Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events
Identifieur interne : 002149 ( Pmc/Corpus ); précédent : 002148; suivant : 002150Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events
Auteurs : Vanessa K. Wong ; Stephen Baker ; Derek J. Pickard ; Julian Parkhill ; Andrew J. Page ; Nicholas A. Feasey ; Robert A. Kingsley ; Nicholas R. Thomson ; Jacqueline A. Keane ; François-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 ; Chisomo 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 DouganSource :
- Nature genetics [ 1061-4036 ] ; 2015.
Abstract
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
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DOI: 10.1038/ng.3281
PubMed: 25961941
PubMed Central: 4921243
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PMC:4921243Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Phylogeographical analysis of the dominant multidrug-resistant H58 clade of <italic>Salmonella</italic> Typhi identifies inter- and intracontinental transmission events</title><author><name sortKey="Wong, Vanessa K" sort="Wong, Vanessa K" uniqKey="Wong V" first="Vanessa K" last="Wong">Vanessa K. Wong</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation><affiliation><nlm:aff id="A2">Department of Microbiology, Addenbrooke’s Hospital, Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge, UK</nlm:aff></affiliation></author><author><name sortKey="Baker, Stephen" sort="Baker, Stephen" uniqKey="Baker S" first="Stephen" last="Baker">Stephen Baker</name><affiliation><nlm:aff id="A3">Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam</nlm:aff></affiliation><affiliation><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff></affiliation><affiliation><nlm:aff id="A5">Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK</nlm:aff></affiliation></author><author><name sortKey="Pickard, Derek J" sort="Pickard, Derek J" uniqKey="Pickard D" first="Derek J" last="Pickard">Derek J. Pickard</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation></author><author><name sortKey="Parkhill, Julian" sort="Parkhill, Julian" uniqKey="Parkhill J" first="Julian" last="Parkhill">Julian Parkhill</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation></author><author><name sortKey="Page, Andrew J" sort="Page, Andrew J" uniqKey="Page A" first="Andrew J" last="Page">Andrew J. Page</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation></author><author><name sortKey="Feasey, Nicholas A" sort="Feasey, Nicholas A" uniqKey="Feasey N" first="Nicholas A" last="Feasey">Nicholas A. Feasey</name><affiliation><nlm:aff id="A6">Liverpool School of Tropical Medicine, Liverpool, UK</nlm:aff></affiliation></author><author><name sortKey="Kingsley, Robert A" sort="Kingsley, Robert A" uniqKey="Kingsley R" first="Robert A" last="Kingsley">Robert A. Kingsley</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation><affiliation><nlm:aff id="A7">Institute of Food Research, Norwich Research Park, Norwich, UK</nlm:aff></affiliation></author><author><name sortKey="Thomson, Nicholas R" sort="Thomson, Nicholas R" uniqKey="Thomson N" first="Nicholas R" last="Thomson">Nicholas R. Thomson</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation><affiliation><nlm:aff id="A5">Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK</nlm:aff></affiliation></author><author><name sortKey="Keane, Jacqueline A" sort="Keane, Jacqueline A" uniqKey="Keane J" first="Jacqueline A" last="Keane">Jacqueline A. Keane</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation></author><author><name sortKey="Weill, Francois Xavier" sort="Weill, Francois Xavier" uniqKey="Weill F" first="François-Xavier" last="Weill">François-Xavier Weill</name><affiliation><nlm:aff id="A8">Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, France</nlm:aff></affiliation></author><author><name sortKey="Edwards, David J" sort="Edwards, David J" uniqKey="Edwards D" first="David J" last="Edwards">David J. Edwards</name><affiliation><nlm:aff id="A9">Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia</nlm:aff></affiliation></author><author><name sortKey="Hawkey, Jane" sort="Hawkey, Jane" uniqKey="Hawkey J" first="Jane" last="Hawkey">Jane Hawkey</name><affiliation><nlm:aff id="A9">Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia</nlm:aff></affiliation><affiliation><nlm:aff id="A10">Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria, Australia</nlm:aff></affiliation></author><author><name sortKey="Harris, Simon R" sort="Harris, Simon R" uniqKey="Harris S" first="Simon R" last="Harris">Simon R. Harris</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation></author><author><name sortKey="Mather, Alison E" sort="Mather, Alison E" uniqKey="Mather A" first="Alison E" last="Mather">Alison E. Mather</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation></author><author><name sortKey="Cain, Amy K" sort="Cain, Amy K" uniqKey="Cain A" first="Amy K" last="Cain">Amy K. Cain</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation></author><author><name sortKey="Hadfield, James" sort="Hadfield, James" uniqKey="Hadfield J" first="James" last="Hadfield">James Hadfield</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation></author><author><name sortKey="Hart, Peter J" sort="Hart, Peter J" uniqKey="Hart P" first="Peter J" last="Hart">Peter J. Hart</name><affiliation><nlm:aff id="A11">Institute of Biomedical Research, School of Immunity and Infection, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, UK</nlm:aff></affiliation></author><author><name sortKey="Thieu, Nga Tran Vu" sort="Thieu, Nga Tran Vu" uniqKey="Thieu N" first="Nga Tran Vu" last="Thieu">Nga Tran Vu Thieu</name><affiliation><nlm:aff id="A3">Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam</nlm:aff></affiliation></author><author><name sortKey="Klemm, Elizabeth J" sort="Klemm, Elizabeth J" uniqKey="Klemm E" first="Elizabeth J" last="Klemm">Elizabeth J. Klemm</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation></author><author><name sortKey="Glinos, Dafni A" sort="Glinos, Dafni A" uniqKey="Glinos D" first="Dafni A" last="Glinos">Dafni A. Glinos</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation></author><author><name sortKey="Breiman, Robert F" sort="Breiman, Robert F" uniqKey="Breiman R" first="Robert F" last="Breiman">Robert F. Breiman</name><affiliation><nlm:aff id="A12">Kenya Medical Research Institute (KEMRI), Nairobi, Kenya</nlm:aff></affiliation><affiliation><nlm:aff id="A13">Centers for Disease Control and Prevention, Atlanta, Georgia, USA</nlm:aff></affiliation><affiliation><nlm:aff id="A14">Emory Global Health Institute, Atlanta, Georgia, USA</nlm:aff></affiliation></author><author><name sortKey="Watson, Conall H" sort="Watson, Conall H" uniqKey="Watson C" first="Conall H" last="Watson">Conall H. Watson</name><affiliation><nlm:aff id="A15">Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK</nlm:aff></affiliation></author><author><name sortKey="Kariuki, Samuel" sort="Kariuki, Samuel" uniqKey="Kariuki