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
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]

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.

Domaines: Santé publique et épidémiologie

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, 2016, 7, pp.12827. ⟨10.1038/ncomms12827⟩. ⟨pasteur-01422000⟩