AustralieFrV1, Main, Exploration, bibRecord, 002A13

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

Identifieur interne : 002A13 ( Main/Exploration ); précédent : 002A12; suivant : 002A14

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

Auteurs : Vanessa K. Wong [Royaume-Uni] ; Stephen Baker [Viêt Nam, Royaume-Uni] ; Derek J. Pickard [Royaume-Uni] ; Julian Parkhill [Royaume-Uni] ; Andrew J. Page [Royaume-Uni] ; Nicholas A. Feasey [Royaume-Uni] ; Robert A. Kingsley [Royaume-Uni] ; Nicholas R. Thomson [Royaume-Uni] ; Jacqueline A. Keane [Royaume-Uni] ; François-Xavier Weill [France] ; David J. Edwards [Australie] ; Jane Hawkey [Australie] ; Simon R. Harris [Royaume-Uni] ; Alison E. Mather [Royaume-Uni] ; Amy K. Cain [Royaume-Uni] ; James Hadfield [Royaume-Uni] ; Peter J. Hart [Royaume-Uni] ; Nga Tran Vu Thieu [Viêt Nam] ; Elizabeth J. Klemm [Royaume-Uni] ; Dafni A. Glinos [Royaume-Uni] ; Robert F. Breiman [Kenya, États-Unis] ; Conall H. Watson [Royaume-Uni] ; Samuel Kariuki [Royaume-Uni, Kenya] ; Melita A. Gordon [Royaume-Uni] ; Robert S. Heyderman [Malawi] ; Chinyere Okoro [Royaume-Uni] ; Jan Jacobs [Belgique] ; Octavie Lunguya ; W John Edmunds [Royaume-Uni] ; Chisomo Msefula [Malawi] ; Jose A. Chabalgoity [Uruguay] ; Mike Kama [Fidji] ; Kylie Jenkins [Fidji] ; Shanta Dutta [Inde] ; Florian Marks [Corée du Sud] ; Josefina Campos [Argentine] ; Corinne Thompson [Viêt Nam, Royaume-Uni] ; Stephen Obaro [États-Unis, Nigeria] ; Calman A. Maclennan [Royaume-Uni, Italie] ; Christiane Dolecek [Royaume-Uni] ; Karen H. Keddy [Afrique du Sud] ; Anthony M. Smith [Afrique du Sud] ; Christopher M. Parry [Royaume-Uni, Japon] ; Abhilasha Karkey [Népal] ; E Kim Mulholland [Royaume-Uni, Australie] ; James I. Campbell [Viêt Nam, Royaume-Uni] ; Sabina Dongol [Népal] ; Buddha Basnyat [Népal] ; Muriel Dufour [Nouvelle-Zélande] ; Don Bandaranayake [Nouvelle-Zélande] ; Take Toleafoa Naseri [Samoa] ; Shalini Pravin Singh [Fidji] ; Mochammad Hatta [Indonésie] ; Paul Newton [Royaume-Uni, Laos] ; Robert S. Onsare [Kenya] ; Lupeoletalalei Isaia [Samoa] ; David Dance [Royaume-Uni, Laos] ; Viengmon Davong [Laos] ; Guy Thwaites [Viêt Nam, Royaume-Uni] ; Lalith Wijedoru [Thaïlande, Royaume-Uni] ; John A. Crump [Nouvelle-Zélande] ; Elizabeth De Pinna [Royaume-Uni] ; Satheesh Nair [Royaume-Uni] ; Eric J. Nilles [Fidji] ; Duy Pham Thanh [Viêt Nam] ; Paul Turner [Royaume-Uni, Thaïlande, Cambodge] ; Sona Soeng [Cambodge] ; Mary Valcanis [Australie] ; Joan Powling [Australie] ; Karolina Dimovski [Australie] ; Geoff Hogg [Australie] ; Jeremy Farrar [Viêt Nam, Royaume-Uni] ; Kathryn E. Holt [Australie] ; Gordon Dougan [Royaume-Uni]

Source :

Nature genetics [ 1061-4036 ] ; 2015.

RBID : PMC:4921243

Descripteurs français

KwdFr :
- Analyse de séquence d'ADN, Antibactériens (pharmacologie), Antibactériens (usage thérapeutique), Données de séquences moléculaires, Fièvre typhoïde (microbiologie), Fièvre typhoïde (traitement médicamenteux), Fièvre typhoïde (transmission), Génome bactérien, Humains, Multirésistance bactérienne aux médicaments, Phylogénie, Phylogéographie, Quinoléines (pharmacologie), Quinoléines (usage thérapeutique), Salmonella typhi (génétique).
MESH :
- génétique : Salmonella typhi.
- microbiologie : Fièvre typhoïde.
- pharmacologie : Antibactériens, Quinoléines.
- traitement médicamenteux : Fièvre typhoïde.
- usage thérapeutique : Antibactériens, Fièvre typhoïde, Quinoléines.
- Analyse de séquence d'ADN, Données de séquences moléculaires, Génome bactérien, Humains, Multirésistance bactérienne aux médicaments, Phylogénie, Phylogéographie.

English descriptors

KwdEn :
- Anti-Bacterial Agents (pharmacology), Anti-Bacterial Agents (therapeutic use), Drug Resistance, Multiple, Bacterial, Genome, Bacterial, Humans, Molecular Sequence Data, Phylogeny, Phylogeography, Quinolines (pharmacology), Quinolines (therapeutic use), Salmonella typhi (genetics), Sequence Analysis, DNA, Typhoid Fever (drug therapy), Typhoid Fever (microbiology), Typhoid Fever (transmission).
MESH :
- chemical , pharmacology : Anti-Bacterial Agents, Quinolines.
- chemical , therapeutic use : Anti-Bacterial Agents, Quinolines.
- drug therapy : Typhoid Fever.
- genetics : Salmonella typhi.
- microbiology : Typhoid Fever.
- transmission : Typhoid Fever.
- Drug Resistance, Multiple, Bacterial, Genome, Bacterial, Humans, Molecular Sequence Data, Phylogeny, Phylogeography, Sequence Analysis, DNA.

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 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.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4921243

DOI: 10.1038/ng.3281
PubMed: 25961941
PubMed Central: 4921243

Affiliations:

Afrique du Sud, Argentine, Australie, Belgique, Cambodge, Corée du Sud, Fidji, France, Inde, Indonésie, Italie, Japon, Kenya, Laos, Malawi, Nigeria, Nouvelle-Zélande, Népal, Royaume-Uni, Samoa, Thaïlande, Uruguay, Viêt Nam, États-Unis
Angleterre, Gauteng, Grand Londres, Géorgie (États-Unis), Midlands de l'Ouest, Nebraska, Oxfordshire, Région capitale de Séoul, Victoria (État), Île-de-France
Birmingham, Johannesbourg, Londres, Melbourne, Oxford, Paris, Séoul
Université de Birmingham, Université de Melbourne, Université du Witwatersrand

