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 4 W. John Edmunds 21 Samuel Kariuki 22 Melita A. Gordon 23, 14 Robert S. Heyderman 24, 23 Chinyere Okoro 25 Jan Jacobs 26 Octavie Lunguya 27, 28 Chisomo Msefula 29, 23 Jose A. Chabalgoity 30 Mike Kama 31 Kylie Jenkins 32 Shanta Dutta 33 Florian Marks Josefina Campos 34 Corinne Thompson 3, 5 Stephen Obaro 35 Calman A. Maclennan 2 Christiane Dolecek 36 Karen H. Keddy 37, 38 Anthony M. Smith 37 Christopher M. Parry 13, 4, 39 Abhilasha Karkey Don Dongol Buddha Basnyat Amit Arjyal E. Kim Mulholland James I. Campbell 40 Muriel Dufour Don Bandaranayake Take N. Toleafoa Shalini Pravin Singh 41 Mochammad Hatta Paul Newton 42, 43 David Dance Viengmon Davong Robert S. Onsare 22 Lupeoletalalelei Isaia Guy Thwaites 5, 3 Lalith Wijedoru John A. Crump Elizabeth De Pinna 44 Satheesh Nair 44 Eric J. Nilles 45 Duy Pham Thanh 3, 46, 4 Paul Turner Sona Soeng Mary Valcanis Joan Powling Karolina Dimovski Geoff Hogg Jeremy Farrar 3 Alison E. Mather 2 Ben Amos
1 Addenbrooke's Hospital
2 The Wellcome Trust Sanger Institute [Cambridge]
3 The hospital for tropical diseases
4 LSHTM - London School of Hygiene and Tropical Medicine
5 Centre for Tropical Medicine
6 Cardiff University
7 HPA Collaborating Centre, Medical Microbiology, St George's Healthcare NHS Trust
8 Public Health Laboratory London
9 Division of infection
10 Centre for Sytems Genomics
11 Department of Engineering [Cambridge]
12 Department of Biochemistry and Molecular Biology
13 Liverpool School of Tropical Medicine
14 Institute of Infection and Global Health
15 Institute of Food Research [Norwich]
16 Institute for Astronomy [Honolulu]
17 BPE - Bactéries pathogènes entériques
18 ACOML - Atmospheric Chemistry Observations and Modeling Laboratory
19 INM-8
20 Global Disease Detection Division
21 DAMTP/CMS - Department of Applied Mathematics and Theoretical Physics / Centre for Mathematical Sciences
22 Centre for Microbiology Research
23 Malawi-Liverpool-Wellcome Trust Clinical Research Programme
Institute of Infection and Global Health, University of Liverpool
24 Division of Infection & Immunity
25 The Department of Medicine
26 KU Leuven - Catholic University of Leuven
27 Institut National de Recherche Biomédicale
28 National Institute of Biomedical Research
29 University of Malawi
30 Facultad de Medicina
31 LAOG - Laboratoire d'Astrophysique de Grenoble
32 IHU-LIRYC
33 IPR - Institut de Physique de Rennes
34 Enteropathogen division
35 Alpert Medical School
36 Wellcome trust Major Overseas Programme
37 Centre for Enteric Diseases
38 Faculty of Health Sciences
39 School of Tropical Medicine
40 York University - Department of Mathematics and Statistics
41 Department of Mathematical Sciences [Varanasi]
42 LOMWRU - Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit
43 Centre for Tropical Medicine and Global Health
44 Gastrointestinal Bacteria Reference Unit
45 Pacific Technical Support Division
46 Centre for Tropical Medicine
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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