S" first="Samuel" last="Kariuki">Samuel Kariuki</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation><affiliation><nlm:aff id="A12">Kenya Medical Research Institute (KEMRI), Nairobi, Kenya</nlm:aff></affiliation></author><author><name sortKey="Gordon, Melita A" sort="Gordon, Melita A" uniqKey="Gordon M" first="Melita A" last="Gordon">Melita A. Gordon</name><affiliation><nlm:aff id="A16">Institute of Infection and Global Health, University of Liverpool, Liverpool, UK</nlm:aff></affiliation></author><author><name sortKey="Heyderman, Robert S" sort="Heyderman, Robert S" uniqKey="Heyderman R" first="Robert S" last="Heyderman">Robert S. Heyderman</name><affiliation><nlm:aff id="A17">Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi</nlm:aff></affiliation></author><author><name sortKey="Okoro, Chinyere" sort="Okoro, Chinyere" uniqKey="Okoro C" first="Chinyere" last="Okoro">Chinyere Okoro</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation></author><author><name sortKey="Jacobs, Jan" sort="Jacobs, Jan" uniqKey="Jacobs J" first="Jan" last="Jacobs">Jan Jacobs</name><affiliation><nlm:aff id="A18">Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium</nlm:aff></affiliation><affiliation><nlm:aff id="A19">Department of Microbiology and Immunology, Katholieke Universiteit (KU) Leuven, University of Leuven, Leuven, Belgium</nlm:aff></affiliation></author><author><name sortKey="Lunguya, Octavie" sort="Lunguya, Octavie" uniqKey="Lunguya O" first="Octavie" last="Lunguya">Octavie Lunguya</name><affiliation><nlm:aff id="A20">National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo</nlm:aff></affiliation><affiliation><nlm:aff id="A21">University Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo</nlm:aff></affiliation></author><author><name sortKey="Edmunds, W John" sort="Edmunds, W John" uniqKey="Edmunds W" first="W John" last="Edmunds">W John Edmunds</name><affiliation><nlm:aff id="A15">Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK</nlm:aff></affiliation></author><author><name sortKey="Msefula, Chisomo" sort="Msefula, Chisomo" uniqKey="Msefula C" first="Chisomo" last="Msefula">Chisomo Msefula</name><affiliation><nlm:aff id="A17">Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi</nlm:aff></affiliation><affiliation><nlm:aff id="A22">Microbiology Department, College of Medicine, University of Malawi, Blantyre, Malawi</nlm:aff></affiliation></author><author><name sortKey="Chabalgoity, Jose A" sort="Chabalgoity, Jose A" uniqKey="Chabalgoity J" first="Jose A" last="Chabalgoity">Jose A. Chabalgoity</name><affiliation><nlm:aff id="A23">Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Montevideo, Uruguay</nlm:aff></affiliation></author><author><name sortKey="Kama, Mike" sort="Kama, Mike" uniqKey="Kama M" first="Mike" last="Kama">Mike Kama</name><affiliation><nlm:aff id="A24">Ministry of Health, Suva, Fiji</nlm:aff></affiliation></author><author><name sortKey="Jenkins, Kylie" sort="Jenkins, Kylie" uniqKey="Jenkins K" first="Kylie" last="Jenkins">Kylie Jenkins</name><affiliation><nlm:aff id="A25">Fiji Health Sector Support Program, Suva, Fiji</nlm:aff></affiliation></author><author><name sortKey="Dutta, Shanta" sort="Dutta, Shanta" uniqKey="Dutta S" first="Shanta" last="Dutta">Shanta Dutta</name><affiliation><nlm:aff id="A26">National Institute of Cholera and Enteric Diseases, Kolkata, India</nlm:aff></affiliation></author><author><name sortKey="Marks, Florian" sort="Marks, Florian" uniqKey="Marks F" first="Florian" last="Marks">Florian Marks</name><affiliation><nlm:aff id="A27">International Vaccine Institute, Department of Epidemiology, Seoul, Republic of Korea</nlm:aff></affiliation></author><author><name sortKey="Campos, Josefina" sort="Campos, Josefina" uniqKey="Campos J" first="Josefina" last="Campos">Josefina Campos</name><affiliation><nlm:aff id="A28">Enteropathogen Division, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) Carlos G. Malbran Institute, Buenos Aires, Argentina</nlm:aff></affiliation></author><author><name sortKey="Thompson, Corinne" sort="Thompson, Corinne" uniqKey="Thompson C" first="Corinne" last="Thompson">Corinne Thompson</name><affiliation><nlm:aff id="A3">Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam</nlm:aff></affiliation><affiliation><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff></affiliation></author><author><name sortKey="Obaro, Stephen" sort="Obaro, Stephen" uniqKey="Obaro S" first="Stephen" last="Obaro">Stephen Obaro</name><affiliation><nlm:aff id="A29">Division of Pediatric Infectious Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA</nlm:aff></affiliation><affiliation><nlm:aff id="A30">University of Abuja Teaching Hospital, Abuja, Nigeria</nlm:aff></affiliation><affiliation><nlm:aff id="A31">Bingham University, Karu, Nigeria</nlm:aff></affiliation></author><author><name sortKey="Maclennan, Calman A" sort="Maclennan, Calman A" uniqKey="Maclennan C" first="Calman A" last="Maclennan">Calman A. Maclennan</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation><affiliation><nlm:aff id="A11">Institute of Biomedical Research, School of Immunity and Infection, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, UK</nlm:aff></affiliation><affiliation><nlm:aff id="A32">Novartis Vaccines Institute for Global Health, Siena, Italy</nlm:aff></affiliation></author><author><name sortKey="Dolecek, Christiane" sort="Dolecek, Christiane" uniqKey="Dolecek C" first="Christiane" last="Dolecek">Christiane Dolecek</name><affiliation><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff></affiliation></author><author><name sortKey="Keddy, Karen H" sort="Keddy, Karen H" uniqKey="Keddy K" first="Karen H" last="Keddy">Karen H. Keddy</name><affiliation><nlm:aff id="A33">Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service, University of the Witwatersrand, Johannesburg, South Africa</nlm:aff></affiliation></author><author><name sortKey="Smith, Anthony M" sort="Smith, Anthony M" uniqKey="Smith A" first="Anthony M" last="Smith">Anthony M. Smith</name><affiliation><nlm:aff id="A33">Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service, University of the Witwatersrand, Johannesburg, South Africa</nlm:aff></affiliation></author><author><name sortKey="Parry, Christopher M" sort="Parry, Christopher M" uniqKey="Parry C" first="Christopher M" last="Parry">Christopher M. Parry</name><affiliation><nlm:aff id="A34">Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK</nlm:aff></affiliation><affiliation><nlm:aff id="A35">Graduate School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan</nlm:aff></affiliation></author><author><name sortKey="Karkey, Abhilasha" sort="Karkey, Abhilasha" uniqKey="Karkey A" first="Abhilasha" last="Karkey">Abhilasha Karkey</name><affiliation><nlm:aff id="A36">Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal</nlm:aff></affiliation></author><author><name sortKey="Mulholland, E Kim" sort="Mulholland, E Kim" uniqKey="Mulholland E" first="E Kim" last="Mulholland">E Kim Mulholland</name><affiliation><nlm:aff