Le document en format XML

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<author><name sortKey="Hawkey, Jane" sort="Hawkey, Jane" uniqKey="Hawkey J" first="Jane" last="Hawkey">Jane Hawkey</name>
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<author><name sortKey="Mather, Alison E" sort="Mather, Alison E" uniqKey="Mather A" first="Alison E" last="Mather">Alison E. Mather</name>
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<author><name sortKey="Cain, Amy K" sort="Cain, Amy K" uniqKey="Cain A" first="Amy K" last="Cain">Amy K. Cain</name>
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<author><name sortKey="Hart, Peter J" sort="Hart, Peter J" uniqKey="Hart P" first="Peter J" last="Hart">Peter J. Hart</name>
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<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>
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<author><name sortKey="Klemm, Elizabeth J" sort="Klemm, Elizabeth J" uniqKey="Klemm E" first="Elizabeth J" last="Klemm">Elizabeth J. Klemm</name>
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<author><name sortKey="Glinos, Dafni A" sort="Glinos, Dafni A" uniqKey="Glinos D" first="Dafni A" last="Glinos">Dafni A. Glinos</name>
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<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton</wicri:regionArea>
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<author><name sortKey="Breiman, Robert F" sort="Breiman, Robert F" uniqKey="Breiman R" first="Robert F" last="Breiman">Robert F. Breiman</name>
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<country xml:lang="fr">Kenya</country>
<wicri:regionArea>Kenya Medical Research Institute (KEMRI), Nairobi</wicri:regionArea>
<wicri:noRegion>Nairobi</wicri:noRegion>
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<affiliation wicri:level="2"><nlm:aff id="A13">Centers for Disease Control and Prevention, Atlanta, Georgia, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Centers for Disease Control and Prevention, Atlanta, Georgia</wicri:regionArea>
<placeName><region type="state">Géorgie (États-Unis)</region>
</placeName>
</affiliation>
<affiliation wicri:level="2"><nlm:aff id="A14">Emory Global Health Institute, Atlanta, Georgia, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Emory Global Health Institute, Atlanta, Georgia</wicri:regionArea>
<placeName><region type="state">Géorgie (États-Unis)</region>
</placeName>
</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 wicri:level="3"><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>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London</wicri:regionArea>
<placeName><settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
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</author>
<author><name sortKey="Kariuki, Samuel" sort="Kariuki, Samuel" uniqKey="Kariuki S" first="Samuel" last="Kariuki">Samuel Kariuki</name>
<affiliation wicri:level="1"><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff>
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<wicri:noRegion>Hinxton</wicri:noRegion>
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<affiliation wicri:level="1"><nlm:aff id="A12">Kenya Medical Research Institute (KEMRI), Nairobi, Kenya</nlm:aff>
<country xml:lang="fr">Kenya</country>
<wicri:regionArea>Kenya Medical Research Institute (KEMRI), Nairobi</wicri:regionArea>
<wicri:noRegion>Nairobi</wicri:noRegion>
</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 wicri:level="1"><nlm:aff id="A16">Institute of Infection and Global Health, University of Liverpool, Liverpool, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Institute of Infection and Global Health, University of Liverpool, Liverpool</wicri:regionArea>
<wicri:noRegion>Liverpool</wicri:noRegion>
</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 wicri:level="1"><nlm:aff id="A17">Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi</nlm:aff>
<country xml:lang="fr">Malawi</country>
<wicri:regionArea>Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre</wicri:regionArea>
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</author>
<author><name sortKey="Okoro, Chinyere" sort="Okoro, Chinyere" uniqKey="Okoro C" first="Chinyere" last="Okoro">Chinyere Okoro</name>
<affiliation wicri:level="1"><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton</wicri:regionArea>
<wicri:noRegion>Hinxton</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Jacobs, Jan" sort="Jacobs, Jan" uniqKey="Jacobs J" first="Jan" last="Jacobs">Jan Jacobs</name>
<affiliation wicri:level="1"><nlm:aff id="A18">Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium</nlm:aff>
<country xml:lang="fr">Belgique</country>
<wicri:regionArea>Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp</wicri:regionArea>
<wicri:noRegion>Antwerp</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A19">Department of Microbiology and Immunology, Katholieke Universiteit (KU) Leuven, University of Leuven, Leuven, Belgium</nlm:aff>
<country xml:lang="fr">Belgique</country>
<wicri:regionArea>Department of Microbiology and Immunology, Katholieke Universiteit (KU) Leuven, University of Leuven, Leuven</wicri:regionArea>
<wicri:noRegion>Leuven</wicri:noRegion>
</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>
<wicri:noCountry code="subfield">Democratic Republic of the Congo</wicri:noCountry>
</affiliation>
<affiliation><nlm:aff id="A21">University Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo</nlm:aff>
<wicri:noCountry code="subfield">Democratic Republic of the Congo</wicri:noCountry>
</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 wicri:level="3"><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>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London</wicri:regionArea>
<placeName><settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Msefula, Chisomo" sort="Msefula, Chisomo" uniqKey="Msefula C" first="Chisomo" last="Msefula">Chisomo Msefula</name>
<affiliation wicri:level="1"><nlm:aff id="A17">Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi</nlm:aff>
<country xml:lang="fr">Malawi</country>
<wicri:regionArea>Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre</wicri:regionArea>
<wicri:noRegion>Blantyre</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A22">Microbiology Department, College of Medicine, University of Malawi, Blantyre, Malawi</nlm:aff>
<country xml:lang="fr">Malawi</country>
<wicri:regionArea>Microbiology Department, College of Medicine, University of Malawi, Blantyre</wicri:regionArea>
<wicri:noRegion>Blantyre</wicri:noRegion>
</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 wicri:level="1"><nlm:aff id="A23">Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Montevideo, Uruguay</nlm:aff>
<country xml:lang="fr">Uruguay</country>
<wicri:regionArea>Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Montevideo</wicri:regionArea>
<wicri:noRegion>Montevideo</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Kama, Mike" sort="Kama, Mike" uniqKey="Kama M" first="Mike" last="Kama">Mike Kama</name>
<affiliation wicri:level="1"><nlm:aff id="A24">Ministry of Health, Suva, Fiji</nlm:aff>
<country xml:lang="fr">Fidji</country>
<wicri:regionArea>Ministry of Health, Suva</wicri:regionArea>
<wicri:noRegion>Suva</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Jenkins, Kylie" sort="Jenkins, Kylie" uniqKey="Jenkins K" first="Kylie" last="Jenkins">Kylie Jenkins</name>
<affiliation wicri:level="1"><nlm:aff id="A25">Fiji Health Sector Support Program, Suva, Fiji</nlm:aff>
<country xml:lang="fr">Fidji</country>
<wicri:regionArea>Fiji Health Sector Support Program, Suva</wicri:regionArea>
<wicri:noRegion>Suva</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Dutta, Shanta" sort="Dutta, Shanta" uniqKey="Dutta S" first="Shanta" last="Dutta">Shanta Dutta</name>
<affiliation wicri:level="1"><nlm:aff id="A26">National Institute of Cholera and Enteric Diseases, Kolkata, India</nlm:aff>
<country xml:lang="fr">Inde</country>
<wicri:regionArea>National Institute of Cholera and Enteric Diseases, Kolkata</wicri:regionArea>
<wicri:noRegion>Kolkata</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Marks, Florian" sort="Marks, Florian" uniqKey="Marks F" first="Florian" last="Marks">Florian Marks</name>
<affiliation wicri:level="3"><nlm:aff id="A27">International Vaccine Institute, Department of Epidemiology, Seoul, Republic of Korea</nlm:aff>
<country xml:lang="fr">Corée du Sud</country>
<wicri:regionArea>International Vaccine Institute, Department of Epidemiology, Seoul</wicri:regionArea>
<placeName><settlement type="city">Séoul</settlement>
<region type="capital">Région capitale de Séoul</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Campos, Josefina" sort="Campos, Josefina" uniqKey="Campos J" first="Josefina" last="Campos">Josefina Campos</name>
<affiliation wicri:level="1"><nlm:aff id="A28">Enteropathogen Division, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) Carlos G. Malbran Institute, Buenos Aires, Argentina</nlm:aff>
