Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events

Vanessa K. Wong; Stephen Baker; Derek J. Pickard; Julian Parkhill; Andrew J. Page; Nicholas A. Feasey; Robert A. Kingsley; Nicholas R. Thomson; Jacqueline A. Keanel; Francois-Xavier Weill; David J. Edwards; Jane Hawkey; Simon R. Harris; Alison E. Mather; Amy K. Cain; James Hadfield; Peter J. Hart; Nga Tran Vu Thieu; Elizabeth J. Klemm; Dafni A. Glinos; Robert F. Breiman; Conall H. Watson; Samuel Kariuki; Melita A. Gordon; Robert S. Heyderman; Chinyere Okoro; Jan Jacobs; Octavie Lunguya; W. John Edmunds; Chisorno Msefula; Jose A. Chabalgoity; Mike Kama; Kylie Jenkins; Shanta Dutta; Florian Marks; Josefina Campos; Corinne Thompson; Stephen Obaro; Calman A. MacLennan; Christiane Dolecek; Karen H. Keddy; Anthony M. Smith; Christopher M. Parry; Abhilasha Karkey; E. Kim Mulholland; James I. Campbell; Sabina Dongol; Buddha Basnyat; Muriel Dufour; Don Bandaranayake; Take Toleafoa Naseri; Shalini Pravin Singh; Mochammad Hatta; Paul Newton; Robert S. Onsare; Lupeoletalalei Isaia; David Dance; Viengmon Davong; Guy Thwaites; Lalith Wijedoru; John A. Crump; Elizabeth De Pinna; Satheesh Nair; Eric J. Nilles; Duy Pham Thanh; Paul Turner; Sona Soeng; Mary Valcanis; Joan Powling; Karolina Dimovski; Geoff Hogg; Jeremy Farrar; Kathryn E. Holt; Gordon Dougan

doi:10.1038/ng.3281

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Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events

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Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events

Vanessa K. Wong, Stephen Baker, Derek J. Pickard, Julian Parkhill, Andrew J. Page, Nicholas A. Feasey, Robert A. Kingsley, Nicholas R. Thomson, Jacqueline A. Keanel, Francois-Xavier Weill, …

Nature genetics, Vol.47(6), pp.632-639

01/06/2015

DOI: https://doi.org/10.1038/ng.3281

Abstract

Genetics & Heredity

Life Sciences & Biomedicine

Science & Technology

The emergence of multidrug-resistant (MDR) typhoid is a major global health threat affecting many countries where the disease is endemic. Here whole-genome sequence analysis of 1,832 Salmonella enterica serovar Typhi (S. Typhi) identifies a single dominant MDR lineage, H58, that has emerged and spread throughout Asia and Africa over the last 30 years. Our analysis identifies numerous transmissions of H58, including multiple transfers from Asia to Africa and an ongoing, unrecognized MDR epidemic within Africa itself. Notably, our analysis indicates that H58 lineages are displacing antibiotic-sensitive isolates, transforming the global population structure of this pathogen. H58 isolates can harbor a complex MDR element residing either on transmissible IncHI1 plasmids or within multiple chromosomal integration sites. We also identify new mutations that define the H58 lineage. This phylogeographical analysis provides a framework to facilitate global management of MDR typhoid and is applicable to similar MDR lineages emerging in other bacterial species.