id="A5">Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK</nlm:aff></affiliation><affiliation><nlm:aff id="A37">Murdoch Childrens Research Institute, Melbourne, Victoria, Australia</nlm:aff></affiliation></author><author><name sortKey="Campbell, James I" sort="Campbell, James I" uniqKey="Campbell J" first="James I" last="Campbell">James I. Campbell</name><affiliation><nlm:aff id="A3">Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam</nlm:aff></affiliation><affiliation><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff></affiliation></author><author><name sortKey="Dongol, Sabina" sort="Dongol, Sabina" uniqKey="Dongol S" first="Sabina" last="Dongol">Sabina Dongol</name><affiliation><nlm:aff id="A36">Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal</nlm:aff></affiliation></author><author><name sortKey="Basnyat, Buddha" sort="Basnyat, Buddha" uniqKey="Basnyat B" first="Buddha" last="Basnyat">Buddha Basnyat</name><affiliation><nlm:aff id="A36">Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal</nlm:aff></affiliation></author><author><name sortKey="Dufour, Muriel" sort="Dufour, Muriel" uniqKey="Dufour M" first="Muriel" last="Dufour">Muriel Dufour</name><affiliation><nlm:aff id="A38">Enteric and Leptospira Reference Laboratory, Institute of Environmental Science and Research, Ltd. (ESR), Porirua, New Zealand</nlm:aff></affiliation></author><author><name sortKey="Bandaranayake, Don" sort="Bandaranayake, Don" uniqKey="Bandaranayake D" first="Don" last="Bandaranayake">Don Bandaranayake</name><affiliation><nlm:aff id="A39">National Centre for Biosecurity and Infectious Disease, Institute of Environmental Science and Research, Porirua, New Zealand</nlm:aff></affiliation></author><author><name sortKey="Naseri, Take Toleafoa" sort="Naseri, Take Toleafoa" uniqKey="Naseri T" first="Take Toleafoa" last="Naseri">Take Toleafoa Naseri</name><affiliation><nlm:aff id="A40">Samoa Ministry of Health, Apia, Samoa</nlm:aff></affiliation></author><author><name sortKey="Singh, Shalini Pravin" sort="Singh, Shalini Pravin" uniqKey="Singh S" first="Shalini Pravin" last="Singh">Shalini Pravin Singh</name><affiliation><nlm:aff id="A41">National Influenza Center, World Health Organization, Center for Communicable Disease Control, Suva, Fiji</nlm:aff></affiliation></author><author><name sortKey="Hatta, Mochammad" sort="Hatta, Mochammad" uniqKey="Hatta M" first="Mochammad" last="Hatta">Mochammad Hatta</name><affiliation><nlm:aff id="A42">Department of Microbiology, Hasanuddin University, Makassar, Indonesia</nlm:aff></affiliation></author><author><name sortKey="Newton, Paul" sort="Newton, Paul" uniqKey="Newton P" first="Paul" last="Newton">Paul Newton</name><affiliation><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff></affiliation><affiliation><nlm:aff id="A43">Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos</nlm:aff></affiliation></author><author><name sortKey="Onsare, Robert S" sort="Onsare, Robert S" uniqKey="Onsare R" first="Robert S" last="Onsare">Robert S. Onsare</name><affiliation><nlm:aff id="A12">Kenya Medical Research Institute (KEMRI), Nairobi, Kenya</nlm:aff></affiliation></author><author><name sortKey="Isaia, Lupeoletalalei" sort="Isaia, Lupeoletalalei" uniqKey="Isaia L" first="Lupeoletalalei" last="Isaia">Lupeoletalalei Isaia</name><affiliation><nlm:aff id="A44">National Health Services, Tupua Tamasese Meaole Hospital, Apia, Samoa</nlm:aff></affiliation></author><author><name sortKey="Dance, David" sort="Dance, David" uniqKey="Dance D" first="David" last="Dance">David Dance</name><affiliation><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff></affiliation><affiliation><nlm:aff id="A43">Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos</nlm:aff></affiliation></author><author><name sortKey="Davong, Viengmon" sort="Davong, Viengmon" uniqKey="Davong V" first="Viengmon" last="Davong">Viengmon Davong</name><affiliation><nlm:aff id="A43">Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos</nlm:aff></affiliation></author><author><name sortKey="Thwaites, Guy" sort="Thwaites, Guy" uniqKey="Thwaites G" first="Guy" last="Thwaites">Guy Thwaites</name><affiliation><nlm:aff id="A3">Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam</nlm:aff></affiliation><affiliation><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff></affiliation></author><author><name sortKey="Wijedoru, Lalith" sort="Wijedoru, Lalith" uniqKey="Wijedoru L" first="Lalith" last="Wijedoru">Lalith Wijedoru</name><affiliation><nlm:aff id="A45">Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand</nlm:aff></affiliation><affiliation><nlm:aff id="A46">Paediatric Emergency Medicine, Chelsea and Westminster Hospital, London, UK</nlm:aff></affiliation></author><author><name sortKey="Crump, John A" sort="Crump, John A" uniqKey="Crump J" first="John A" last="Crump">John A. Crump</name><affiliation><nlm:aff id="A47">Centre for International Health and Otago International Health Research Network, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand</nlm:aff></affiliation></author><author><name sortKey="De Pinna, Elizabeth" sort="De Pinna, Elizabeth" uniqKey="De Pinna E" first="Elizabeth" last="De Pinna">Elizabeth De Pinna</name><affiliation><nlm:aff id="A48"><italic>Salmonella</italic> Reference Service, Public Health England, Colindale, London, UK</nlm:aff></affiliation></author><author><name sortKey="Nair, Satheesh" sort="Nair, Satheesh" uniqKey="Nair S" first="Satheesh" last="Nair">Satheesh Nair</name><affiliation><nlm:aff id="A48"><italic>Salmonella</italic> Reference Service, Public Health England, Colindale, London, UK</nlm:aff></affiliation></author><author><name sortKey="Nilles, Eric J" sort="Nilles, Eric J" uniqKey="Nilles E" first="Eric J" last="Nilles">Eric J. Nilles</name><affiliation><nlm:aff id="A49">Emerging Disease Surveillance and Response, Division of Pacific Technical Support, World Health Organization, Suva, Fiji</nlm:aff></affiliation></author><author><name sortKey="Thanh, Duy Pham" sort="Thanh, Duy Pham" uniqKey="Thanh D" first="Duy Pham" last="Thanh">Duy Pham Thanh</name><affiliation><nlm:aff id="A3">Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam</nlm:aff></affiliation></author><author><name sortKey="Turner, Paul" sort="Turner, Paul" uniqKey="Turner P" first="Paul" last="Turner">Paul Turner</name><affiliation><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff></affiliation><affiliation><nlm:aff id="A45">Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand</nlm:aff></affiliation><affiliation><nlm:aff id="A50">Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia</nlm:aff></affiliation></author><author><name sortKey="Soeng, Sona" sort="Soeng, Sona" uniqKey="Soeng S" first="Sona" last="Soeng">Sona Soeng</name><affiliation><nlm:aff id="A50">Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia</nlm:aff></affiliation></author><author><name sortKey="Valcanis, Mary" sort="Valcanis, Mary" uniqKey="Valcanis M" first="Mary" last="Valcanis">Mary Valcanis</name><affiliation><nlm:aff