella disease is Salmonella Typhimurium sequence type (ST)313. It has been proposed that antimicrobial resistance and genome degradation has contributed to the success of ST313 lineages in Africa, but the evolutionary trajectory of such changes was unclear. Here, to define the evolutionary dynamics of ST313, we sub-sampled from two comprehensive collections of Salmonella isolates from African patients with bloodstream infections, spanning 1966 to 2018. The resulting 680 genome sequences led to the discovery of a pan-susceptible ST313 lineage (ST313 L3), which emerged in Malawi in 2016 and is closely related to ST313 variants that cause gastrointestinal disease in the United Kingdom and Brazil. Genomic analysis revealed degradation events in important virulence genes in ST313 L3, which had not occurred in other ST313 lineages. Despite arising only recently in the clinic, ST313 L3 is a phylogenetic intermediate between ST313 L1 and L2, with a characteristic accessory genome. Our in-depth genotypic and phenotypic characterization identifies the crucial loss-of-function genetic events that occurred during the stepwise evolution of invasive S. Typhimurium across Africa.",
keywords = "ENTERICA SEROVAR TYPHIMURIUM, DRUG-RESISTANCE, IDENTIFICATION, ALIGNMENT, TOOL, VIRULENCE, PROPHAGE, DISEASE, SETS",
author = "Pulford, {Caisey V.} and Perez-Sepulveda, {Blanca M.} and Roc{\'i}o Canals and Bevington, {Jessica A.} and Bengtsson, {Rebecca J.} and Nicolas Wenner and Rodwell, {Ella V.} and Benjamin Kumwenda and Xiaojun Zhu and Bennett, {Rebecca J.} and Stenhouse, {George E.} and {Malaka De Silva}, P. and Webster, {Hermione J.} and Bengoechea, {Jose A.} and Amy Dumigan and Alicia Tran-Dien and Reenesh Prakash and Banda, {Happy C.} and Lovemore Alufandika and Mautanga, {Mike P.} and Arthur Bowers-Barnard and Beliavskaia, {Alexandra Y.} and Predeus, {Alexander V.} and Rowe, {Will P.M.} and Darby, {Alistair C.} and Neil Hall and Weill, {Fran{\c c}ois Xavier} and Gordon, {Melita A.} and Feasey, {Nicholas A.} and Baker, {Kate S.} and Hinton, {Jay C.D.}",
note = "Publisher Copyright: {\textcopyright} 2020, The Author(s).",
year = "2021",
month = mar,
doi = "10.1038/s41564-020-00836-1",
language = "English",
volume = "6",
pages = "327--338",
journal = "Nature Microbiology",
issn = "2058-5276",
publisher = "Nature Publishing Group",
number = "3",

}

RIS

TY - JOUR

T1 - Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa

AU - Pulford, Caisey V.

AU - Perez-Sepulveda, Blanca M.

AU - Canals, Rocío

AU - Bevington, Jessica A.

AU - Bengtsson, Rebecca J.

AU - Wenner, Nicolas

AU - Rodwell, Ella V.

AU - Kumwenda, Benjamin

AU - Zhu, Xiaojun

AU - Bennett, Rebecca J.

AU - Stenhouse, George E.

AU - Malaka De Silva, P.

AU - Webster, Hermione J.

AU - Bengoechea, Jose A.

AU - Dumigan, Amy

AU - Tran-Dien, Alicia

AU - Prakash, Reenesh

AU - Banda, Happy C.

AU - Alufandika, Lovemore

AU - Mautanga, Mike P.

AU - Bowers-Barnard, Arthur

AU - Beliavskaia, Alexandra Y.

AU - Predeus, Alexander V.

AU - Rowe, Will P.M.

AU - Darby, Alistair C.

AU - Hall, Neil

AU - Weill, François Xavier

AU - Gordon, Melita A.

AU - Feasey, Nicholas A.

AU - Baker, Kate S.

AU - Hinton, Jay C.D.

N1 - Publisher Copyright: © 2020, The Author(s).

PY - 2021/3

Y1 - 2021/3

N2 - Bloodstream infections caused by nontyphoidal Salmonella are a major public health concern in Africa, causing ~49,600 deaths every year. The most common Salmonella enterica pathovariant associated with invasive nontyphoidal Salmonella disease is Salmonella Typhimurium sequence type (ST)313. It has been proposed that antimicrobial resistance and genome degradation has contributed to the success of ST313 lineages in Africa, but the evolutionary trajectory of such changes was unclear. Here, to define the evolutionary dynamics of ST313, we sub-sampled from two comprehensive collections of Salmonella isolates from African patients with bloodstream infections, spanning 1966 to 2018. The resulting 680 genome sequences led to the discovery of a pan-susceptible ST313 lineage (ST313 L3), which emerged in Malawi in 2016 and is closely related to ST313 variants that cause gastrointestinal disease in the United Kingdom and Brazil. Genomic analysis revealed degradation events in important virulence genes in ST313 L3, which had not occurred in other ST313 lineages. Despite arising only recently in the clinic, ST313 L3 is a phylogenetic intermediate between ST313 L1 and L2, with a characteristic accessory genome. Our in-depth genotypic and phenotypic characterization identifies the crucial loss-of-function genetic events that occurred during the stepwise evolution of invasive S. Typhimurium across Africa.

AB - Bloodstream infections caused by nontyphoidal Salmonella are a major public health concern in Africa, causing ~49,600 deaths every year. The most common Salmonella enterica pathovariant associated with invasive nontyphoidal Salmonella disease is Salmonella Typhimurium sequence type (ST)313. It has been proposed that antimicrobial resistance and genome degradation has contributed to the success of ST313 lineages in Africa, but the evolutionary trajectory of such changes was unclear. Here, to define the evolutionary dynamics of ST313, we sub-sampled from two comprehensive collections of Salmonella isolates from African patients with bloodstream infections, spanning 1966 to 2018. The resulting 680 genome sequences led to the discovery of a pan-susceptible ST313 lineage (ST313 L3), which emerged in Malawi in 2016 and is closely related to ST313 variants that cause gastrointestinal disease in the United Kingdom and Brazil. Genomic analysis revealed degradation events in important virulence genes in ST313 L3, which had not occurred in other ST313 lineages. Despite arising only recently in the clinic, ST313 L3 is a phylogenetic intermediate between ST313 L1 and L2, with a characteristic accessory genome. Our in-depth genotypic and phenotypic characterization identifies the crucial loss-of-function genetic events that occurred during the stepwise evolution of invasive S. Typhimurium across Africa.

KW - ENTERICA SEROVAR TYPHIMURIUM

KW - DRUG-RESISTANCE

KW - IDENTIFICATION

KW - ALIGNMENT

KW - TOOL

KW - VIRULENCE

KW - PROPHAGE

KW - DISEASE

KW - SETS

UR - http://www.scopus.com/inward/record.url?scp=85097902874&partnerID=8YFLogxK

UR - https://www.mendeley.com/catalogue/512cd890-f6be-3368-ad8a-9c12ae3f6e7c/

U2 - 10.1038/s41564-020-00836-1

DO - 10.1038/s41564-020-00836-1

M3 - Article

C2 - 33349664

AN - SCOPUS:85097902874

VL - 6

SP - 327

EP - 338

JO - Nature Microbiology

JF - Nature Microbiology

SN - 2058-5276

IS - 3

ER -

ID: 88620341