<country xml:lang="fr">Argentine</country>
<wicri:regionArea>Enteropathogen Division, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) Carlos G. Malbran Institute, Buenos Aires</wicri:regionArea>
<wicri:noRegion>Buenos Aires</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Thompson, Corinne" sort="Thompson, Corinne" uniqKey="Thompson C" first="Corinne" last="Thompson">Corinne Thompson</name>
<affiliation wicri:level="1"><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>
<country xml:lang="fr">Viêt Nam</country>
<wicri:regionArea>Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City</wicri:regionArea>
<wicri:noRegion>Ho Chi Minh City</wicri:noRegion>
</affiliation>
<affiliation wicri:level="3"><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford</wicri:regionArea>
<placeName><settlement type="city">Oxford</settlement>
<region type="country">Angleterre</region>
<region type="comté" nuts="2">Oxfordshire</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Obaro, Stephen" sort="Obaro, Stephen" uniqKey="Obaro S" first="Stephen" last="Obaro">Stephen Obaro</name>
<affiliation wicri:level="2"><nlm:aff id="A29">Division of Pediatric Infectious Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Pediatric Infectious Diseases, University of Nebraska Medical Center, Omaha, Nebraska</wicri:regionArea>
<placeName><region type="state">Nebraska</region>
</placeName>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A30">University of Abuja Teaching Hospital, Abuja, Nigeria</nlm:aff>
<country xml:lang="fr">Nigeria</country>
<wicri:regionArea>University of Abuja Teaching Hospital, Abuja</wicri:regionArea>
<wicri:noRegion>Abuja</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A31">Bingham University, Karu, Nigeria</nlm:aff>
<country xml:lang="fr">Nigeria</country>
<wicri:regionArea>Bingham University, Karu</wicri:regionArea>
<wicri:noRegion>Karu</wicri:noRegion>
</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 wicri:level="1"><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton</wicri:regionArea>
<wicri:noRegion>Hinxton</wicri:noRegion>
</affiliation>
<affiliation wicri:level="4"><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>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Institute of Biomedical Research, School of Immunity and Infection, College of Medicine and Dental Sciences, University of Birmingham, Birmingham</wicri:regionArea>
<placeName><settlement type="city">Birmingham</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Midlands de l'Ouest</region>
<settlement type="city">Birmingham</settlement>
</placeName>
<orgName type="university">Université de Birmingham</orgName>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A32">Novartis Vaccines Institute for Global Health, Siena, Italy</nlm:aff>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>Novartis Vaccines Institute for Global Health, Siena</wicri:regionArea>
<wicri:noRegion>Siena</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Dolecek, Christiane" sort="Dolecek, Christiane" uniqKey="Dolecek C" first="Christiane" last="Dolecek">Christiane Dolecek</name>
<affiliation wicri:level="3"><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford</wicri:regionArea>
<placeName><settlement type="city">Oxford</settlement>
<region type="country">Angleterre</region>
<region type="comté" nuts="2">Oxfordshire</region>
</placeName>
</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 wicri:level="4"><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>
<country xml:lang="fr">Afrique du Sud</country>
<wicri:regionArea>Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service, University of the Witwatersrand, Johannesburg</wicri:regionArea>
<orgName type="university">Université du Witwatersrand</orgName>
<placeName><settlement type="city">Johannesbourg</settlement>
<region type="region" nuts="2">Gauteng</region>
</placeName>
</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 wicri:level="4"><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>
<country xml:lang="fr">Afrique du Sud</country>
<wicri:regionArea>Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service, University of the Witwatersrand, Johannesburg</wicri:regionArea>
<orgName type="university">Université du Witwatersrand</orgName>
<placeName><settlement type="city">Johannesbourg</settlement>
<region type="region" nuts="2">Gauteng</region>
</placeName>
</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 wicri:level="3"><nlm:aff id="A34">Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Department of Clinical Research, London School of Hygiene and Tropical Medicine, London</wicri:regionArea>
<placeName><settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
</placeName>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A35">Graduate School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>Graduate School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki</wicri:regionArea>
<wicri:noRegion>Nagasaki</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Karkey, Abhilasha" sort="Karkey, Abhilasha" uniqKey="Karkey A" first="Abhilasha" last="Karkey">Abhilasha Karkey</name>
<affiliation wicri:level="1"><nlm:aff id="A36">Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal</nlm:aff>
<country xml:lang="fr">Népal</country>
<wicri:regionArea>Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu</wicri:regionArea>
<wicri:noRegion>Kathmandu</wicri:noRegion>
</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 wicri:level="3"><nlm:aff id="A5">Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London</wicri:regionArea>
<placeName><settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
</placeName>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A37">Murdoch Childrens Research Institute, Melbourne, Victoria, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Murdoch Childrens Research Institute, Melbourne, Victoria</wicri:regionArea>
<wicri:noRegion>Victoria</wicri:noRegion>
</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 wicri:level="1"><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>
<country xml:lang="fr">Viêt Nam</country>
<wicri:regionArea>Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City</wicri:regionArea>
<wicri:noRegion>Ho Chi Minh City</wicri:noRegion>
</affiliation>
<affiliation wicri:level="3"><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford</wicri:regionArea>
<placeName><settlement type="city">Oxford</settlement>
<region type="country">Angleterre</region>
<region type="comté" nuts="2">Oxfordshire</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Dongol, Sabina" sort="Dongol, Sabina" uniqKey="Dongol S" first="Sabina" last="Dongol">Sabina Dongol</name>
<affiliation wicri:level="1"><nlm:aff id="A36">Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal</nlm:aff>
<country xml:lang="fr">Népal</country>
<wicri:regionArea>Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu</wicri:regionArea>
<wicri:noRegion>Kathmandu</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Basnyat, Buddha" sort="Basnyat, Buddha" uniqKey="Basnyat B" first="Buddha" last="Basnyat">Buddha Basnyat</name>
<affiliation wicri:level="1"><nlm:aff id="A36">Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal</nlm:aff>
<country xml:lang="fr">Népal</country>
<wicri:regionArea>Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu</wicri:regionArea>
<wicri:noRegion>Kathmandu</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Dufour, Muriel" sort="Dufour, Muriel" uniqKey="Dufour M" first="Muriel" last="Dufour">Muriel Dufour</name>
<affiliation wicri:level="1"><nlm:aff id="A38">Enteric and Leptospira Reference Laboratory, Institute of Environmental Science and Research, Ltd. (ESR), Porirua, New Zealand</nlm:aff>
<country xml:lang="fr">Nouvelle-Zélande</country>
<wicri:regionArea>Enteric and Leptospira Reference Laboratory, Institute of Environmental Science and Research, Ltd. (ESR), Porirua</wicri:regionArea>
<wicri:noRegion>Porirua</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Bandaranayake, Don" sort="Bandaranayake, Don" uniqKey="Bandaranayake D" first="Don" last="Bandaranayake">Don Bandaranayake</name>
<affiliation wicri:level="1"><nlm:aff id="A39">National Centre for Biosecurity and Infectious Disease, Institute of Environmental Science and Research, Porirua, New Zealand</nlm:aff>
<country xml:lang="fr">Nouvelle-Zélande</country>
<wicri:regionArea>National Centre for Biosecurity and Infectious Disease, Institute of Environmental Science and Research, Porirua</wicri:regionArea>
<wicri:noRegion>Porirua</wicri:noRegion>
</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 wicri:level="1"><nlm:aff id="A40">Samoa Ministry of Health, Apia, Samoa</nlm:aff>
<country xml:lang="fr">Samoa</country>
<wicri:regionArea>Samoa Ministry of Health, Apia</wicri:regionArea>
<wicri:noRegion>Apia</wicri:noRegion>