id="A51">Microbiological Diagnostic Unit–Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia</nlm:aff></affiliation></author><author><name sortKey="Powling, Joan" sort="Powling, Joan" uniqKey="Powling J" first="Joan" last="Powling">Joan Powling</name><affiliation><nlm:aff id="A51">Microbiological Diagnostic Unit–Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia</nlm:aff></affiliation></author><author><name sortKey="Dimovski, Karolina" sort="Dimovski, Karolina" uniqKey="Dimovski K" first="Karolina" last="Dimovski">Karolina Dimovski</name><affiliation><nlm:aff id="A51">Microbiological Diagnostic Unit–Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia</nlm:aff></affiliation></author><author><name sortKey="Hogg, Geoff" sort="Hogg, Geoff" uniqKey="Hogg G" first="Geoff" last="Hogg">Geoff Hogg</name><affiliation><nlm:aff id="A51">Microbiological Diagnostic Unit–Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia</nlm:aff></affiliation></author><author><name sortKey="Farrar, Jeremy" sort="Farrar, Jeremy" uniqKey="Farrar J" first="Jeremy" last="Farrar">Jeremy Farrar</name><affiliation><nlm:aff id="A3">Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam</nlm:aff></affiliation><affiliation><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff></affiliation></author><author><name sortKey="Holt, Kathryn E" sort="Holt, Kathryn E" uniqKey="Holt K" first="Kathryn E" last="Holt">Kathryn E. Holt</name><affiliation><nlm:aff id="A9">Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia</nlm:aff></affiliation></author><author><name sortKey="Dougan, Gordon" sort="Dougan, Gordon" uniqKey="Dougan G" first="Gordon" last="Dougan">Gordon Dougan</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25961941</idno><idno type="pmc">4921243</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4921243</idno><idno type="RBID">PMC:4921243</idno><idno type="doi">10.1038/ng.3281</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">002149</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">002149</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Phylogeographical analysis of the dominant multidrug-resistant H58 clade of <italic>Salmonella</italic> Typhi identifies inter- and intracontinental transmission events</title><author><name sortKey="Wong, Vanessa K" sort="Wong, Vanessa K" uniqKey="Wong V" first="Vanessa K" last="Wong">Vanessa K. Wong</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation><affiliation><nlm:aff id="A2">Department of Microbiology, Addenbrooke’s Hospital, Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge, UK</nlm:aff></affiliation></author><author><name sortKey="Baker, Stephen" sort="Baker, Stephen" uniqKey="Baker S" first="Stephen" last="Baker">Stephen Baker</name><affiliation><nlm:aff id="A3">Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam</nlm:aff></affiliation><affiliation><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff></affiliation><affiliation><nlm:aff id="A5">Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK</nlm:aff></affiliation></author><author><name sortKey="Pickard, Derek J" sort="Pickard, Derek J" uniqKey="Pickard D" first="Derek J" last="Pickard">Derek J. Pickard</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation></author><author><name sortKey="Parkhill, Julian" sort="Parkhill, Julian" uniqKey="Parkhill J" first="Julian" last="Parkhill">Julian Parkhill</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation></author><author><name sortKey="Page, Andrew J" sort="Page, Andrew J" uniqKey="Page A" first="Andrew J" last="Page">Andrew J. Page</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation></author><author><name sortKey="Feasey, Nicholas A" sort="Feasey, Nicholas A" uniqKey="Feasey N" first="Nicholas A" last="Feasey">Nicholas A. Feasey</name><affiliation><nlm:aff id="A6">Liverpool School of Tropical Medicine, Liverpool, UK</nlm:aff></affiliation></author><author><name sortKey="Kingsley, Robert A" sort="Kingsley, Robert A" uniqKey="Kingsley R" first="Robert A" last="Kingsley">Robert A. Kingsley</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation><affiliation><nlm:aff id="A7">Institute of Food Research, Norwich Research Park, Norwich, UK</nlm:aff></affiliation></author><author><name sortKey="Thomson, Nicholas R" sort="Thomson, Nicholas R" uniqKey="Thomson N" first="Nicholas R" last="Thomson">Nicholas R. Thomson</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation><affiliation><nlm:aff id="A5">Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK</nlm:aff></affiliation></author><author><name sortKey="Keane, Jacqueline A" sort="Keane, Jacqueline A" uniqKey="Keane J" first="Jacqueline A" last="Keane">Jacqueline A. Keane</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation></author><author><name sortKey="Weill, Francois Xavier" sort="Weill, Francois Xavier" uniqKey="Weill F" first="François-Xavier" last="Weill">François-Xavier Weill</name><affiliation><nlm:aff id="A8">Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, France</nlm:aff></affiliation></author><author><name sortKey="Edwards, David J" sort="Edwards, David J" uniqKey="Edwards D" first="David J" last="Edwards">David J. Edwards</name><affiliation><nlm:aff id="A9">Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia</nlm:aff></affiliation></author><author><name sortKey="Hawkey, Jane" sort="Hawkey, Jane" uniqKey="Hawkey J" first="Jane" last="Hawkey">Jane Hawkey</name><affiliation><nlm:aff id="A9">Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia</nlm:aff></affiliation><affiliation><nlm:aff id="A10">Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria, Australia</nlm:aff></affiliation></author><author><name sortKey="Harris, Simon R" sort="Harris, Simon R" uniqKey="Harris S" first="Simon R" last="Harris">Simon R. Harris</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation></author><author><name sortKey="Mather, Alison E" sort="Mather, Alison E" uniqKey="Mather A" first="Alison E" last="Mather">Alison E. Mather</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation></author><author><name sortKey="Cain, Amy K" sort="Cain, Amy K" uniqKey="Cain A" first="Amy K" last="Cain">Amy K. Cain</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation></author><author><name sortKey="Hadfield, James" sort="Hadfield, James" uniqKey="Hadfield J" first="James" last="Hadfield">James Hadfield</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation></author><author><name sortKey="Hart, Peter J" sort="Hart, Peter J" uniqKey="Hart P" first="Peter J" last="Hart">Peter J. Hart</name><affiliation><nlm:aff id="A11">Institute of Biomedical Research, School of Immunity and Infection, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, UK</nlm:aff></affiliation></author><author><name sortKey="Thieu, Nga Tran Vu" sort="Thieu, Nga Tran Vu" uniqKey="Thieu N" first="Nga Tran Vu" last="Thieu">Nga Tran Vu Thieu</name><affiliation><nlm:aff id="A3">Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam</nlm:aff></affiliation></author><author><name