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

42 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)

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10.1038/ncomms12827

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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, [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

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.

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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.",

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