An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid

Vanessa K. Wong; Stephen Baker; Thomas R. Connor; Derek Pickard; Andrew J. Page; Jayshree Dave; Niamh Murphy; Richard Holliman; Armine Sefton; Michael Millar; Zoe A. Dyson; Gordon Dougan; Kathryn E. Holt; Julian Parkhill; Robert A. Kingsley; Nicholas R. Thomson; Jacqueline A. Keane; James Hadfield; Elizabeth J. Klemm; Simon R. Harris; Amy K. Cain; Samuel Kariuki; Chinyere Okoro; Calman A. MacLennan; Nga Tran Vu Thieu; Duy Pham Thanh; Corinne Thompson; Christiane Dolecek; James I. Campbell; Guy Thwaites; Jeremy Farrar; Paul N. Newton; David Dance; Paul Turner; E. Kim Mulholland; Jane Hawkey; David J. Edwards; Nick Feasey; François Xavier Weill; Simon Le Hello; Peter J. Hart; Robert F. Breiman; Robert S. Onsare; Conall H. Watson; W. John Edmunds; Melita A. Gordon; Robert S. Heyderman; Chisomo Msefula; Jan Jacobs; Octavie Lunguya; Jose A. Chabalgoity; Mike Kama; Kylie Jenkins; Shanta Dutta; Florian Marks; Josefina Campos; Stephen Obaro; Karen H. Keddy; Anthony M. Smith; Christopher Parry; Abhilasha Karkey; Sabina Dongol; Buddha Basnyat; Amit Arjyal; Muriel Dufour; Don Bandaranayake; Take N. Toleafoa; Shalini Pravin Singh; Mochammad Hatta; Viengmon Davong; Lupeoletalalelei Isaia; Lalith Wijedoru; John A. Crump; Elizabeth De Pinna; Satheesh Nair; Eric J. Nilles; Sona Soeng; Mary Valcanis; Joan Powling; Karolina Dimovski; Geoff Hogg; Alison E. Mather; Ben Amos

doi:10.1038/ncomms12827

An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid

Vanessa K. Wong
, Stephen Baker
, Thomas R. Connor
, Derek Pickard
, Andrew J. Page
, Jayshree Dave
, Niamh Murphy
, Richard Holliman
, Armine Sefton
, Michael Millar
, Zoe A. Dyson
, Gordon Dougan
, Kathryn E. Holt
, Julian Parkhill
, Robert A. Kingsley
, Nicholas R. Thomson
, Jacqueline A. Keane
, James Hadfield
, Elizabeth J. Klemm
, Simon R. Harris

Amy K. Cain, Samuel Kariuki, Chinyere Okoro, Calman A. MacLennan, Nga Tran Vu Thieu, Duy Pham Thanh, Corinne Thompson, Christiane Dolecek, James I. Campbell, Guy Thwaites, Jeremy Farrar, Paul N. Newton, David Dance, Paul Turner, E. Kim Mulholland, Jane Hawkey, David J. Edwards, Nick Feasey, François Xavier Weill, Simon Le Hello, Peter J. Hart, Robert F. Breiman, Robert S. Onsare, Conall H. Watson, W. John Edmunds, Melita A. Gordon, Robert S. Heyderman, Chisomo Msefula, Jan Jacobs, Octavie Lunguya, Jose A. Chabalgoity, Mike Kama, Kylie Jenkins, Shanta Dutta, Florian Marks, Josefina Campos, Stephen Obaro, Karen H. Keddy, Anthony M. Smith, Christopher Parry, Abhilasha Karkey, Sabina Dongol, Buddha Basnyat, Amit Arjyal, Muriel Dufour, Don Bandaranayake, Take N. Toleafoa, Shalini Pravin Singh, Mochammad Hatta, Viengmon Davong, Lupeoletalalelei Isaia, Lalith Wijedoru, John A. Crump, Elizabeth De Pinna, Satheesh Nair, Eric J. Nilles, Sona Soeng, Mary Valcanis, Joan Powling, Karolina Dimovski, Geoff Hogg, Alison E. Mather, Ben Amos

