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

Autor: Wong, Vanessa K., Baker, Stephen, Connor, Thomas R., Pickard, Derek, Page, Andrew J., Dave, Jayshree, Murphy, Niamh, Holliman, Richard, Sefton, Armine, Millar, Michael, Dyson, Zoe A., Dougan, Gordon, Holt, Kathryn E., Parkhill, Julian, Feasey, Nicholas A., Kingsley, Robert A., Thomson, Nicholas R., Keane, Jacqueline A., Weill, François- Xavier, Le Hello, Simon, Hawkey, Jan, Edwards, David, Harris, Simon R., Cain, Amy K., Hadfield, James, Hart, Peter J., Thieu, Nga Tran Vu, Klemm, Elizabeth, Breiman, Robert F., Watson, Conall H., Edmunds, W. John, Kariuki, Samuel, Gordon, Melita A., Heyderman, Robert S., Okoro, Chinyere, Jacobs, Jan, Lunguya, Octavie, Msefula, Chisomo, Chabalgoity, Jose A., Kama, Mike, Jenkins, Kylie, Dutta, Shanta, Marks, Florian, Campos, Josefina, Thompson, Corinne, Obaro, Stephen, MacLennan, Calman A., Dolecek, Christiane, Keddy, Karen H., Smith, Anthony M., Parry, Christopher M., Karkey, Abhilasha, Dongol, Don, Basnyat, Buddha, Arjyal, Amit, Mulholland, E. Kim, Campbell, James I., Dufour, Muriel, Bandaranayake, Don, Toleafoa, Take N., Singh, Shalini Pravin, Hatta, Mochammad, Newton, Paul, Dance, David, Davong, Viengmon, Onsare, Robert S., Isaia, Lupeoletalalelei, Thwaites, Guy, Wijedoru, Lalith, Crump, John A., de Pinna, Elizabeth, Nair, Satheesh, Nilles, Eric J., Thanh, Duy Pham, Turner, Paul, Soeng, Sona, Valcanis, Mary, Powling, Joan, Dimovski, Karolina, Hogg, Geoff, Farrar, Jeremy, Mather, Alison E., Amos, Ben
Přispěvatelé: Addenbrooke's Hospital, Cambridge University NHS Trust, The Wellcome Trust Sanger Institute [Cambridge], London School of Hygiene and Tropical Medicine (LSHTM), University of Oxford [Oxford], Cardiff University, Barts Health NHS Trust [London, UK], Centre for Sytems Genomics, University of Melbourne, Department of Engineering [Cambridge], University of Cambridge [UK] (CAM), Liverpool School of Tropical Medicine (LSTM), University of Liverpool, Institute of Food Research [Norwich], Institute for Astronomy [Honolulu], University of Hawai‘i [Mānoa] (UHM), Bactéries pathogènes entériques (BPE), Institut Pasteur [Paris], Atmospheric Chemistry Observations and Modeling Laboratory (ACOML), National Center for Atmospheric Research [Boulder] (NCAR), INM-8, Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association-Helmholtz-Gemeinschaft = Helmholtz Association, Global Disease Detection Division, Centers for Disease Control and Prevention, Department of Applied Mathematics and Theoretical Physics (DAMTP), University College of London [London] (UCL), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Institut National de Recherche Biomédicale [Kinshasa] (INRB), University of Malawi, Universidad de la República [Montevideo] (UCUR), IHU-LIRYC, Université Bordeaux Segalen - Bordeaux 2-CHU Bordeaux [Bordeaux], Department of Mathematics and Statistics [Toronto], York University [Toronto], Department of Mathematical Sciences [Varanasi], Banaras Hindu University [Varanasi] (BHU), Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Mahidol University [Bangkok]-Mahosot Hospital, Public Health England [London], Nuffield Department of Clinical Medicine [Oxford], This work was supported by a number of organizations. The Wellcome Trust Sanger Institute authors were funded by Wellcome Trust Award #098051. V.K.W. was supported by the Wellcome Trust (#098051) and the National Institute of HealthResearch (NIHR) Cambridge Biomedical Research Centre (BRC). N.F. was supported by the Wellcome Trust Research Fellowship #WT092152MA. N.F., R.S.H. and this work were supported by a strategic award from the Wellcome Trust for the MLW ClinicalResearch Programme (#101113/Z/13/Z). C.P. was funded by The Wellcome Trust Mahidol University Oxford Tropical Medicine Research Programme, supported by the Wellcome Trust of Great Britain (Major Overseas Programmes—Thailand Unit CoreGrant), the European Society for Paediatric Infectious Diseases and 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/09/Z). Z.A.D. was supported by the WellcomeTrust (Strategic award #106158). K.E.H. was supported by the NHMRC of Australia (fellowship #1061409) and the Victorian Life Sciences Computation Initiative (VLSCI, grant #VR0082). C.A.M. was supported by a Clinical Research Fellowship fromGlaxoSmithKline and PJH by a UK Medical Research Council PhD studentship. This work forms part of an EU FP7 Marie Curie Actions Industry Academia Partnerships and Pathways (IAPP) Consortium Programme, entitled GENDRIVAX (Genome-drivenvaccine development for bacterial infections), involving the Wellcome Trust Sanger Institute, KEMRI Nairobi and Novartis Vaccines Institute for Global Health. The Institut Pasteur (IP) authors were funded by the IP, the Institut de Veille Sanitaire and by theFrench Government ‘Investissement d’Avenir’ programme (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 (MRC, MR/J003999/1).C.O. was supported by Society in Science, The Branco Weiss Fellowship, administered by the ETH Zurich. A.K.C. was supported by the MRC (#G1100100/1). J.J. was supported by the antibiotic resistance surveillance project in DR 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. J.A.C. was supported by the joint US National Institutes of Health-National Science Foundation Ecology and Evolution of Infectious Disease program (#R01 TW009237) and the UK Biotechnology and Biological Sciences Research Council (BBSRC, BB/J010367/1), and by UK BBSRC Zoonoses in Emerging Livestock Systems awards #BB/L017679, #BB/L018926 and #BB/L018845. S.K. was supported by the NIH Grant Number 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 National Institutes of Health (#R01AI097493). C.D. was supported by the University of Oxford-Li Ka Shing Global Health Programme. A.E.M. was supported by a Biotechnology and Biological Sciences Research Councilaward (#BB/M014088/1). P.T. was supported by the Wellcome Trust of Great Britain (Major Overseas Programmes—Thailand Unit Core Grant) and University of Oxford-Li Ka Shing Global Health Foundation., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Dyson, Zoe A [0000-0002-8887-3492], Holt, Kathryn E [0000-0003-3949-2471], Apollo - University of Cambridge Repository, University of Oxford, Biotechnology and Biological Sciences Research Council (BBSRC), Institut Pasteur [Paris] (IP), Universidad de la República [Montevideo] (UDELAR)
Jazyk: angličtina
Rok vydání: 2016
Předmět:
Zdroj: Nature Communications
Nature Communications, Nature Publishing Group, 2016, 7, pp.12827. ⟨10.1038/ncomms12827⟩
Nature Communications, 2016, 7, pp.12827. ⟨10.1038/ncomms12827⟩
Nature Communications, Vol 7, Iss 1, Pp 1-11 (2016)
ISSN: 2041-1723
Popis: 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.
Typhoid fever is caused by Salmonella enterica serovar Typhi (S. Typhi). This study examines ∼2,000 clinical isolates of S. Typhi to show highly structured/geographically restricted genomes except rapidly disseminating H58 subclade, and design a genotyping framework for tracking the disease.
Databáze: OpenAIRE
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