sortKey="Klemm, Elizabeth J" sort="Klemm, Elizabeth J" uniqKey="Klemm E" first="Elizabeth J" last="Klemm">Elizabeth J. Klemm</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation></author><author><name sortKey="Glinos, Dafni A" sort="Glinos, Dafni A" uniqKey="Glinos D" first="Dafni A" last="Glinos">Dafni A. Glinos</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation></author><author><name sortKey="Breiman, Robert F" sort="Breiman, Robert F" uniqKey="Breiman R" first="Robert F" last="Breiman">Robert F. Breiman</name><affiliation><nlm:aff id="A12">Kenya Medical Research Institute (KEMRI), Nairobi, Kenya</nlm:aff></affiliation><affiliation><nlm:aff id="A13">Centers for Disease Control and Prevention, Atlanta, Georgia, USA</nlm:aff></affiliation><affiliation><nlm:aff id="A14">Emory Global Health Institute, Atlanta, Georgia, USA</nlm:aff></affiliation></author><author><name sortKey="Watson, Conall H" sort="Watson, Conall H" uniqKey="Watson C" first="Conall H" last="Watson">Conall H. Watson</name><affiliation><nlm:aff id="A15">Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK</nlm:aff></affiliation></author><author><name sortKey="Kariuki, Samuel" sort="Kariuki, Samuel" uniqKey="Kariuki S" first="Samuel" last="Kariuki">Samuel Kariuki</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation><affiliation><nlm:aff id="A12">Kenya Medical Research Institute (KEMRI), Nairobi, Kenya</nlm:aff></affiliation></author><author><name sortKey="Gordon, Melita A" sort="Gordon, Melita A" uniqKey="Gordon M" first="Melita A" last="Gordon">Melita A. Gordon</name><affiliation><nlm:aff id="A16">Institute of Infection and Global Health, University of Liverpool, Liverpool, UK</nlm:aff></affiliation></author><author><name sortKey="Heyderman, Robert S" sort="Heyderman, Robert S" uniqKey="Heyderman R" first="Robert S" last="Heyderman">Robert S. Heyderman</name><affiliation><nlm:aff id="A17">Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi</nlm:aff></affiliation></author><author><name sortKey="Okoro, Chinyere" sort="Okoro, Chinyere" uniqKey="Okoro C" first="Chinyere" last="Okoro">Chinyere Okoro</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation></author><author><name sortKey="Jacobs, Jan" sort="Jacobs, Jan" uniqKey="Jacobs J" first="Jan" last="Jacobs">Jan Jacobs</name><affiliation><nlm:aff id="A18">Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium</nlm:aff></affiliation><affiliation><nlm:aff id="A19">Department of Microbiology and Immunology, Katholieke Universiteit (KU) Leuven, University of Leuven, Leuven, Belgium</nlm:aff></affiliation></author><author><name sortKey="Lunguya, Octavie" sort="Lunguya, Octavie" uniqKey="Lunguya O" first="Octavie" last="Lunguya">Octavie Lunguya</name><affiliation><nlm:aff id="A20">National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo</nlm:aff></affiliation><affiliation><nlm:aff id="A21">University Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo</nlm:aff></affiliation></author><author><name sortKey="Edmunds, W John" sort="Edmunds, W John" uniqKey="Edmunds W" first="W John" last="Edmunds">W John Edmunds</name><affiliation><nlm:aff id="A15">Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK</nlm:aff></affiliation></author><author><name sortKey="Msefula, Chisomo" sort="Msefula, Chisomo" uniqKey="Msefula C" first="Chisomo" last="Msefula">Chisomo Msefula</name><affiliation><nlm:aff id="A17">Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi</nlm:aff></affiliation><affiliation><nlm:aff id="A22">Microbiology Department, College of Medicine, University of Malawi, Blantyre, Malawi</nlm:aff></affiliation></author><author><name sortKey="Chabalgoity, Jose A" sort="Chabalgoity, Jose A" uniqKey="Chabalgoity J" first="Jose A" last="Chabalgoity">Jose A. Chabalgoity</name><affiliation><nlm:aff id="A23">Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Montevideo, Uruguay</nlm:aff></affiliation></author><author><name sortKey="Kama, Mike" sort="Kama, Mike" uniqKey="Kama M" first="Mike" last="Kama">Mike Kama</name><affiliation><nlm:aff id="A24">Ministry of Health, Suva, Fiji</nlm:aff></affiliation></author><author><name sortKey="Jenkins, Kylie" sort="Jenkins, Kylie" uniqKey="Jenkins K" first="Kylie" last="Jenkins">Kylie Jenkins</name><affiliation><nlm:aff id="A25">Fiji Health Sector Support Program, Suva, Fiji</nlm:aff></affiliation></author><author><name sortKey="Dutta, Shanta" sort="Dutta, Shanta" uniqKey="Dutta S" first="Shanta" last="Dutta">Shanta Dutta</name><affiliation><nlm:aff id="A26">National Institute of Cholera and Enteric Diseases, Kolkata, India</nlm:aff></affiliation></author><author><name sortKey="Marks, Florian" sort="Marks, Florian" uniqKey="Marks F" first="Florian" last="Marks">Florian Marks</name><affiliation><nlm:aff id="A27">International Vaccine Institute, Department of Epidemiology, Seoul, Republic of Korea</nlm:aff></affiliation></author><author><name sortKey="Campos, Josefina" sort="Campos, Josefina" uniqKey="Campos J" first="Josefina" last="Campos">Josefina Campos</name><affiliation><nlm:aff id="A28">Enteropathogen Division, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) Carlos G. Malbran Institute, Buenos Aires, Argentina</nlm:aff></affiliation></author><author><name sortKey="Thompson, Corinne" sort="Thompson, Corinne" uniqKey="Thompson C" first="Corinne" last="Thompson">Corinne Thompson</name><affiliation><nlm:aff id="A3">Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam</nlm:aff></affiliation><affiliation><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff></affiliation></author><author><name sortKey="Obaro, Stephen" sort="Obaro, Stephen" uniqKey="Obaro S" first="Stephen" last="Obaro">Stephen Obaro</name><affiliation><nlm:aff id="A29">Division of Pediatric Infectious Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA</nlm:aff></affiliation><affiliation><nlm:aff id="A30">University of Abuja Teaching Hospital, Abuja, Nigeria</nlm:aff></affiliation><affiliation><nlm:aff id="A31">Bingham University, Karu, Nigeria</nlm:aff></affiliation></author><author><name sortKey="Maclennan, Calman A" sort="Maclennan, Calman A" uniqKey="Maclennan C" first="Calman A" last="Maclennan">Calman A. Maclennan</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation><affiliation><nlm:aff id="A11">Institute of Biomedical Research, School of Immunity and Infection, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, UK</nlm:aff></affiliation><affiliation><nlm:aff id="A32">Novartis Vaccines Institute for Global Health, Siena, Italy</nlm:aff></affiliation></author><author><name sortKey="Dolecek, Christiane" sort="Dolecek, Christiane" uniqKey="Dolecek C" first="Christiane" last="Dolecek">Christiane Dolecek</name><affiliation><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff></affiliation></author><author><name sortKey="Keddy, Karen H" sort="Keddy, Karen H" uniqKey="Keddy K" first="Karen H" last="Keddy">Karen H. Keddy</name><affiliation><nlm:aff id="A33">Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service, University of the