</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 wicri:level="1"><nlm:aff id="A41">National Influenza Center, World Health Organization, Center for Communicable Disease Control, Suva, Fiji</nlm:aff>
<country xml:lang="fr">Fidji</country>
<wicri:regionArea>National Influenza Center, World Health Organization, Center for Communicable Disease Control, Suva</wicri:regionArea>
<wicri:noRegion>Suva</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Hatta, Mochammad" sort="Hatta, Mochammad" uniqKey="Hatta M" first="Mochammad" last="Hatta">Mochammad Hatta</name>
<affiliation wicri:level="1"><nlm:aff id="A42">Department of Microbiology, Hasanuddin University, Makassar, Indonesia</nlm:aff>
<country xml:lang="fr">Indonésie</country>
<wicri:regionArea>Department of Microbiology, Hasanuddin University, Makassar</wicri:regionArea>
<wicri:noRegion>Makassar</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Newton, Paul" sort="Newton, Paul" uniqKey="Newton P" first="Paul" last="Newton">Paul Newton</name>
<affiliation wicri:level="3"><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford</wicri:regionArea>
<placeName><settlement type="city">Oxford</settlement>
<region type="country">Angleterre</region>
<region type="comté" nuts="2">Oxfordshire</region>
</placeName>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A43">Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos</nlm:aff>
<country xml:lang="fr">Laos</country>
<wicri:regionArea>Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane</wicri:regionArea>
<wicri:noRegion>Vientiane</wicri:noRegion>
</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 wicri:level="1"><nlm:aff id="A12">Kenya Medical Research Institute (KEMRI), Nairobi, Kenya</nlm:aff>
<country xml:lang="fr">Kenya</country>
<wicri:regionArea>Kenya Medical Research Institute (KEMRI), Nairobi</wicri:regionArea>
<wicri:noRegion>Nairobi</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Isaia, Lupeoletalalei" sort="Isaia, Lupeoletalalei" uniqKey="Isaia L" first="Lupeoletalalei" last="Isaia">Lupeoletalalei Isaia</name>
<affiliation wicri:level="1"><nlm:aff id="A44">National Health Services, Tupua Tamasese Meaole Hospital, Apia, Samoa</nlm:aff>
<country xml:lang="fr">Samoa</country>
<wicri:regionArea>National Health Services, Tupua Tamasese Meaole Hospital, Apia</wicri:regionArea>
<wicri:noRegion>Apia</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Dance, David" sort="Dance, David" uniqKey="Dance D" first="David" last="Dance">David Dance</name>
<affiliation wicri:level="3"><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford</wicri:regionArea>
<placeName><settlement type="city">Oxford</settlement>
<region type="country">Angleterre</region>
<region type="comté" nuts="2">Oxfordshire</region>
</placeName>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A43">Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos</nlm:aff>
<country xml:lang="fr">Laos</country>
<wicri:regionArea>Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane</wicri:regionArea>
<wicri:noRegion>Vientiane</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Davong, Viengmon" sort="Davong, Viengmon" uniqKey="Davong V" first="Viengmon" last="Davong">Viengmon Davong</name>
<affiliation wicri:level="1"><nlm:aff id="A43">Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos</nlm:aff>
<country xml:lang="fr">Laos</country>
<wicri:regionArea>Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane</wicri:regionArea>
<wicri:noRegion>Vientiane</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Thwaites, Guy" sort="Thwaites, Guy" uniqKey="Thwaites G" first="Guy" last="Thwaites">Guy Thwaites</name>
<affiliation wicri:level="1"><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>
<country xml:lang="fr">Viêt Nam</country>
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</affiliation>
</author>
<author><name sortKey="Wijedoru, Lalith" sort="Wijedoru, Lalith" uniqKey="Wijedoru L" first="Lalith" last="Wijedoru">Lalith Wijedoru</name>
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<country xml:lang="fr">Thaïlande</country>
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</affiliation>
<affiliation wicri:level="3"><nlm:aff id="A46">Paediatric Emergency Medicine, Chelsea and Westminster Hospital, London, UK</nlm:aff>
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</placeName>
</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 wicri:level="1"><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>
<country xml:lang="fr">Nouvelle-Zélande</country>
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</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 wicri:level="3"><nlm:aff id="A48"><italic>Salmonella</italic>
 Reference Service, Public Health England, Colindale, London, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea> Reference Service, Public Health England, Colindale, London</wicri:regionArea>
<placeName><settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Nair, Satheesh" sort="Nair, Satheesh" uniqKey="Nair S" first="Satheesh" last="Nair">Satheesh Nair</name>
<affiliation wicri:level="3"><nlm:aff id="A48"><italic>Salmonella</italic>
 Reference Service, Public Health England, Colindale, London, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea> Reference Service, Public Health England, Colindale, London</wicri:regionArea>
<placeName><settlement type="city">Londres</settlement>
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</placeName>
</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 wicri:level="1"><nlm:aff id="A49">Emerging Disease Surveillance and Response, Division of Pacific Technical Support, World Health Organization, Suva, Fiji</nlm:aff>
<country xml:lang="fr">Fidji</country>
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</author>
<author><name sortKey="Thanh, Duy Pham" sort="Thanh, Duy Pham" uniqKey="Thanh D" first="Duy Pham" last="Thanh">Duy Pham Thanh</name>
<affiliation wicri:level="1"><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>
<country xml:lang="fr">Viêt Nam</country>
<wicri:regionArea>Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City</wicri:regionArea>
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</affiliation>
</author>
<author><name sortKey="Turner, Paul" sort="Turner, Paul" uniqKey="Turner P" first="Paul" last="Turner">Paul Turner</name>
<affiliation wicri:level="3"><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford</wicri:regionArea>
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</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A45">Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand</nlm:aff>
<country xml:lang="fr">Thaïlande</country>
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</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A50">Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia</nlm:aff>
<country xml:lang="fr">Cambodge</country>
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</affiliation>
</author>
<author><name sortKey="Soeng, Sona" sort="Soeng, Sona" uniqKey="Soeng S" first="Sona" last="Soeng">Sona Soeng</name>
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<country xml:lang="fr">Cambodge</country>
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</author>
<author><name sortKey="Valcanis, Mary" sort="Valcanis, Mary" uniqKey="Valcanis M" first="Mary" last="Valcanis">Mary Valcanis</name>
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<country xml:lang="fr">Australie</country>
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</affiliation>
</author>
<author><name sortKey="Powling, Joan" sort="Powling, Joan" uniqKey="Powling J" first="Joan" last="Powling">Joan Powling</name>
<affiliation wicri:level="4"><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>
<country xml:lang="fr">Australie</country>
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</author>
<author><name sortKey="Dimovski, Karolina" sort="Dimovski, Karolina" uniqKey="Dimovski K" first="Karolina" last="Dimovski">Karolina Dimovski</name>
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</author>
<author><name sortKey="Hogg, Geoff" sort="Hogg, Geoff" uniqKey="Hogg G" first="Geoff" last="Hogg">Geoff Hogg</name>
<affiliation wicri:level="4"><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>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>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</wicri:regionArea>
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</author>
<author><name sortKey="Farrar, Jeremy" sort="Farrar, Jeremy" uniqKey="Farrar J" first="Jeremy" last="Farrar">Jeremy Farrar</name>
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<affiliation wicri:level="3"><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
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</author>
<author><name sortKey="Holt, Kathryn E" sort="Holt, Kathryn E" uniqKey="Holt K" first="Kathryn E" last="Holt">Kathryn E. Holt</name>
<affiliation wicri:level="4"><nlm:aff id="A9">Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria</wicri:regionArea>
