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

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

54 Scopus citations

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 (US)
Article number	12827
Journal	Nature communications
Volume	7
DOIs	https://doi.org/10.1038/ncomms12827
State	Published - 2016

ASJC Scopus subject areas

Chemistry(all)
Biochemistry, Genetics and Molecular Biology(all)
Physics and Astronomy(all)

Access to Document

10.1038/ncomms12827

Fingerprint Dive into the research topics of 'An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid'. Together they form a unique fingerprint.

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, [12827]. https://doi.org/10.1038/ncomms12827

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

In: Nature communications, Vol. 7, 12827, 2016.

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

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. https://doi.org/10.1038/ncomms12827

Wong, Vanessa K. ; Baker, Stephen ; Connor, Thomas R. ; Pickard, Derek ; Page, Andrew J. ; Dave, Jayshree ; Murphy, Niamh ; Holliman, Richard ; Sefton, Armine ; Millar, Michael ; Dyson, Zoe A. ; Dougan, Gordon ; Holt, Kathryn E. ; Parkhill, Julian ; Kingsley, Robert A. ; Thomson, Nicholas R. ; Keane, Jacqueline A. ; Hadfield, James ; Klemm, Elizabeth J. ; Harris, Simon R. ; Cain, Amy K. ; Kariuki, Samuel ; Okoro, Chinyere ; MacLennan, Calman A. ; Vu Thieu, Nga Tran ; Thanh, Duy Pham ; Thompson, Corinne ; Dolecek, Christiane ; Campbell, James I. ; Thwaites, Guy ; Farrar, Jeremy ; Newton, Paul N. ; Dance, David ; Turner, Paul ; Mulholland, E. Kim ; Hawkey, Jane ; Edwards, David J. ; Feasey, Nicholas A. ; Weill, François Xavier ; Le Hello, Simon ; Hart, Peter J. ; Breiman, Robert F. ; Onsare, Robert S. ; Watson, Conall H. ; Edmunds, W. John ; Gordon, Melita A. ; Heyderman, Robert S. ; Msefula, Chisomo ; Jacobs, Jan ; Lunguya, Octavie ; Chabalgoity, Jose A. ; Kama, Mike ; Jenkins, Kylie ; Dutta, Shanta ; Marks, Florian ; Campos, Josefina ; Obaro, Stephen ; Keddy, Karen H. ; Smith, Anthony M. ; Parry, Christopher M. ; Karkey, Abhilasha ; Dongol, Sabina ; Basnyat, Buddha ; Arjyal, Amit ; Dufour, Muriel ; Bandaranayake, Don ; Toleafoa, Take N. ; Singh, Shalini Pravin ; Hatta, Mochammad ; Davong, Viengmon ; Isaia, Lupeoletalalelei ; Wijedoru, Lalith ; Crump, John A. ; De Pinna, Elizabeth ; Nair, Satheesh ; Nilles, Eric J. ; Soeng, Sona ; Valcanis, Mary ; Powling, Joan ; Dimovski, Karolina ; Hogg, Geoff ; Mather, Alison E. ; Amos, Ben. / An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid. In: Nature communications. 2016 ; Vol. 7.

@article{35903121b32f40d9803216b751479d39,

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 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 = "Funding Information: This work was supported by a number of organizations. The Wellcome Trust Sanger Institute authors were funded by Wellcome Trust Award #098051. V.K.W. was supported by the Wellcome Trust (#098051) and the National Institute of Health Research (NIHR) Cambridge Biomedical Research Centre (BRC). N.F. was supported by the Wellcome Trust Research Fellowship #WT092152MA. N.F., R.S.H. and this work were supported by a strategic award from the Wellcome Trust for the MLW Clinical Research Programme (#101113/Z/13/Z). C.P. was funded by The Wellcome Trust Mahidol University Oxford Tropical Medicine Research Programme, supported by the Wellcome Trust of Great Britain (Major Overseas Programmes?Thailand Unit Core Grant), the European Society for Paediatric Infectious Diseases and University of Oxford-Li Ka Shing Global Health Foundation. D.D., P.N. and V.D. were supported by the Wellcome Trust (core grant #089275/H/09/Z). Z.A.D. was supported by the Wellcome Trust (Strategic award #106158). K.E.H. was supported by the NHMRC of Australia (fellowship #1061409) and the Victorian Life Sciences Computation Initiative (VLSCI; grant #VR0082). C.A.M. was supported by a Clinical Research Fellowship from GlaxoSmithKline and PJH by a UK Medical Research Council PhD studentship. This work forms part of an EU FP7 Marie Curie Actions Industry Academia Partnerships and Pathways (IAPP) Consortium Programme, entitled GENDRIVAX (Genome-driven vaccine development for bacterial infections), involving the Wellcome Trust Sanger Institute, KEMRI Nairobi and Novartis Vaccines Institute for Global Health. The Institut Pasteur (IP) authors were funded by the IP, the Institut de Veille Sanitaire and by the French Government ?Investissement d?Avenir? programme (Integrative Biology of Emerging Infectious Diseases Laboratory of Excellence, grant #ANR-10-LABX-62-IBEID). C.H.W. was supported by the UK Medical Research Council (MRC; #MR/J003999/1). C.O. was supported by Society in Science, The Branco Weiss Fellowship, administered by the ETH Zurich. A.K.C. was supported by the MRC (#G1100100/1). J.J. was supported by the antibiotic resistance surveillance project in DR Congo, funded by Project 2.01 of the Third Framework Agreement between the Belgian Directorate General of Development Cooperation and the Institute of Tropical Medicine, Antwerp, Belgium. F.M. was supported by a research grant from the Bill and Melinda Gates Foundation. J.A.C. was supported by the joint US National Institutes of Health-National Science Foundation Ecology and Evolution of Infectious Disease program (#R01 TW009237) and the UK Biotechnology and Biological Sciences Research Council (BBSRC; #BB/J010367/1), and by UK BBSRC Zoonoses in Emerging Livestock Systems awards #BB/L017679, #BB/L018926 and #BB/L018845. S.K. was supported by the NIH Grant Number R01 AI099525-02. S.B. is a Sir Henry Dale Fellow, jointly funded by the Wellcome Trust and the Royal Society (#100087/Z/12/Z). S.O. was supported by the National Institute Of Allergy And Infectious Diseases of the National Institutes of Health (#R01AI097493). C.D. was supported by the University of Oxford-Li Ka Shing Global Health Programme. A.E.M. was supported by a Biotechnology and Biological Sciences Research Council award (#BB/M014088/1). P.T. was supported by the Wellcome Trust of Great Britain (Major Overseas Programmes?Thailand Unit Core Grant) and University of Oxford-Li Ka Shing Global Health Foundation.",