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Record Identifier: 9926516495701891
Title: Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events
Creators: Vanessa K. Wong
Stephen Baker
Derek J. Pickard
Julian Parkhill
Andrew J. Page
Nicholas A. Feasey
Robert A. Kingsley
Nicholas R. Thomson
Jacqueline A. Keanel
Francois-Xavier Weill
David J. Edwards
Jane Hawkey
Simon R. Harris
Alison E. Mather
Amy K. Cain
James Hadfield
Peter J. Hart
Nga Tran Vu Thieu
Elizabeth J. Klemm
Dafni A. Glinos
Robert F. Breiman
Conall H. Watson
Samuel Kariuki
Melita A. Gordon
Robert S. Heyderman
Chinyere Okoro
Jan Jacobs
Octavie Lunguya
W. John Edmunds
Chisorno Msefula
Jose A. Chabalgoity
Mike Kama
Kylie Jenkins
Shanta Dutta
Florian Marks
Josefina Campos
Corinne Thompson
Stephen Obaro
Calman A. MacLennan
Christiane Dolecek
Karen H. Keddy
Anthony M. Smith
Christopher M. Parry
Abhilasha Karkey
E. Kim Mulholland
James I. Campbell
Sabina Dongol
Buddha Basnyat
Muriel Dufour
Don Bandaranayake
Take Toleafoa Naseri
Shalini Pravin Singh
Mochammad Hatta
Paul Newton
Robert S. Onsare
Lupeoletalalei Isaia
David Dance
Viengmon Davong
Guy Thwaites
Lalith Wijedoru
John A. Crump
Elizabeth De Pinna
Satheesh Nair
Eric J. Nilles
Duy Pham Thanh
Paul Turner
Sona Soeng
Mary Valcanis
Joan Powling
Karolina Dimovski
Geoff Hogg
Jeremy Farrar
Kathryn E. Holt
Gordon Dougan
Publication Details: Nature genetics, Vol.47(6), pp.632-639
Academic Unit: Centre for International Health
Publisher: Springer Nature
Grant note: Institut de Veille Sanitaire Wellcome Trust G1100100; G9818340 / MRC; UK Research & Innovation (UKRI); Medical Research Council UK (MRC) 098051 / Wellcome Trust award; Wellcome Trust University of Oxford-Li Ka Shing Global Health Foundation WT092152MA / Wellcome Trust research fellowship; Wellcome Trust Wellcome Trust Mahidol University Oxford Tropical Medicine Research Programme; Wellcome Trust Society in Science Branco Weiss Fellowship 089275/H/091Z / Wellcome Trust UK Medical Research Council PhD studentship; UK Research & Innovation (UKRI); Medical Research Council UK (MRC) 1330800 / Direct For Biological Sciences; Div Of Molecular and Cellular Bioscience; National Science Foundation (NSF); NSF - Directorate for Biological Sciences (BIO) 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) ANR-10-LABX-62-IBEID / French government 'Investissement d'Avenir' program (Integrative Biology of Emerging Infectious Diseases Laboratory of Excellence); Agence Nationale de la Recherche (ANR) R01 AI097493 / National Institute of Allergy and Infectious Diseases of the US 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) 2.01 / Institute of Tropical Medicine (Antwerp, Belgium) BB/J010367/1; BB/L018845/1; BB/L018926/1 / Biotechnology and Biological Sciences Research Council; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC) MR/J003999/1; G1100100/1 / UK Medical Research Council; UK Research & Innovation (UKRI); Medical Research Council UK (MRC) Wellcome Trust (Major Overseas Programmes-Thailand Unit Core Grant); Wellcome Trust 101113/Z/13/Z / Wellcome Trust for the Malawi-Liverpool Wellcome Trust Clinical Research Programme R01 AI099525-02 / US National Institutes of Health grant; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA 1061409 / National Health and Medical Research Council of Australia; National Health & Medical Research Council (NHMRC) of Australia 2.01 / Belgian Directorate General of Development Cooperation Clinical Research Fellowship from GlaxoSmithKline Institut Pasteur 100087/Z/12/Z / Royal Society European Society for Paediatric Infectious Diseases BB/L018926/1; BB/L018845/1; BB/J010367/1 / BBSRC; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC) R01 TW009237 / US National Institutes of Health-National Science Foundation Ecology and Evolution of Infectious Disease program G9818340; G1100100; 1263989 / Medical Research Council; UK Research & Innovation (UKRI); Medical Research Council UK (MRC) antibiotic resistance surveillance project in the Democratic Republic of the Congo 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) Bill and Melinda Gates Foundation; Bill & Melinda Gates Foundation
Date published ; e-published: 01/06/2015
Language: English
Resource Type: Journal article

Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events

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