Witwatersrand, Johannesburg, South Africa</nlm:aff></affiliation></author><author><name sortKey="Smith, Anthony M" sort="Smith, Anthony M" uniqKey="Smith A" first="Anthony M" last="Smith">Anthony M. Smith</name><affiliation><nlm:aff id="A33">Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service, University of the Witwatersrand, Johannesburg, South Africa</nlm:aff></affiliation></author><author><name sortKey="Parry, Christopher M" sort="Parry, Christopher M" uniqKey="Parry C" first="Christopher M" last="Parry">Christopher M. Parry</name><affiliation><nlm:aff id="A34">Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK</nlm:aff></affiliation><affiliation><nlm:aff id="A35">Graduate School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan</nlm:aff></affiliation></author><author><name sortKey="Karkey, Abhilasha" sort="Karkey, Abhilasha" uniqKey="Karkey A" first="Abhilasha" last="Karkey">Abhilasha Karkey</name><affiliation><nlm:aff id="A36">Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal</nlm:aff></affiliation></author><author><name sortKey="Mulholland, E Kim" sort="Mulholland, E Kim" uniqKey="Mulholland E" first="E Kim" last="Mulholland">E Kim Mulholland</name><affiliation><nlm:aff id="A5">Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK</nlm:aff></affiliation><affiliation><nlm:aff id="A37">Murdoch Childrens Research Institute, Melbourne, Victoria, Australia</nlm:aff></affiliation></author><author><name sortKey="Campbell, James I" sort="Campbell, James I" uniqKey="Campbell J" first="James I" last="Campbell">James I. Campbell</name><affiliation><nlm:aff id="A3">Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam</nlm:aff></affiliation><affiliation><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff></affiliation></author><author><name sortKey="Dongol, Sabina" sort="Dongol, Sabina" uniqKey="Dongol S" first="Sabina" last="Dongol">Sabina Dongol</name><affiliation><nlm:aff id="A36">Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal</nlm:aff></affiliation></author><author><name sortKey="Basnyat, Buddha" sort="Basnyat, Buddha" uniqKey="Basnyat B" first="Buddha" last="Basnyat">Buddha Basnyat</name><affiliation><nlm:aff id="A36">Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal</nlm:aff></affiliation></author><author><name sortKey="Dufour, Muriel" sort="Dufour, Muriel" uniqKey="Dufour M" first="Muriel" last="Dufour">Muriel Dufour</name><affiliation><nlm:aff id="A38">Enteric and Leptospira Reference Laboratory, Institute of Environmental Science and Research, Ltd. (ESR), Porirua, New Zealand</nlm:aff></affiliation></author><author><name sortKey="Bandaranayake, Don" sort="Bandaranayake, Don" uniqKey="Bandaranayake D" first="Don" last="Bandaranayake">Don Bandaranayake</name><affiliation><nlm:aff id="A39">National Centre for Biosecurity and Infectious Disease, Institute of Environmental Science and Research, Porirua, New Zealand</nlm:aff></affiliation></author><author><name sortKey="Naseri, Take Toleafoa" sort="Naseri, Take Toleafoa" uniqKey="Naseri T" first="Take Toleafoa" last="Naseri">Take Toleafoa Naseri</name><affiliation><nlm:aff id="A40">Samoa Ministry of Health, Apia, Samoa</nlm:aff></affiliation></author><author><name sortKey="Singh, Shalini Pravin" sort="Singh, Shalini Pravin" uniqKey="Singh S" first="Shalini Pravin" last="Singh">Shalini Pravin Singh</name><affiliation><nlm:aff id="A41">National Influenza Center, World Health Organization, Center for Communicable Disease Control, Suva, Fiji</nlm:aff></affiliation></author><author><name sortKey="Hatta, Mochammad" sort="Hatta, Mochammad" uniqKey="Hatta M" first="Mochammad" last="Hatta">Mochammad Hatta</name><affiliation><nlm:aff id="A42">Department of Microbiology, Hasanuddin University, Makassar, Indonesia</nlm:aff></affiliation></author><author><name sortKey="Newton, Paul" sort="Newton, Paul" uniqKey="Newton P" first="Paul" last="Newton">Paul Newton</name><affiliation><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff></affiliation><affiliation><nlm:aff id="A43">Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos</nlm:aff></affiliation></author><author><name sortKey="Onsare, Robert S" sort="Onsare, Robert S" uniqKey="Onsare R" first="Robert S" last="Onsare">Robert S. Onsare</name><affiliation><nlm:aff id="A12">Kenya Medical Research Institute (KEMRI), Nairobi, Kenya</nlm:aff></affiliation></author><author><name sortKey="Isaia, Lupeoletalalei" sort="Isaia, Lupeoletalalei" uniqKey="Isaia L" first="Lupeoletalalei" last="Isaia">Lupeoletalalei Isaia</name><affiliation><nlm:aff id="A44">National Health Services, Tupua Tamasese Meaole Hospital, Apia, Samoa</nlm:aff></affiliation></author><author><name sortKey="Dance, David" sort="Dance, David" uniqKey="Dance D" first="David" last="Dance">David Dance</name><affiliation><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff></affiliation><affiliation><nlm:aff id="A43">Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos</nlm:aff></affiliation></author><author><name sortKey="Davong, Viengmon" sort="Davong, Viengmon" uniqKey="Davong V" first="Viengmon" last="Davong">Viengmon Davong</name><affiliation><nlm:aff id="A43">Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos</nlm:aff></affiliation></author><author><name sortKey="Thwaites, Guy" sort="Thwaites, Guy" uniqKey="Thwaites G" first="Guy" last="Thwaites">Guy Thwaites</name><affiliation><nlm:aff id="A3">Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam</nlm:aff></affiliation><affiliation><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff></affiliation></author><author><name sortKey="Wijedoru, Lalith" sort="Wijedoru, Lalith" uniqKey="Wijedoru L" first="Lalith" last="Wijedoru">Lalith Wijedoru</name><affiliation><nlm:aff id="A45">Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand</nlm:aff></affiliation><affiliation><nlm:aff id="A46">Paediatric Emergency Medicine, Chelsea and Westminster Hospital, London, UK</nlm:aff></affiliation></author><author><name sortKey="Crump, John A" sort="Crump, John A" uniqKey="Crump J" first="John A" last="Crump">John A. Crump</name><affiliation><nlm:aff id="A47">Centre for International Health and Otago International Health Research Network, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand</nlm:aff></affiliation></author><author><name sortKey="De Pinna, Elizabeth" sort="De Pinna, Elizabeth" uniqKey="De Pinna E" first="Elizabeth" last="De Pinna">Elizabeth De Pinna</name><affiliation><nlm:aff id="A48"><italic>Salmonella</italic> Reference Service, Public Health England, Colindale, London, UK</nlm:aff></affiliation></author><author><name sortKey="Nair, Satheesh" sort="Nair, Satheesh" uniqKey="Nair S" first="Satheesh" last="Nair">Satheesh Nair</name><affiliation><nlm:aff id="A48"><italic>Salmonella</italic> Reference Service, Public Health England, Colindale, London, UK</nlm:aff></affiliation></author><author><name sortKey="Nilles, Eric J" sort="Nilles, Eric J" uniqKey="Nilles E" first="Eric J" last="Nilles">Eric J. Nilles</name><affiliation><nlm:aff id="A49">Emerging