<orgName type="university">Université de Melbourne</orgName>
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</placeName>
</affiliation>
</author>
<author><name sortKey="Dougan, Gordon" sort="Dougan, Gordon" uniqKey="Dougan G" first="Gordon" last="Dougan">Gordon Dougan</name>
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<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>
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<affiliation wicri:level="1"><nlm:aff id="A2">Department of Microbiology, Addenbrooke’s Hospital, Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Department of Microbiology, Addenbrooke’s Hospital, Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge</wicri:regionArea>
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</author>
<author><name sortKey="Baker, Stephen" sort="Baker, Stephen" uniqKey="Baker S" first="Stephen" last="Baker">Stephen Baker</name>
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<country xml:lang="fr">Viêt Nam</country>
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<affiliation wicri:level="3"><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford</wicri:regionArea>
<placeName><settlement type="city">Oxford</settlement>
<region type="country">Angleterre</region>
<region type="comté" nuts="2">Oxfordshire</region>
</placeName>
</affiliation>
<affiliation wicri:level="3"><nlm:aff id="A5">Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London</wicri:regionArea>
<placeName><settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
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</placeName>
</affiliation>
</author>
<author><name sortKey="Pickard, Derek J" sort="Pickard, Derek J" uniqKey="Pickard D" first="Derek J" last="Pickard">Derek J. Pickard</name>
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<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton</wicri:regionArea>
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</author>
<author><name sortKey="Parkhill, Julian" sort="Parkhill, Julian" uniqKey="Parkhill J" first="Julian" last="Parkhill">Julian Parkhill</name>
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<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton</wicri:regionArea>
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</affiliation>
</author>
<author><name sortKey="Page, Andrew J" sort="Page, Andrew J" uniqKey="Page A" first="Andrew J" last="Page">Andrew J. Page</name>
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<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton</wicri:regionArea>
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</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 wicri:level="1"><nlm:aff id="A6">Liverpool School of Tropical Medicine, Liverpool, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Liverpool School of Tropical Medicine, Liverpool</wicri:regionArea>
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</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 wicri:level="1"><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton</wicri:regionArea>
<wicri:noRegion>Hinxton</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A7">Institute of Food Research, Norwich Research Park, Norwich, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Institute of Food Research, Norwich Research Park, Norwich</wicri:regionArea>
<wicri:noRegion>Norwich</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Thomson, Nicholas R" sort="Thomson, Nicholas R" uniqKey="Thomson N" first="Nicholas R" last="Thomson">Nicholas R. Thomson</name>
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<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton</wicri:regionArea>
<wicri:noRegion>Hinxton</wicri:noRegion>
</affiliation>
<affiliation wicri:level="3"><nlm:aff id="A5">Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London</wicri:regionArea>
<placeName><settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Keane, Jacqueline A" sort="Keane, Jacqueline A" uniqKey="Keane J" first="Jacqueline A" last="Keane">Jacqueline A. Keane</name>
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<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton</wicri:regionArea>
<wicri:noRegion>Hinxton</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Weill, Francois Xavier" sort="Weill, Francois Xavier" uniqKey="Weill F" first="François-Xavier" last="Weill">François-Xavier Weill</name>
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<country xml:lang="fr">France</country>
<wicri:regionArea>Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris</wicri:regionArea>
<placeName><region type="region">Île-de-France</region>
<region type="old region">Île-de-France</region>
<settlement type="city">Paris</settlement>
</placeName>
</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 wicri:level="4"><nlm:aff id="A9">Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria</wicri:regionArea>
<orgName type="university">Université de Melbourne</orgName>
<placeName><settlement type="city">Melbourne</settlement>
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</placeName>
</affiliation>
</author>
<author><name sortKey="Hawkey, Jane" sort="Hawkey, Jane" uniqKey="Hawkey J" first="Jane" last="Hawkey">Jane Hawkey</name>
<affiliation wicri:level="4"><nlm:aff id="A9">Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria</wicri:regionArea>
<orgName type="university">Université de Melbourne</orgName>
<placeName><settlement type="city">Melbourne</settlement>
<region type="état">Victoria (État)</region>
</placeName>
</affiliation>
<affiliation wicri:level="4"><nlm:aff id="A10">Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria</wicri:regionArea>
<orgName type="university">Université de Melbourne</orgName>
<placeName><settlement type="city">Melbourne</settlement>
<region type="état">Victoria (État)</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Harris, Simon R" sort="Harris, Simon R" uniqKey="Harris S" first="Simon R" last="Harris">Simon R. Harris</name>
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<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton</wicri:regionArea>
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</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 wicri:level="1"><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton</wicri:regionArea>
<wicri:noRegion>Hinxton</wicri:noRegion>
</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 wicri:level="1"><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton</wicri:regionArea>
<wicri:noRegion>Hinxton</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Hadfield, James" sort="Hadfield, James" uniqKey="Hadfield J" first="James" last="Hadfield">James Hadfield</name>
<affiliation wicri:level="1"><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton</wicri:regionArea>
<wicri:noRegion>Hinxton</wicri:noRegion>
</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 wicri:level="4"><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>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Institute of Biomedical Research, School of Immunity and Infection, College of Medicine and Dental Sciences, University of Birmingham, Birmingham</wicri:regionArea>
<placeName><settlement type="city">Birmingham</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Midlands de l'Ouest</region>
<settlement type="city">Birmingham</settlement>
</placeName>
<orgName type="university">Université de Birmingham</orgName>
</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 wicri:level="1"><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>
<country xml:lang="fr">Viêt Nam</country>
<wicri:regionArea>Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City</wicri:regionArea>
<wicri:noRegion>Ho Chi Minh City</wicri:noRegion>
</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 wicri:level="1"><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton</wicri:regionArea>
<wicri:noRegion>Hinxton</wicri:noRegion>
</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 wicri:level="1"><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton</wicri:regionArea>
<wicri:noRegion>Hinxton</wicri:noRegion>
</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 wicri:level="1"><nlm:aff id="A12">Kenya Medical Research Institute (KEMRI), Nairobi, Kenya</nlm:aff>
<country xml:lang="fr">Kenya</country>
<wicri:regionArea>Kenya Medical Research Institute (KEMRI), Nairobi</wicri:regionArea>
<wicri:noRegion>Nairobi</wicri:noRegion>
</affiliation>
<affiliation wicri:level="2"><nlm:aff id="A13">Centers for Disease Control and Prevention, Atlanta, Georgia, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Centers for Disease Control and Prevention, Atlanta, Georgia</wicri:regionArea>
<placeName><region type="state">Géorgie (États-Unis)</region>
</placeName>
</affiliation>
<affiliation wicri:level="2"><nlm:aff id="A14">Emory Global Health Institute, Atlanta, Georgia, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Emory Global Health Institute, Atlanta, Georgia</wicri:regionArea>
