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

Vanessa K. Wong 1, 2 Stephen Baker 3, 4, 5 Thomas R. Connor 6 Derek Pickard 2 Andrew J. Page 2 Jayshree Dave 7, 8 Niamh Murphy 8 Richard Holliman 8 Armine Sefton 9 Michael Millar 9 Zoe A. Dyson 10 Gordon Dougan 11 Kathryn E. Holt 12, 10 Julian Parkhill 2 Nicholas A. Feasey 13, 14 Robert A. Kingsley 15, 2 Nicholas R. Thomson 2 Jacqueline A. Keane 16 François- Xavier Weill 17 Simon Le Hello 17 Jan Hawkey David Edwards 18 Simon R. Harris 2 Amy K. Cain 19 James Hadfield Peter J. Hart Nga Tran Vu Thieu Elizabeth Klemm 2 Robert F. Breiman 20 Conall H. Watson 21 W. John Edmunds 22 Samuel Kariuki 23 Melita A. Gordon 24, 14 Robert S. Heyderman 25, 24 Chinyere Okoro 26 Jan Jacobs 27 Octavie Lunguya 28, 29 Chisomo Msefula 30, 24 Jose A. Chabalgoity 31 Mike Kama 32 Kylie Jenkins 33 Shanta Dutta 34 Florian Marks Josefina Campos 35 Corinne Thompson 3, 5 Stephen Obaro 36 Calman A. Maclennan 2 Christiane Dolecek 37 Karen H. Keddy 38, 39 Anthony M. Smith 38 Christopher M. Parry 13, 4, 40 Abhilasha Karkey Don Dongol Buddha Basnyat Amit Arjyal E. Kim Mulholland James I. Campbell 41 Muriel Dufour Don Bandaranayake Take N. Toleafoa Shalini Pravin Singh 42 Mochammad Hatta Paul Newton 43, 44 David Dance Viengmon Davong Robert S. Onsare 23 Lupeoletalalelei Isaia Guy Thwaites 5, 3 Lalith Wijedoru John A. Crump Elizabeth De Pinna 45 Satheesh Nair 45 Eric J. Nilles 46 Duy Pham Thanh 3, 47, 4 Paul Turner Sona Soeng Mary Valcanis Joan Powling Karolina Dimovski Geoff Hogg Jeremy Farrar 3 Alison E. Mather 2 Ben Amos
24 Malawi-Liverpool-Wellcome Trust Clinical Research Programme
Institute of Infection and Global Health, University of Liverpool
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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Nature Communications, Nature Publishing Group, 2016, 7, pp.12827. 〈10.1038/ncomms12827〉
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Vanessa K. Wong, Stephen Baker, Thomas R. Connor, Derek Pickard, Andrew J. Page, et al.. An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid. Nature Communications, Nature Publishing Group, 2016, 7, pp.12827. 〈10.1038/ncomms12827〉. 〈pasteur-01422000〉

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