An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid - Archive ouverte HAL Access content directly
Journal Articles Nature Communications Year : 2016

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
Jayshree Dave
  • Function : Author
Niamh Murphy
  • Function : Author
Richard Holliman
  • Function : Author
Kathryn E. Holt
  • Function : Author
Jan Hawkey
  • Function : Author
Amy K. Cain
  • Function : Author
James Hadfield
  • Function : Author
Peter J. Hart
  • Function : Author
Nga Tran Vu Thieu
  • Function : Author
Samuel Kariuki
  • Function : Author
Mike Kama
  • Function : Author
Kylie Jenkins
  • Function : Author
Shanta Dutta
  • Function : Author
Florian Marks
  • Function : Author
Josefina Campos
  • Function : Author
Corinne Thompson
  • Function : Author
Stephen Obaro
  • Function : Author
Christiane Dolecek
  • Function : Author
Karen H. Keddy
  • Function : Author
Anthony M. Smith
  • Function : Author
Abhilasha Karkey
  • Function : Author
Don Dongol
  • Function : Author
Buddha Basnyat
  • Function : Author
Amit Arjyal
  • Function : Author
E. Kim Mulholland
  • Function : Author
Muriel Dufour
  • Function : Author
Don Bandaranayake
  • Function : Author
Take N. Toleafoa
  • Function : Author
Mochammad Hatta
  • Function : Author
David Dance
  • Function : Author
Viengmon Davong
  • Function : Author
Robert S. Onsare
  • Function : Author
Lupeoletalalelei Isaia
  • Function : Author
Guy Thwaites
  • Function : Author
Lalith Wijedoru
  • Function : Author
John A. Crump
  • Function : Author
Eric J. Nilles
  • Function : Author
Paul Turner
  • Function : Author
Sona Soeng
  • Function : Author
Mary Valcanis
  • Function : Author
Joan Powling
  • Function : Author
Karolina Dimovski
  • Function : Author
Geoff Hogg
  • Function : Author
Jeremy Farrar
  • Function : Author
Ben Amos
  • Function : Author

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.
Fichier principal
Vignette du fichier
ncomms12827.pdf (2.77 Mo) Télécharger le fichier
Origin : Publication funded by an institution
Loading...

Dates and versions

pasteur-01422000 , version 1 (23-12-2016)

Licence

Attribution - NonCommercial - ShareAlike - CC BY 4.0

Identifiers

Cite

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⟩

Collections

PASTEUR ANR
342 View
212 Download

Altmetric

Share

Gmail Facebook Twitter LinkedIn More