<placeName><region type="state">Géorgie (États-Unis)</region>
</placeName>
</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 wicri:level="3"><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>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London</wicri:regionArea>
<placeName><settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Kariuki, Samuel" sort="Kariuki, Samuel" uniqKey="Kariuki S" first="Samuel" last="Kariuki">Samuel Kariuki</name>
<affiliation wicri:level="1"><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton</wicri:regionArea>
<wicri:noRegion>Hinxton</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A12">Kenya Medical Research Institute (KEMRI), Nairobi, Kenya</nlm:aff>
<country xml:lang="fr">Kenya</country>
<wicri:regionArea>Kenya Medical Research Institute (KEMRI), Nairobi</wicri:regionArea>
<wicri:noRegion>Nairobi</wicri:noRegion>
</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 wicri:level="1"><nlm:aff id="A16">Institute of Infection and Global Health, University of Liverpool, Liverpool, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Institute of Infection and Global Health, University of Liverpool, Liverpool</wicri:regionArea>
<wicri:noRegion>Liverpool</wicri:noRegion>
</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 wicri:level="1"><nlm:aff id="A17">Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi</nlm:aff>
<country xml:lang="fr">Malawi</country>
<wicri:regionArea>Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre</wicri:regionArea>
<wicri:noRegion>Blantyre</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Okoro, Chinyere" sort="Okoro, Chinyere" uniqKey="Okoro C" first="Chinyere" last="Okoro">Chinyere Okoro</name>
<affiliation wicri:level="1"><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton</wicri:regionArea>
<wicri:noRegion>Hinxton</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Jacobs, Jan" sort="Jacobs, Jan" uniqKey="Jacobs J" first="Jan" last="Jacobs">Jan Jacobs</name>
<affiliation wicri:level="1"><nlm:aff id="A18">Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium</nlm:aff>
<country xml:lang="fr">Belgique</country>
<wicri:regionArea>Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp</wicri:regionArea>
<wicri:noRegion>Antwerp</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A19">Department of Microbiology and Immunology, Katholieke Universiteit (KU) Leuven, University of Leuven, Leuven, Belgium</nlm:aff>
<country xml:lang="fr">Belgique</country>
<wicri:regionArea>Department of Microbiology and Immunology, Katholieke Universiteit (KU) Leuven, University of Leuven, Leuven</wicri:regionArea>
<wicri:noRegion>Leuven</wicri:noRegion>
</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>
<wicri:noCountry code="subfield">Democratic Republic of the Congo</wicri:noCountry>
</affiliation>
<affiliation><nlm:aff id="A21">University Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo</nlm:aff>
<wicri:noCountry code="subfield">Democratic Republic of the Congo</wicri:noCountry>
</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 wicri:level="3"><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>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London</wicri:regionArea>
<placeName><settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Msefula, Chisomo" sort="Msefula, Chisomo" uniqKey="Msefula C" first="Chisomo" last="Msefula">Chisomo Msefula</name>
<affiliation wicri:level="1"><nlm:aff id="A17">Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi</nlm:aff>
<country xml:lang="fr">Malawi</country>
<wicri:regionArea>Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre</wicri:regionArea>
<wicri:noRegion>Blantyre</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A22">Microbiology Department, College of Medicine, University of Malawi, Blantyre, Malawi</nlm:aff>
<country xml:lang="fr">Malawi</country>
<wicri:regionArea>Microbiology Department, College of Medicine, University of Malawi, Blantyre</wicri:regionArea>
<wicri:noRegion>Blantyre</wicri:noRegion>
</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 wicri:level="1"><nlm:aff id="A23">Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Montevideo, Uruguay</nlm:aff>
<country xml:lang="fr">Uruguay</country>
<wicri:regionArea>Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Montevideo</wicri:regionArea>
<wicri:noRegion>Montevideo</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Kama, Mike" sort="Kama, Mike" uniqKey="Kama M" first="Mike" last="Kama">Mike Kama</name>
<affiliation wicri:level="1"><nlm:aff id="A24">Ministry of Health, Suva, Fiji</nlm:aff>
<country xml:lang="fr">Fidji</country>
<wicri:regionArea>Ministry of Health, Suva</wicri:regionArea>
<wicri:noRegion>Suva</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Jenkins, Kylie" sort="Jenkins, Kylie" uniqKey="Jenkins K" first="Kylie" last="Jenkins">Kylie Jenkins</name>
<affiliation wicri:level="1"><nlm:aff id="A25">Fiji Health Sector Support Program, Suva, Fiji</nlm:aff>
<country xml:lang="fr">Fidji</country>
<wicri:regionArea>Fiji Health Sector Support Program, Suva</wicri:regionArea>
<wicri:noRegion>Suva</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Dutta, Shanta" sort="Dutta, Shanta" uniqKey="Dutta S" first="Shanta" last="Dutta">Shanta Dutta</name>
<affiliation wicri:level="1"><nlm:aff id="A26">National Institute of Cholera and Enteric Diseases, Kolkata, India</nlm:aff>
<country xml:lang="fr">Inde</country>
<wicri:regionArea>National Institute of Cholera and Enteric Diseases, Kolkata</wicri:regionArea>
<wicri:noRegion>Kolkata</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Marks, Florian" sort="Marks, Florian" uniqKey="Marks F" first="Florian" last="Marks">Florian Marks</name>
<affiliation wicri:level="3"><nlm:aff id="A27">International Vaccine Institute, Department of Epidemiology, Seoul, Republic of Korea</nlm:aff>
<country xml:lang="fr">Corée du Sud</country>
<wicri:regionArea>International Vaccine Institute, Department of Epidemiology, Seoul</wicri:regionArea>
<placeName><settlement type="city">Séoul</settlement>
<region type="capital">Région capitale de Séoul</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Campos, Josefina" sort="Campos, Josefina" uniqKey="Campos J" first="Josefina" last="Campos">Josefina Campos</name>
<affiliation wicri:level="1"><nlm:aff id="A28">Enteropathogen Division, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) Carlos G. Malbran Institute, Buenos Aires, Argentina</nlm:aff>
<country xml:lang="fr">Argentine</country>
<wicri:regionArea>Enteropathogen Division, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) Carlos G. Malbran Institute, Buenos Aires</wicri:regionArea>
<wicri:noRegion>Buenos Aires</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Thompson, Corinne" sort="Thompson, Corinne" uniqKey="Thompson C" first="Corinne" last="Thompson">Corinne Thompson</name>
<affiliation wicri:level="1"><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>
<country xml:lang="fr">Viêt Nam</country>
<wicri:regionArea>Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City</wicri:regionArea>
<wicri:noRegion>Ho Chi Minh City</wicri:noRegion>
</affiliation>
<affiliation wicri:level="3"><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford</wicri:regionArea>
<placeName><settlement type="city">Oxford</settlement>
<region type="country">Angleterre</region>
<region type="comté" nuts="2">Oxfordshire</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Obaro, Stephen" sort="Obaro, Stephen" uniqKey="Obaro S" first="Stephen" last="Obaro">Stephen Obaro</name>
<affiliation wicri:level="2"><nlm:aff id="A29">Division of Pediatric Infectious Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Pediatric Infectious Diseases, University of Nebraska Medical Center, Omaha, Nebraska</wicri:regionArea>
<placeName><region type="state">Nebraska</region>
</placeName>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A30">University of Abuja Teaching Hospital, Abuja, Nigeria</nlm:aff>
<country xml:lang="fr">Nigeria</country>
<wicri:regionArea>University of Abuja Teaching Hospital, Abuja</wicri:regionArea>
<wicri:noRegion>Abuja</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A31">Bingham University, Karu, Nigeria</nlm:aff>
<country xml:lang="fr">Nigeria</country>
<wicri:regionArea>Bingham University, Karu</wicri:regionArea>
<wicri:noRegion>Karu</wicri:noRegion>
</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 wicri:level="1"><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton</wicri:regionArea>
<wicri:noRegion>Hinxton</wicri:noRegion>
</affiliation>
<affiliation wicri:level="4"><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>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Institute of Biomedical Research, School of Immunity and Infection, College of Medicine and Dental Sciences, University of Birmingham, Birmingham</wicri:regionArea>