Clinical Sciences

Wellcome Sanger Institute
Cambridge University Hospitals NHS Foundation Trust
University of Oxford
London School of Hygiene and Tropical Medicine
Cardiff University
UK Health Security Agency
Barts Health NHS Trust
University of Melbourne
Quadram Institute
Kenya Medical Research Institute
University of Birmingham
Lao PDR
Mahidol University
Angkor Hospital for Children
Murdoch Children's Research Institute
Institut Pasteur Paris
Centers for Disease Control and Prevention
Emory University
University of Liverpool
University of Malawi
University College London
Institute of Tropical Medicine Antwerp
KU Leuven
National Institute for Biomedical Research
University Hospital of Kinshasa
Universidad de la República
Ministry of Health
National Institute of Cholera and Enteric Diseases India
International Vaccine Institute, Seoul
Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán"
University of Nebraska Medical Center
University of Abuja, Gwagwalada
Bingham University
University of the Witwatersrand
Nagasaki University
ESR
Samoa Ministry of Health
World Health Organization
Universitas Hasanuddin
Tupua Tamasese Meaole Hospital
Chelsea and Westminster Hospital NHS Foundation Trust
University of Otago
University of Cambridge
St Augustine’s Hospital

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

138 Citations (Scopus)

Abstract

The population of Salmonella enterica serovar Typhi (S. Typhi), the causative agent of typhoid fever, exhibits limited DNA sequence variation, which complicates efforts to rationally discriminate individual isolates. Here we utilize data from whole-genome sequences (WGS) of nearly 2,000 isolates sourced from over 60 countries to generate a robust genotyping scheme that is phylogenetically informative and compatible with a range of assays. These data show that, with the exception of the rapidly disseminating H58 subclade (now designated genotype 4.3.1), the global S. Typhi population is highly structured and includes dozens of subclades that display geographical restriction. The genotyping approach presented here can be used to interrogate local S. Typhi populations and help identify recent introductions of S. Typhi into new or previously endemic locations, providing information on their likely geographical source. This approach can be used to classify clinical isolates and provides a universal framework for further experimental investigations.

Original language	English
Article number	12827
Journal	Nature Communications
Volume	7
DOIs	https://doi.org/10.1038/ncomms12827
Publication status	Published - 1 Jan 2016

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SDG 3 Good Health and Well-being

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Wong, V. K., Baker, S., Connor, T. R., Pickard, D., Page, A. J., Dave, J., Murphy, N., Holliman, R., Sefton, A., Millar, M., Dyson, Z. A., Dougan, G., Holt, K. E., Parkhill, J., Kingsley, R. A., Thomson, N. R., Keane, J. A., Hadfield, J., Klemm, E. J., ... Amos, B. (2016). An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid. Nature Communications, 7, Article 12827. https://doi.org/10.1038/ncomms12827

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title = "An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid",

abstract = "The population of Salmonella enterica serovar Typhi (S. Typhi), the causative agent of typhoid fever, exhibits limited DNA sequence variation, which complicates efforts to rationally discriminate individual isolates. Here we utilize data from whole-genome sequences (WGS) of nearly 2,000 isolates sourced from over 60 countries to generate a robust genotyping scheme that is phylogenetically informative and compatible with a range of assays. These data show that, with the exception of the rapidly disseminating H58 subclade (now designated genotype 4.3.1), the global S. Typhi population is highly structured and includes dozens of subclades that display geographical restriction. The genotyping approach presented here can be used to interrogate local S. Typhi populations and help identify recent introductions of S. Typhi into new or previously endemic locations, providing information on their likely geographical source. This approach can be used to classify clinical isolates and provides a universal framework for further experimental investigations.",