Disease Surveillance and Response, Division of Pacific Technical Support, World Health Organization, Suva, Fiji</nlm:aff></affiliation></author><author><name sortKey="Thanh, Duy Pham" sort="Thanh, Duy Pham" uniqKey="Thanh D" first="Duy Pham" last="Thanh">Duy Pham Thanh</name><affiliation><nlm:aff id="A3">Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam</nlm:aff></affiliation></author><author><name sortKey="Turner, Paul" sort="Turner, Paul" uniqKey="Turner P" first="Paul" last="Turner">Paul Turner</name><affiliation><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff></affiliation><affiliation><nlm:aff id="A45">Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand</nlm:aff></affiliation><affiliation><nlm:aff id="A50">Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia</nlm:aff></affiliation></author><author><name sortKey="Soeng, Sona" sort="Soeng, Sona" uniqKey="Soeng S" first="Sona" last="Soeng">Sona Soeng</name><affiliation><nlm:aff id="A50">Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia</nlm:aff></affiliation></author><author><name sortKey="Valcanis, Mary" sort="Valcanis, Mary" uniqKey="Valcanis M" first="Mary" last="Valcanis">Mary Valcanis</name><affiliation><nlm:aff id="A51">Microbiological Diagnostic Unit–Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia</nlm:aff></affiliation></author><author><name sortKey="Powling, Joan" sort="Powling, Joan" uniqKey="Powling J" first="Joan" last="Powling">Joan Powling</name><affiliation><nlm:aff id="A51">Microbiological Diagnostic Unit–Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia</nlm:aff></affiliation></author><author><name sortKey="Dimovski, Karolina" sort="Dimovski, Karolina" uniqKey="Dimovski K" first="Karolina" last="Dimovski">Karolina Dimovski</name><affiliation><nlm:aff id="A51">Microbiological Diagnostic Unit–Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia</nlm:aff></affiliation></author><author><name sortKey="Hogg, Geoff" sort="Hogg, Geoff" uniqKey="Hogg G" first="Geoff" last="Hogg">Geoff Hogg</name><affiliation><nlm:aff id="A51">Microbiological Diagnostic Unit–Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia</nlm:aff></affiliation></author><author><name sortKey="Farrar, Jeremy" sort="Farrar, Jeremy" uniqKey="Farrar J" first="Jeremy" last="Farrar">Jeremy Farrar</name><affiliation><nlm:aff id="A3">Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam</nlm:aff></affiliation><affiliation><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff></affiliation></author><author><name sortKey="Holt, Kathryn E" sort="Holt, Kathryn E" uniqKey="Holt K" first="Kathryn E" last="Holt">Kathryn E. Holt</name><affiliation><nlm:aff id="A9">Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia</nlm:aff></affiliation></author><author><name sortKey="Dougan, Gordon" sort="Dougan, Gordon" uniqKey="Dougan G" first="Gordon" last="Dougan">Gordon Dougan</name><affiliation><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff></affiliation></author></analytic><series><title level="j">Nature genetics</title><idno type="ISSN">1061-4036</idno><idno type="eISSN">1546-1718</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p id="P1">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 <italic>Salmonella enterica</italic> serovar Typhi (<italic>S.</italic> 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.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<pmc-dir>properties manuscript</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-journal-id">9216904</journal-id><journal-id journal-id-type="pubmed-jr-id">2419</journal-id><journal-id journal-id-type="nlm-ta">Nat Genet</journal-id><journal-id journal-id-type="iso-abbrev">Nat. Genet.</journal-id><journal-title-group><journal-title>Nature genetics</journal-title></journal-title-group><issn pub-type="ppub">1061-4036</issn><issn pub-type="epub">1546-1718</issn></journal-meta><article-meta><article-id pub-id-type="pmid">25961941</article-id><article-id pub-id-type="pmc">4921243</article-id><article-id pub-id-type="doi">10.1038/ng.3281</article-id><article-id pub-id-type="manuscript">NIHMS793848</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Phylogeographical analysis of the dominant multidrug-resistant H58 clade of <italic>Salmonella</italic> Typhi identifies inter- and intracontinental transmission events</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Wong</surname><given-names>Vanessa K</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref ref-type="aff" rid="A2">2</xref></contrib><contrib 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rid="A4">4</xref></contrib><contrib contrib-type="author"><name><surname>Wijedoru</surname><given-names>Lalith</given-names></name><xref ref-type="aff" rid="A45">45</xref><xref ref-type="aff" rid="A46">46</xref></contrib><contrib contrib-type="author"><name><surname>Crump</surname><given-names>John A</given-names></name><xref ref-type="aff" rid="A47">47</xref></contrib><contrib contrib-type="author"><name><surname>De Pinna</surname><given-names>Elizabeth</given-names></name><xref ref-type="aff" rid="A48">48</xref></contrib><contrib contrib-type="author"><name><surname>Nair</surname><given-names>Satheesh</given-names></name><xref ref-type="aff" rid="A48">48</xref></contrib><contrib contrib-type="author"><name><surname>Nilles</surname><given-names>Eric J</given-names></name><xref ref-type="aff" rid="A49">49</xref></contrib><contrib contrib-type="author"><name><surname>Thanh</surname><given-names>Duy Pham</given-names></name><xref ref-type="aff" rid="A3">3</xref></contrib><contrib contrib-type="author"><name><surname>Turner</surname><given-names>Paul</given-names></name><xref ref-type="aff" rid="A4">4</xref><xref ref-type="aff" rid="A45">45</xref><xref ref-type="aff" rid="A50">50</xref></contrib><contrib contrib-type="author"><name><surname>Soeng</surname><given-names>Sona</given-names></name><xref ref-type="aff" rid="A50">50</xref></contrib><contrib contrib-type="author"><name><surname>Valcanis</surname><given-names>Mary</given-names></name><xref ref-type="aff" rid="A51">51</xref></contrib><contrib contrib-type="author"><name><surname>Powling</surname><given-names>Joan</given-names></name><xref ref-type="aff" rid="A51">51</xref></contrib><contrib contrib-type="author"><name><surname>Dimovski</surname><given-names>Karolina</given-names></name><xref ref-type="aff" rid="A51">51</xref></contrib><contrib contrib-type="author"><name><surname>Hogg</surname><given-names>Geoff</given-names></name><xref ref-type="aff" rid="A51">51</xref></contrib><contrib contrib-type="author"><name><surname>Farrar</surname><given-names>Jeremy</given-names></name><xref ref-type="aff" rid="A3">3</xref><xref ref-type="aff" rid="A4">4</xref></contrib><contrib contrib-type="author"><name><surname>Holt</surname><given-names>Kathryn E</given-names></name><xref ref-type="aff" rid="A9">9</xref><xref rid="FN2" ref-type="author-notes">52</xref></contrib><contrib contrib-type="author"><name><surname>Dougan</surname><given-names>Gordon</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref