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

Vanessa K. Wong; Stephen Baker; Thomas R. Connor; Derek Pickard; Andrew J. Page; Jayshree Dave; Niamh Murphy; Richard Holliman; Armine Sefton; Michael Millar; Zoe A. Dyson; Gordon Dougan; Kathryn E. Holt; Int Typhoid Consortium; John Crump

doi:10.1038/ncomms12827

Back

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

Journal article

Open access

Peer reviewed

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

Vanessa K. Wong, Stephen Baker, Thomas R. Connor, Derek Pickard, Andrew J. Page, Jayshree Dave, Niamh Murphy, Richard Holliman, Armine Sefton, Michael Millar, …

Nature communications, Vol.7(1), pp.12827-12827

05/10/2016

DOI: https://doi.org/10.1038/ncomms12827

Abstract

Multidisciplinary Sciences

Science & Technology

Science & Technology - Other Topics

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.

Files and links (1)

url

https://doi.org/10.1038/ncomms12827View

Published (Version of record) Open

Metrics

1 Record Views

See more details

Details

Record Identifier: 9926515308601891
Title: An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid
Creators: Vanessa K. Wong
Stephen Baker
Thomas R. Connor
Derek Pickard
Andrew J. Page
Jayshree Dave
Niamh Murphy
Richard Holliman
Armine Sefton
Michael Millar
Zoe A. Dyson
Gordon Dougan
Kathryn E. Holt
Int Typhoid Consortium
John Crump
Publication Details: Nature communications, Vol.7(1), pp.12827-12827
Academic Unit: Centre for International Health
Publisher: NATURE PORTFOLIO
Grant note: CL-2015-14-006 / National Institute for Health Research; National Institutes of Health Research (NIHR) Institut de Veille Sanitaire G1100100 / Medical Research Council; UK Research & Innovation (UKRI); Medical Research Council UK (MRC) ANR-10-LABX-62-IBEID / French Government 'Investissement d'Avenir' programme (Integrative Biology of Emerging Infectious Diseases Laboratory of Excellence); Agence Nationale de la Recherche (ANR) 1061409 / NHMRC of Australia; National Health & Medical Research Council (NHMRC) of Australia University of Oxford-Li Ka Shing Global Health Foundation Institute of Tropical Medicine, Antwerp, Belgium BB/L018926/1; BB/M014088/1; BB/J010367/1 / BBSRC; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC) Wellcome Trust Mahidol University Oxford Tropical Medicine Research Programme - Wellcome Trust of Great Britain (Major Overseas Programmes-Thailand Unit Core Grant) University of Oxford-Li Ka Shing Global Health Programme G1100100 / MRC; UK Research & Innovation (UKRI); Medical Research Council UK (MRC) UK Medical Research Council; UK Research & Innovation (UKRI); Medical Research Council UK (MRC) BB/J010367/1 / UK Biotechnology and Biological Sciences Research Council (BBSRC); UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC) VR0082 / Victorian Life Sciences Computation Initiative (VLSCI) 098051; WT092152MA; 101113/Z/13/Z; 089275/H/09/Z; 106158; 100087/Z/12/Z / Wellcome Trust Belgian Directorate General of Development Cooperation, Antwerp, Belgium BB/M014088/1 / Biotechnology and Biological Sciences Research Council; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC) 100087/Z/12/Z / Royal Society European Society for Paediatric Infectious Diseases R01 TW009237 / US National Institutes of Health-National Science Foundation Ecology and Evolution of Infectious Disease program 101113/Z/13/Z; 089275/H/09/Z / Wellcome Trust National Institute of Health Research (NIHR) Cambridge Biomedical Research Centre (BRC); National Institutes of Health Research (NIHR) GlaxoSmithKline R01AI097493 / National Institute Of Allergy And Infectious Diseases of the National Institutes of Health; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Allergy & Infectious Diseases (NIAID) Wellcome Trust of Great Britain (Major Overseas Programmes-Thailand Unit Core Grant); Wellcome Trust IP Society in Science, The Branco Weiss Fellowship R01 AI099525-02 / NIH; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA G1100100/1 / MRC; UK Research & Innovation (UKRI); Medical Research Council UK (MRC) BB/L017679; BB/L018926; BB/L018845 / UK BBSRC Zoonoses in Emerging Livestock Systems awards; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC) MR/J003999/1 / UK Medical Research Council (MRC); UK Research & Innovation (UKRI); Medical Research Council UK (MRC) Bill and Melinda Gates Foundation; Bill & Melinda Gates Foundation
Date published ; e-published: 05/10/2016
Language: English
Resource Type: Journal article

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

Abstract

Files and links (1)

Metrics

Details

Usage Policy