<placeName><settlement type="city">Birmingham</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Midlands de l'Ouest</region>
<settlement type="city">Birmingham</settlement>
</placeName>
<orgName type="university">Université de Birmingham</orgName>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A32">Novartis Vaccines Institute for Global Health, Siena, Italy</nlm:aff>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>Novartis Vaccines Institute for Global Health, Siena</wicri:regionArea>
<wicri:noRegion>Siena</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Dolecek, Christiane" sort="Dolecek, Christiane" uniqKey="Dolecek C" first="Christiane" last="Dolecek">Christiane Dolecek</name>
<affiliation wicri:level="3"><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford</wicri:regionArea>
<placeName><settlement type="city">Oxford</settlement>
<region type="country">Angleterre</region>
<region type="comté" nuts="2">Oxfordshire</region>
</placeName>
</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 wicri:level="4"><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>
<country xml:lang="fr">Afrique du Sud</country>
<wicri:regionArea>Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service, University of the Witwatersrand, Johannesburg</wicri:regionArea>
<orgName type="university">Université du Witwatersrand</orgName>
<placeName><settlement type="city">Johannesbourg</settlement>
<region type="region" nuts="2">Gauteng</region>
</placeName>
</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 wicri:level="4"><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>
<country xml:lang="fr">Afrique du Sud</country>
<wicri:regionArea>Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service, University of the Witwatersrand, Johannesburg</wicri:regionArea>
<orgName type="university">Université du Witwatersrand</orgName>
<placeName><settlement type="city">Johannesbourg</settlement>
<region type="region" nuts="2">Gauteng</region>
</placeName>
</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 wicri:level="3"><nlm:aff id="A34">Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Department of Clinical Research, London School of Hygiene and Tropical Medicine, London</wicri:regionArea>
<placeName><settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
</placeName>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A35">Graduate School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>Graduate School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki</wicri:regionArea>
<wicri:noRegion>Nagasaki</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Karkey, Abhilasha" sort="Karkey, Abhilasha" uniqKey="Karkey A" first="Abhilasha" last="Karkey">Abhilasha Karkey</name>
<affiliation wicri:level="1"><nlm:aff id="A36">Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal</nlm:aff>
<country xml:lang="fr">Népal</country>
<wicri:regionArea>Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu</wicri:regionArea>
<wicri:noRegion>Kathmandu</wicri:noRegion>
</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 wicri:level="3"><nlm:aff id="A5">Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London</wicri:regionArea>
<placeName><settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
</placeName>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A37">Murdoch Childrens Research Institute, Melbourne, Victoria, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Murdoch Childrens Research Institute, Melbourne, Victoria</wicri:regionArea>
<wicri:noRegion>Victoria</wicri:noRegion>
</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 wicri:level="1"><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>
<country xml:lang="fr">Viêt Nam</country>
<wicri:regionArea>Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City</wicri:regionArea>
<wicri:noRegion>Ho Chi Minh City</wicri:noRegion>
</affiliation>
<affiliation wicri:level="3"><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford</wicri:regionArea>
<placeName><settlement type="city">Oxford</settlement>
<region type="country">Angleterre</region>
<region type="comté" nuts="2">Oxfordshire</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Dongol, Sabina" sort="Dongol, Sabina" uniqKey="Dongol S" first="Sabina" last="Dongol">Sabina Dongol</name>
<affiliation wicri:level="1"><nlm:aff id="A36">Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal</nlm:aff>
<country xml:lang="fr">Népal</country>
<wicri:regionArea>Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu</wicri:regionArea>
<wicri:noRegion>Kathmandu</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Basnyat, Buddha" sort="Basnyat, Buddha" uniqKey="Basnyat B" first="Buddha" last="Basnyat">Buddha Basnyat</name>
<affiliation wicri:level="1"><nlm:aff id="A36">Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal</nlm:aff>
<country xml:lang="fr">Népal</country>
<wicri:regionArea>Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu</wicri:regionArea>
<wicri:noRegion>Kathmandu</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Dufour, Muriel" sort="Dufour, Muriel" uniqKey="Dufour M" first="Muriel" last="Dufour">Muriel Dufour</name>
<affiliation wicri:level="1"><nlm:aff id="A38">Enteric and Leptospira Reference Laboratory, Institute of Environmental Science and Research, Ltd. (ESR), Porirua, New Zealand</nlm:aff>
<country xml:lang="fr">Nouvelle-Zélande</country>
<wicri:regionArea>Enteric and Leptospira Reference Laboratory, Institute of Environmental Science and Research, Ltd. (ESR), Porirua</wicri:regionArea>
<wicri:noRegion>Porirua</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Bandaranayake, Don" sort="Bandaranayake, Don" uniqKey="Bandaranayake D" first="Don" last="Bandaranayake">Don Bandaranayake</name>
<affiliation wicri:level="1"><nlm:aff id="A39">National Centre for Biosecurity and Infectious Disease, Institute of Environmental Science and Research, Porirua, New Zealand</nlm:aff>
<country xml:lang="fr">Nouvelle-Zélande</country>
<wicri:regionArea>National Centre for Biosecurity and Infectious Disease, Institute of Environmental Science and Research, Porirua</wicri:regionArea>
<wicri:noRegion>Porirua</wicri:noRegion>
</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 wicri:level="1"><nlm:aff id="A40">Samoa Ministry of Health, Apia, Samoa</nlm:aff>
<country xml:lang="fr">Samoa</country>
<wicri:regionArea>Samoa Ministry of Health, Apia</wicri:regionArea>
<wicri:noRegion>Apia</wicri:noRegion>
</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 wicri:level="1"><nlm:aff id="A41">National Influenza Center, World Health Organization, Center for Communicable Disease Control, Suva, Fiji</nlm:aff>
<country xml:lang="fr">Fidji</country>
<wicri:regionArea>National Influenza Center, World Health Organization, Center for Communicable Disease Control, Suva</wicri:regionArea>
<wicri:noRegion>Suva</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Hatta, Mochammad" sort="Hatta, Mochammad" uniqKey="Hatta M" first="Mochammad" last="Hatta">Mochammad Hatta</name>
<affiliation wicri:level="1"><nlm:aff id="A42">Department of Microbiology, Hasanuddin University, Makassar, Indonesia</nlm:aff>
<country xml:lang="fr">Indonésie</country>
<wicri:regionArea>Department of Microbiology, Hasanuddin University, Makassar</wicri:regionArea>
<wicri:noRegion>Makassar</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Newton, Paul" sort="Newton, Paul" uniqKey="Newton P" first="Paul" last="Newton">Paul Newton</name>
<affiliation wicri:level="3"><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford</wicri:regionArea>
<placeName><settlement type="city">Oxford</settlement>
<region type="country">Angleterre</region>
<region type="comté" nuts="2">Oxfordshire</region>
</placeName>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A43">Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos</nlm:aff>
<country xml:lang="fr">Laos</country>
<wicri:regionArea>Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane</wicri:regionArea>
<wicri:noRegion>Vientiane</wicri:noRegion>
</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 wicri:level="1"><nlm:aff id="A12">Kenya Medical Research Institute (KEMRI), Nairobi, Kenya</nlm:aff>
<country xml:lang="fr">Kenya</country>
<wicri:regionArea>Kenya Medical Research Institute (KEMRI), Nairobi</wicri:regionArea>
<wicri:noRegion>Nairobi</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Isaia, Lupeoletalalei" sort="Isaia, Lupeoletalalei" uniqKey="Isaia L" first="Lupeoletalalei" last="Isaia">Lupeoletalalei Isaia</name>
<affiliation wicri:level="1"><nlm:aff id="A44">National Health Services, Tupua Tamasese Meaole Hospital, Apia, Samoa</nlm:aff>
<country xml:lang="fr">Samoa</country>
<wicri:regionArea>National Health Services, Tupua Tamasese Meaole Hospital, Apia</wicri:regionArea>
<wicri:noRegion>Apia</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Dance, David" sort="Dance, David" uniqKey="Dance D" first="David" last="Dance">David Dance</name>
