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

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Funding Acknowledgements

This work was supported by the Wellcome Trust. We would like to thank the members of the Pathogen Informatics Team and the core sequencing teams at the Wellcome Trust Sanger Institute (Cambridge, UK). We are grateful to D. Harris for his superb work in managing the sequence data. We also thank L. Fabre for her excellent technical assistance.This work was supported by a number of organizations. The authors affiliated with the Wellcome Trust Sanger Institute were funded by Wellcome Trust award 098051; N.A.F. was supported by Wellcome Trust research fellowship WT092152MA. N.A.F., R.S.H. and this work were supported by a strategic award from the Wellcome Trust for the Malawi-Liverpool Wellcome Trust Clinical Research Programme (101113/Z/13/Z). C.M.P. was funded by the Wellcome Trust Mahidol University Oxford Tropical Medicine Research Programme, supported by the Wellcome Trust (Major Overseas Programmes-Thailand Unit Core Grant), the European Society for Paediatric Infectious Diseases and the University of Oxford-Li Ka Shing Global Health Foundation. D.D., P.N. and V.D. were supported by the Wellcome Trust (core grant 089275/H/091Z). K.E.H. was supported by the National Health and Medical Research Council of Australia (fellowship 1061409) and the Victorian Life Sciences Computation Initiative (VLSCI; grant VR0082). C.A.M. was supported by a Clinical Research Fellowship from GlaxoSmithKline, and P.J.H. was supported by a UK Medical Research Council PhD studentship. This work forms part of a European Union Framework Programme 7 Marie Curie Actions Industry Academia Partnerships and Pathways (LAPP) Consortium Programme, entitled GENDRIVAX (Genome-Driven Vaccine Development for Bacterial Infections), involving the Wellcome Trust Sanger Institute, KEMRI Nairobi and the Novartis Vaccines Institute for Global Health. The authors affiliated with the Institut Pasteur were funded by the Institut Pasteur, the Institut de Veille Sanitaire and the French government 'Investissement d'Avenir' program (Integrative Biology of Emerging Infectious Diseases Laboratory of Excellence, grant ANR-10-LABX-62-IBEID). C.H.W. was supported by the UK Medical Research Council (MR/J003999/1). CO. was supported by Society in Science and the Branco Weiss Fellowship, administered by ETH Zurich. A.K.C. was supported by the UK Medical Research Council (G1100100/1). J.J. was supported by the antibiotic resistance surveillance project in the Democratic Republic of the Congo, funded by project 2.01 of the Third Framework Agreement between the Belgian Directorate General of Development Cooperation and the Institute of Tropical Medicine (Antwerp, Belgium). F.M. was supported by a research grant from the Bill and Melinda Gates Foundation. The findings and conclusions contained within this publication are those of the authors and do not necessarily reflect positions or policies of the Bill and Melinda Gates Foundation. J.A. Crump was supported by the joint US National Institutes of Health-National Science Foundation Ecology and Evolution of Infectious Disease program (R01 TW009237), the UK Biotechnology and Biological Sciences Research Council (BBSRC; BB/J010367/1) and UK BBSRC Zoonoses in Emerging Livestock Systems awards BB/L017679, BB/L018926 and BB/L018845. S.K. was supported by US National Institutes of Health grant R01 AI099525-02. S.B. is a Sir Henry Dale Fellow, jointly funded by the Wellcome Trust and the Royal Society (100087/Z/12/Z). S.O. was supported by the National Institute of Allergy and Infectious Diseases of the US National Institutes of Health (R01 AI097493). The content is solely the responsibility of the authors and does not necessarily represent the official views of the US National Institutes of Health. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. C.D.was supported by the University of Oxford-Li Ka Shing Global Health Foundation.