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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 Kylie Jenkins 24 Shanta Dutta 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 25 Muriel Dufour Don Bandaranayake Take N. Toleafoa Shalini Pravin Singh 26 Mochammad Hatta Paul Newton 27 David Dance Viengmon Davong Robert S. Onsare Lupeoletalalelei Isaia Guy Thwaites Lalith Wijedoru John A. Crump Elizabeth de Pinna 28 Satheesh Nair 28 Eric J. Nilles Duy Pham Thanh 29, 3 Paul Turner Sona Soeng Mary Valcanis Joan Powling Karolina Dimovski Geoff Hogg Jeremy Farrar Alison E. Mather 2 Ben Amos
1 Addenbrooke's Hospital
2 The Wellcome Trust Sanger Institute [Cambridge]
3 LSHTM - London School of Hygiene and Tropical Medicine
4 University of Oxford [Oxford]
5 Cardiff University
6 Barts Health NHS Trust [London, UK]
7 Centre for Sytems Genomics
8 Department of Engineering [Cambridge]
9 LSTM - Liverpool School of Tropical Medicine
10 University of Liverpool
11 Institute of Food Research [Norwich]
12 Institute for Astronomy [Honolulu]
13 BPE - Bactéries pathogènes entériques
14 ACOML - Atmospheric Chemistry Observations and Modeling Laboratory
15 INM-8
16 Global Disease Detection Division
17 DAMTP - Department of Applied Mathematics and Theoretical Physics
18 UCL - University College of London [London]
19 CAM - University of Cambridge [UK]
20 KU Leuven - Catholic University of Leuven - Katholieke Universiteit Leuven
21 INRB - Institut National de Recherche Biomédicale [Kinshasa]
22 University of Malawi
23 UDELAR - Universidad de la República [Montevideo]
24 IHU-LIRYC
25 Department of Mathematics and Statistics [Toronto]
26 Department of Mathematical Sciences [Varanasi]
27 LOMWRU - Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit
28 Public Health England [London]
29 Nuffield Department of Clinical Medicine [Oxford]
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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