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

Vanessa K. Wong 1, 2 Stephen Baker 3, 4 Thomas R. Connor 5 Derek Pickard 2 Andrew J. Page 2 Jayshree Dave Niamh Murphy Richard Holliman Armine Sefton 6 Michael Millar 6 Zoe A. Dyson 7 Gordon Dougan 8 Kathryn E. Holt Julian Parkhill 2 Nicholas A. Feasey 9, 10 Robert A. Kingsley 11, 2 Nicholas R. Thomson 2 Jacqueline A. Keane 12 François- Xavier Weill 13 Simon Le Hello 13 Jan Hawkey David Edwards 14 Simon R. Harris 2 Amy K. Cain 15 James Hadfield Peter J. Hart Nga Tran Vu Thieu Elizabeth Klemm 2 Robert F. Breiman 16 Conall H. Watson 3 W. John Edmunds 17 Samuel Kariuki Melita A. Gordon 10 Robert S. Heyderman 18, 10 Chinyere Okoro 19 Jan Jacobs 20 Octavie Lunguya 21 Chisomo Msefula 22 Jose A. Chabalgoity 23 Mike Kama 24 Kylie Jenkins 25 Shanta Dutta 26 Florian Marks Josefina Campos Corinne Thompson Stephen Obaro Calman A. Maclennan 2 Christiane Dolecek Karen H. Keddy Anthony M. Smith Christopher M. Parry 9, 3 Abhilasha Karkey Don Dongol Buddha Basnyat Amit Arjyal E. Kim Mulholland James I. Campbell 27 Muriel Dufour Don Bandaranayake Take N. Toleafoa Shalini Pravin Singh 28 Mochammad Hatta Paul Newton 29 David Dance Viengmon Davong Robert S. Onsare Lupeoletalalelei Isaia Guy Thwaites Lalith Wijedoru John A. Crump Elizabeth de Pinna 30 Satheesh Nair 30 Eric J. Nilles Duy Pham Thanh 31, 3 Paul Turner Sona Soeng Mary Valcanis Joan Powling Karolina Dimovski Geoff Hogg Jeremy Farrar Alison E. Mather 2 Ben Amos
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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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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