year = "2016",

doi = "10.1038/ncomms12827",

language = "English (US)",

volume = "7",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Publishing Group",

}

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 - Funding Information: This work was supported by a number of organizations. The Wellcome Trust Sanger Institute authors were funded by Wellcome Trust Award #098051. V.K.W. was supported by the Wellcome Trust (#098051) and the National Institute of Health Research (NIHR) Cambridge Biomedical Research Centre (BRC). N.F. was supported by the Wellcome Trust Research Fellowship #WT092152MA. N.F., R.S.H. and this work were supported by a strategic award from the Wellcome Trust for the MLW Clinical Research Programme (#101113/Z/13/Z). C.P. was funded by The Wellcome Trust Mahidol University Oxford Tropical Medicine Research Programme, supported by the Wellcome Trust of Great Britain (Major Overseas Programmes?Thailand Unit Core Grant), the European Society for Paediatric Infectious Diseases and University of Oxford-Li Ka Shing Global Health Foundation. D.D., P.N. and V.D. were supported by the Wellcome Trust (core grant #089275/H/09/Z). Z.A.D. was supported by the Wellcome Trust (Strategic award #106158). K.E.H. was supported by the NHMRC of Australia (fellowship #1061409) and the Victorian Life Sciences Computation Initiative (VLSCI; grant #VR0082). C.A.M. was supported by a Clinical Research Fellowship from GlaxoSmithKline and PJH by a UK Medical Research Council PhD studentship. This work forms part of an EU FP7 Marie Curie Actions Industry Academia Partnerships and Pathways (IAPP) Consortium Programme, entitled GENDRIVAX (Genome-driven vaccine development for bacterial infections), involving the Wellcome Trust Sanger Institute, KEMRI Nairobi and Novartis Vaccines Institute for Global Health. The Institut Pasteur (IP) authors were funded by the IP, the Institut de Veille Sanitaire and by the French Government ?Investissement d?Avenir? programme (Integrative Biology of Emerging Infectious Diseases Laboratory of Excellence, grant #ANR-10-LABX-62-IBEID). C.H.W. was supported by the UK Medical Research Council (MRC; #MR/J003999/1). C.O. was supported by Society in Science, The Branco Weiss Fellowship, administered by the ETH Zurich. A.K.C. was supported by the MRC (#G1100100/1). J.J. was supported by the antibiotic resistance surveillance project in DR Congo, funded by Project 2.01 of the Third Framework Agreement between the Belgian Directorate General of Development Cooperation and the Institute of Tropical Medicine, Antwerp, Belgium. F.M. was supported by a research grant from the Bill and Melinda Gates Foundation. J.A.C. was supported by the joint US National Institutes of Health-National Science Foundation Ecology and Evolution of Infectious Disease program (#R01 TW009237) and the UK Biotechnology and Biological Sciences Research Council (BBSRC; #BB/J010367/1), and by UK BBSRC Zoonoses in Emerging Livestock Systems awards #BB/L017679, #BB/L018926 and #BB/L018845. S.K. was supported by the NIH Grant Number R01 AI099525-02. S.B. is a Sir Henry Dale Fellow, jointly funded by the Wellcome Trust and the Royal Society (#100087/Z/12/Z). S.O. was supported by the National Institute Of Allergy And Infectious Diseases of the National Institutes of Health (#R01AI097493). C.D. was supported by the University of Oxford-Li Ka Shing Global Health Programme. A.E.M. was supported by a Biotechnology and Biological Sciences Research Council award (#BB/M014088/1). P.T. was supported by the Wellcome Trust of Great Britain (Major Overseas Programmes?Thailand Unit Core Grant) and University of Oxford-Li Ka Shing Global Health Foundation.

PY - 2016

Y1 - 2016

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.

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

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

U2 - 10.1038/ncomms12827

DO - 10.1038/ncomms12827

M3 - Article

C2 - 27703135

AN - SCOPUS:84991011519

VL - 7

JO - Nature Communications

JF - Nature Communications

SN - 2041-1723

M1 - 12827

ER -