author = "Wong, \{Vanessa K.\} and Stephen Baker and Connor, \{Thomas R.\} and Derek Pickard and Page, \{Andrew J.\} and Jayshree Dave and Niamh Murphy and Richard Holliman and Armine Sefton and Michael Millar and Dyson, \{Zoe A.\} and Gordon Dougan and Holt, \{Kathryn E.\} and Julian Parkhill and Kingsley, \{Robert A.\} and Thomson, \{Nicholas R.\} and Keane, \{Jacqueline A.\} and James Hadfield and Klemm, \{Elizabeth J.\} and Harris, \{Simon R.\} and Cain, \{Amy K.\} and Samuel Kariuki and Chinyere Okoro and MacLennan, \{Calman A.\} and \{Vu Thieu\}, \{Nga Tran\} and Thanh, \{Duy Pham\} and Corinne Thompson and Christiane Dolecek and Campbell, \{James I.\} and Guy Thwaites and Jeremy Farrar and Newton, \{Paul N.\} and David Dance and Paul Turner and Mulholland, \{E. Kim\} and Jane Hawkey and Edwards, \{David J.\} and Nick Feasey and Weill, \{Fran{\c c}ois Xavier\} and \{Le Hello\}, Simon and Hart, \{Peter J.\} and Breiman, \{Robert F.\} and Onsare, \{Robert S.\} and Watson, \{Conall H.\} and Edmunds, \{W. John\} and Gordon, \{Melita A.\} and Heyderman, \{Robert S.\} and Chisomo Msefula and Jan Jacobs and Octavie Lunguya and Chabalgoity, \{Jose A.\} and Mike Kama and Kylie Jenkins and Shanta Dutta and Florian Marks and Josefina Campos and Stephen Obaro and Keddy, \{Karen H.\} and Smith, \{Anthony M.\} and Christopher Parry and Abhilasha Karkey and Sabina Dongol and Buddha Basnyat and Amit Arjyal and Muriel Dufour and Don Bandaranayake and Toleafoa, \{Take N.\} and Singh, \{Shalini Pravin\} and Mochammad Hatta and Viengmon Davong and Lupeoletalalelei Isaia and Lalith Wijedoru and Crump, \{John A.\} and \{De Pinna\}, Elizabeth and Satheesh Nair and Nilles, \{Eric J.\} and Sona Soeng and Mary Valcanis and Joan Powling and Karolina Dimovski and Geoff Hogg and Mather, \{Alison E.\} and Ben Amos",

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day = "1",

doi = "10.1038/ncomms12827",

language = "English",

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journal = "Nature Communications",

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Wong, VK, Baker, S, Connor, TR, Pickard, D, Page, AJ, Dave, J, Murphy, N, Holliman, R, Sefton, A, Millar, M, Dyson, ZA, Dougan, G, Holt, KE, Parkhill, J, Kingsley, RA, Thomson, NR, Keane, JA, Hadfield, J, Klemm, EJ, Harris, SR, Cain, AK, Kariuki, S, Okoro, C, MacLennan, CA, Vu Thieu, NT, Thanh, DP, Thompson, C, Dolecek, C, Campbell, JI, Thwaites, G, Farrar, J, Newton, PN, Dance, D, Turner, P, Mulholland, EK, Hawkey, J, Edwards, DJ, Feasey, N, Weill, FX, Le Hello, S, Hart, PJ, Breiman, RF, Onsare, RS, Watson, CH, Edmunds, WJ, Gordon, MA, Heyderman, RS, Msefula, C, Jacobs, J, Lunguya, O, Chabalgoity, JA, Kama, M, Jenkins, K, Dutta, S, Marks, F, Campos, J, Obaro, S, Keddy, KH, Smith, AM, Parry, C, Karkey, A, Dongol, S, Basnyat, B, Arjyal, A, Dufour, M, Bandaranayake, D, Toleafoa, TN, Singh, SP, Hatta, M, Davong, V, Isaia, L, Wijedoru, L, Crump, JA, De Pinna, E, Nair, S, Nilles, EJ, Soeng, S, Valcanis, M, Powling, J, Dimovski, K, Hogg, G, Mather, AE & Amos, B 2016, 'An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid', Nature Communications, vol. 7, 12827. https://doi.org/10.1038/ncomms12827

TY - JOUR

T1 - An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid

AU - Wong, Vanessa K.

AU - Baker, Stephen

AU - Connor, Thomas R.

AU - Pickard, Derek

AU - Page, Andrew J.

AU - Dave, Jayshree

AU - Murphy, Niamh

AU - Holliman, Richard

AU - Sefton, Armine

AU - Millar, Michael

AU - Dyson, Zoe A.

AU - Dougan, Gordon

AU - Holt, Kathryn E.

AU - Parkhill, Julian

AU - Kingsley, Robert A.

AU - Thomson, Nicholas R.

AU - Keane, Jacqueline A.