rid="FN2" ref-type="author-notes">52</xref></contrib></contrib-group><aff id="A1"><label>1</label>Wellcome Trust Sanger Institute, Hinxton, UK</aff><aff id="A2"><label>2</label>Department of Microbiology, Addenbrooke’s Hospital, Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge, UK</aff><aff id="A3"><label>3</label>Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam</aff><aff id="A4"><label>4</label>Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</aff><aff id="A5"><label>5</label>Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK</aff><aff id="A6"><label>6</label>Liverpool School of Tropical Medicine, Liverpool, UK</aff><aff id="A7"><label>7</label>Institute of Food Research, Norwich Research Park, Norwich, UK</aff><aff id="A8"><label>8</label>Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, France</aff><aff id="A9"><label>9</label>Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia</aff><aff id="A10"><label>10</label>Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria, Australia</aff><aff id="A11"><label>11</label>Institute of Biomedical Research, School of Immunity and Infection, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, UK</aff><aff id="A12"><label>12</label>Kenya Medical Research Institute (KEMRI), Nairobi, Kenya</aff><aff id="A13"><label>13</label>Centers for Disease Control and Prevention, Atlanta, Georgia, USA</aff><aff id="A14"><label>14</label>Emory Global Health Institute, Atlanta, Georgia, USA</aff><aff id="A15"><label>15</label>Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK</aff><aff id="A16"><label>16</label>Institute of Infection and Global Health, University of Liverpool, Liverpool, UK</aff><aff id="A17"><label>17</label>Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi</aff><aff id="A18"><label>18</label>Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium</aff><aff id="A19"><label>19</label>Department of Microbiology and Immunology, Katholieke Universiteit (KU) Leuven, University of Leuven, Leuven, Belgium</aff><aff id="A20"><label>20</label>National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo</aff><aff id="A21"><label>21</label>University Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo</aff><aff id="A22"><label>22</label>Microbiology Department, College of Medicine, University of Malawi, Blantyre, Malawi</aff><aff id="A23"><label>23</label>Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Montevideo, Uruguay</aff><aff id="A24"><label>24</label>Ministry of Health, Suva, Fiji</aff><aff id="A25"><label>25</label>Fiji Health Sector Support Program, Suva, Fiji</aff><aff id="A26"><label>26</label>National Institute of Cholera and Enteric Diseases, Kolkata, India</aff><aff id="A27"><label>27</label>International Vaccine Institute, Department of Epidemiology, Seoul, Republic of Korea</aff><aff id="A28"><label>28</label>Enteropathogen Division, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) Carlos G. Malbran Institute, Buenos Aires, Argentina</aff><aff id="A29"><label>29</label>Division of Pediatric Infectious Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA</aff><aff id="A30"><label>30</label>University of Abuja Teaching Hospital, Abuja, Nigeria</aff><aff id="A31"><label>31</label>Bingham University, Karu, Nigeria</aff><aff id="A32"><label>32</label>Novartis Vaccines Institute for Global Health, Siena, Italy</aff><aff id="A33"><label>33</label>Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service, University of the Witwatersrand, Johannesburg, South Africa</aff><aff id="A34"><label>34</label>Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK</aff><aff id="A35"><label>35</label>Graduate School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan</aff><aff id="A36"><label>36</label>Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal</aff><aff id="A37"><label>37</label>Murdoch Childrens Research Institute, Melbourne, Victoria, Australia</aff><aff id="A38"><label>38</label>Enteric and Leptospira Reference Laboratory, Institute of Environmental Science and Research, Ltd. (ESR), Porirua, New Zealand</aff><aff id="A39"><label>39</label>National Centre for Biosecurity and Infectious Disease, Institute of Environmental Science and Research, Porirua, New Zealand</aff><aff id="A40"><label>40</label>Samoa Ministry of Health, Apia, Samoa</aff><aff id="A41"><label>41</label>National Influenza Center, World Health Organization, Center for Communicable Disease Control, Suva, Fiji</aff><aff id="A42"><label>42</label>Department of Microbiology, Hasanuddin University, Makassar, Indonesia</aff><aff id="A43"><label>43</label>Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos</aff><aff id="A44"><label>44</label>National Health Services, Tupua Tamasese Meaole Hospital, Apia, Samoa</aff><aff id="A45"><label>45</label>Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand</aff><aff id="A46"><label>46</label>Paediatric Emergency Medicine, Chelsea and Westminster Hospital, London, UK</aff><aff id="A47"><label>47</label>Centre for International Health and Otago International Health Research Network, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand</aff><aff id="A48"><label>48</label><italic>Salmonella</italic> Reference Service, Public Health England, Colindale, London, UK</aff><aff id="A49"><label>49</label>Emerging Disease Surveillance and Response, Division of Pacific Technical Support, World Health Organization, Suva, Fiji</aff><aff id="A50"><label>50</label>Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia</aff><aff id="A51"><label>51</label>Microbiological Diagnostic Unit–Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia</aff><author-notes><corresp id="FN1">Correspondence should be addressed to V.K.W. (<email>vw1@sanger.ac.uk</email>)</corresp><fn id="FN2" fn-type="equal"><label>52</label><p>These authors contributed equally to this work.</p></fn></author-notes><pub-date pub-type="nihms-submitted"><day>10</day><month>6</month><year>2016</year></pub-date><pub-date pub-type="epub"><day>11</day><month>5</month><year>2015</year></pub-date><pub-date pub-type="ppub"><month>6</month><year>2015</year></pub-date><pub-date pub-type="pmc-release"><day>26</day><month>6</month><year>2016</year></pub-date><volume>47</volume><issue>6</issue><fpage>632</fpage><lpage>639</lpage><pmc-comment>elocation-id from pubmed: 10.1038/ng.3281</pmc-comment>
<permissions><license license-type="permissions-link"><license-p>Reprints and permissions informatiopn is available online at <ext-link ext-link-type="uri" xlink:href="http://www.nature.com/reprints/index.html">http://www.nature.com/reprints/index.html</ext-link>.</license-p></license></permissions><abstract><p id="P1">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 <italic>Salmonella enterica</italic> serovar Typhi (<italic>S.</italic> 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.</p></abstract></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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