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; Nicholas A. 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 M. 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. HarrisAmy 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, Nicholas A. 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 M. 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

^*Corresponding author for this work

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

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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
Pages (from-to)	1-11
Number of pages	11
Journal	Nature Communications
Volume	7
DOIs	https://doi.org/10.1038/ncomms12827
Publication status	Published - 5 Oct 2016
Externally published	Yes

Bibliographical note

Copyright the Author(s) 2016. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

Keywords

Cluster Analysis
DNA, Bacterial
Genotype
Geography
Haplotypes
Humans
Phylogeny
Polymorphism, Single Nucleotide
Salmonella typhi/genetics
Sequence Analysis, DNA/methods
Typhoid Fever/microbiology

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10.1038/ncomms12827

Publisher VersionFinal published version, 2.81 MBLicence: CC BY

Cite this

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, 1-11. 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.",

keywords = "Cluster Analysis, DNA, Bacterial, Genotype, Geography, Haplotypes, Humans, Phylogeny, Polymorphism, Single Nucleotide, Salmonella typhi/genetics, Sequence Analysis, DNA/methods, Typhoid Fever/microbiology",

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 Feasey, {Nicholas A.} 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 Parry, {Christopher M.} 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",

note = "Copyright the Author(s) 2016. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher. ",

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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, NA, 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, CM, 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, pp. 1-11. 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, Nicholas A.

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 M.

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

N1 - Copyright the Author(s) 2016. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

PY - 2016/10/5

Y1 - 2016/10/5

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.

KW - Cluster Analysis

KW - DNA, Bacterial

KW - Genotype

KW - Geography

KW - Haplotypes

KW - Humans

KW - Phylogeny

KW - Polymorphism, Single Nucleotide

KW - Salmonella typhi/genetics

KW - Sequence Analysis, DNA/methods

KW - Typhoid Fever/microbiology

UR - http://www.scopus.com/inward/record.url?scp=84991011519&partnerID=8YFLogxK

U2 - 10.1038/ncomms12827

DO - 10.1038/ncomms12827

M3 - Article

C2 - 27703135

AN - SCOPUS:84991011519

SN - 2041-1723

VL - 7

SP - 1

EP - 11

JO - Nature Communications

JF - Nature Communications

M1 - 12827

ER -

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

Abstract

Bibliographical note

Keywords

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