AU - Hadfield, James

AU - Klemm, Elizabeth J.

AU - Harris, Simon R.

AU - Cain, Amy K.

AU - Kariuki, Samuel

AU - Okoro, Chinyere

AU - MacLennan, Calman A.

AU - Vu Thieu, Nga Tran

AU - Thanh, Duy Pham

AU - Thompson, Corinne

AU - Dolecek, Christiane

AU - Campbell, James I.

AU - Thwaites, Guy

AU - Farrar, Jeremy

AU - Newton, Paul N.

AU - Dance, David

AU - Turner, Paul

AU - Mulholland, E. Kim

AU - Hawkey, Jane

AU - Edwards, David J.

AU - Feasey, Nick

AU - Weill, François Xavier

AU - Le Hello, Simon

AU - Hart, Peter J.

AU - Breiman, Robert F.

AU - Onsare, Robert S.

AU - Watson, Conall H.

AU - Edmunds, W. John

AU - Gordon, Melita A.

AU - Heyderman, Robert S.

AU - Msefula, Chisomo

AU - Jacobs, Jan

AU - Lunguya, Octavie

AU - Chabalgoity, Jose A.

AU - Kama, Mike

AU - Jenkins, Kylie

AU - Dutta, Shanta

AU - Marks, Florian

AU - Campos, Josefina

AU - Obaro, Stephen

AU - Keddy, Karen H.

AU - Smith, Anthony M.

AU - Parry, Christopher

AU - Karkey, Abhilasha

AU - Dongol, Sabina

AU - Basnyat, Buddha

AU - Arjyal, Amit

AU - Dufour, Muriel

AU - Bandaranayake, Don

AU - Toleafoa, Take N.

AU - Singh, Shalini Pravin

AU - Hatta, Mochammad

AU - Davong, Viengmon

AU - Isaia, Lupeoletalalelei

AU - Wijedoru, Lalith

AU - Crump, John A.

AU - De Pinna, Elizabeth

AU - Nair, Satheesh

AU - Nilles, Eric J.

AU - Soeng, Sona

AU - Valcanis, Mary

AU - Powling, Joan

AU - Dimovski, Karolina

AU - Hogg, Geoff

AU - Mather, Alison E.

AU - Amos, Ben

PY - 2016/1/1

Y1 - 2016/1/1

N2 - The population of Salmonella enterica serovar Typhi (S. Typhi), the causative agent of typhoid fever, exhibits limited DNA sequence variation, which complicates efforts to rationally discriminate individual isolates. Here we utilize data from whole-genome sequences (WGS) of nearly 2,000 isolates sourced from over 60 countries to generate a robust genotyping scheme that is phylogenetically informative and compatible with a range of assays. These data show that, with the exception of the rapidly disseminating H58 subclade (now designated genotype 4.3.1), the global S. Typhi population is highly structured and includes dozens of subclades that display geographical restriction. The genotyping approach presented here can be used to interrogate local S. Typhi populations and help identify recent introductions of S. Typhi into new or previously endemic locations, providing information on their likely geographical source. This approach can be used to classify clinical isolates and provides a universal framework for further experimental investigations.

AB - The population of Salmonella enterica serovar Typhi (S. Typhi), the causative agent of typhoid fever, exhibits limited DNA sequence variation, which complicates efforts to rationally discriminate individual isolates. Here we utilize data from whole-genome sequences (WGS) of nearly 2,000 isolates sourced from over 60 countries to generate a robust genotyping scheme that is phylogenetically informative and compatible with a range of assays. These data show that, with the exception of the rapidly disseminating H58 subclade (now designated genotype 4.3.1), the global S. Typhi population is highly structured and includes dozens of subclades that display geographical restriction. The genotyping approach presented here can be used to interrogate local S. Typhi populations and help identify recent introductions of S. Typhi into new or previously endemic locations, providing information on their likely geographical source. This approach can be used to classify clinical isolates and provides a universal framework for further experimental investigations.

U2 - 10.1038/ncomms12827

DO - 10.1038/ncomms12827

M3 - Article

SN - 2041-1723

VL - 7

JO - Nature Communications

JF - Nature Communications

M1 - 12827

ER -

An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid

Abstract

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