<affiliation wicri:level="3"><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford</wicri:regionArea>
<placeName><settlement type="city">Oxford</settlement>
<region type="country">Angleterre</region>
<region type="comté" nuts="2">Oxfordshire</region>
</placeName>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A43">Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos</nlm:aff>
<country xml:lang="fr">Laos</country>
<wicri:regionArea>Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane</wicri:regionArea>
<wicri:noRegion>Vientiane</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Davong, Viengmon" sort="Davong, Viengmon" uniqKey="Davong V" first="Viengmon" last="Davong">Viengmon Davong</name>
<affiliation wicri:level="1"><nlm:aff id="A43">Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos</nlm:aff>
<country xml:lang="fr">Laos</country>
<wicri:regionArea>Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane</wicri:regionArea>
<wicri:noRegion>Vientiane</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Thwaites, Guy" sort="Thwaites, Guy" uniqKey="Thwaites G" first="Guy" last="Thwaites">Guy Thwaites</name>
<affiliation wicri:level="1"><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>
<country xml:lang="fr">Viêt Nam</country>
<wicri:regionArea>Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City</wicri:regionArea>
<wicri:noRegion>Ho Chi Minh City</wicri:noRegion>
</affiliation>
<affiliation wicri:level="3"><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford</wicri:regionArea>
<placeName><settlement type="city">Oxford</settlement>
<region type="country">Angleterre</region>
<region type="comté" nuts="2">Oxfordshire</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Wijedoru, Lalith" sort="Wijedoru, Lalith" uniqKey="Wijedoru L" first="Lalith" last="Wijedoru">Lalith Wijedoru</name>
<affiliation wicri:level="1"><nlm:aff id="A45">Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand</nlm:aff>
<country xml:lang="fr">Thaïlande</country>
<wicri:regionArea>Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok</wicri:regionArea>
<wicri:noRegion>Bangkok</wicri:noRegion>
</affiliation>
<affiliation wicri:level="3"><nlm:aff id="A46">Paediatric Emergency Medicine, Chelsea and Westminster Hospital, London, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Paediatric Emergency Medicine, Chelsea and Westminster Hospital, London</wicri:regionArea>
<placeName><settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
</placeName>
</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 wicri:level="1"><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>
<country xml:lang="fr">Nouvelle-Zélande</country>
<wicri:regionArea>Centre for International Health and Otago International Health Research Network, Dunedin School of Medicine, University of Otago, Dunedin</wicri:regionArea>
<wicri:noRegion>Dunedin</wicri:noRegion>
</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 wicri:level="3"><nlm:aff id="A48"><italic>Salmonella</italic>
 Reference Service, Public Health England, Colindale, London, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea> Reference Service, Public Health England, Colindale, London</wicri:regionArea>
<placeName><settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Nair, Satheesh" sort="Nair, Satheesh" uniqKey="Nair S" first="Satheesh" last="Nair">Satheesh Nair</name>
<affiliation wicri:level="3"><nlm:aff id="A48"><italic>Salmonella</italic>
 Reference Service, Public Health England, Colindale, London, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea> Reference Service, Public Health England, Colindale, London</wicri:regionArea>
<placeName><settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
</placeName>
</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 wicri:level="1"><nlm:aff id="A49">Emerging Disease Surveillance and Response, Division of Pacific Technical Support, World Health Organization, Suva, Fiji</nlm:aff>
<country xml:lang="fr">Fidji</country>
<wicri:regionArea>Emerging Disease Surveillance and Response, Division of Pacific Technical Support, World Health Organization, Suva</wicri:regionArea>
<wicri:noRegion>Suva</wicri:noRegion>
</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 wicri:level="1"><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>
<country xml:lang="fr">Viêt Nam</country>
<wicri:regionArea>Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City</wicri:regionArea>
<wicri:noRegion>Ho Chi Minh City</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Turner, Paul" sort="Turner, Paul" uniqKey="Turner P" first="Paul" last="Turner">Paul Turner</name>
<affiliation wicri:level="3"><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford</wicri:regionArea>
<placeName><settlement type="city">Oxford</settlement>
<region type="country">Angleterre</region>
<region type="comté" nuts="2">Oxfordshire</region>
</placeName>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A45">Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand</nlm:aff>
<country xml:lang="fr">Thaïlande</country>
<wicri:regionArea>Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok</wicri:regionArea>
<wicri:noRegion>Bangkok</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A50">Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia</nlm:aff>
<country xml:lang="fr">Cambodge</country>
<wicri:regionArea>Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap</wicri:regionArea>
<wicri:noRegion>Siem Reap</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Soeng, Sona" sort="Soeng, Sona" uniqKey="Soeng S" first="Sona" last="Soeng">Sona Soeng</name>
<affiliation wicri:level="1"><nlm:aff id="A50">Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia</nlm:aff>
<country xml:lang="fr">Cambodge</country>
<wicri:regionArea>Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap</wicri:regionArea>
<wicri:noRegion>Siem Reap</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Valcanis, Mary" sort="Valcanis, Mary" uniqKey="Valcanis M" first="Mary" last="Valcanis">Mary Valcanis</name>
<affiliation wicri:level="4"><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>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>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</wicri:regionArea>
<orgName type="university">Université de Melbourne</orgName>
<placeName><settlement type="city">Melbourne</settlement>
<region type="état">Victoria (État)</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Powling, Joan" sort="Powling, Joan" uniqKey="Powling J" first="Joan" last="Powling">Joan Powling</name>
<affiliation wicri:level="4"><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>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>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</wicri:regionArea>
<orgName type="university">Université de Melbourne</orgName>
<placeName><settlement type="city">Melbourne</settlement>
<region type="état">Victoria (État)</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Dimovski, Karolina" sort="Dimovski, Karolina" uniqKey="Dimovski K" first="Karolina" last="Dimovski">Karolina Dimovski</name>
<affiliation wicri:level="4"><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>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>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</wicri:regionArea>
<orgName type="university">Université de Melbourne</orgName>
<placeName><settlement type="city">Melbourne</settlement>
<region type="état">Victoria (État)</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Hogg, Geoff" sort="Hogg, Geoff" uniqKey="Hogg G" first="Geoff" last="Hogg">Geoff Hogg</name>
<affiliation wicri:level="4"><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>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>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</wicri:regionArea>
<orgName type="university">Université de Melbourne</orgName>
<placeName><settlement type="city">Melbourne</settlement>
<region type="état">Victoria (État)</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Farrar, Jeremy" sort="Farrar, Jeremy" uniqKey="Farrar J" first="Jeremy" last="Farrar">Jeremy Farrar</name>
<affiliation wicri:level="1"><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>
<country xml:lang="fr">Viêt Nam</country>
<wicri:regionArea>Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City</wicri:regionArea>
<wicri:noRegion>Ho Chi Minh City</wicri:noRegion>
</affiliation>
<affiliation wicri:level="3"><nlm:aff id="A4">Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford</wicri:regionArea>
<placeName><settlement type="city">Oxford</settlement>
<region type="country">Angleterre</region>
<region type="comté" nuts="2">Oxfordshire</region>
</placeName>
</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 wicri:level="4"><nlm:aff id="A9">Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria</wicri:regionArea>
<orgName type="university">Université de Melbourne</orgName>
<placeName><settlement type="city">Melbourne</settlement>
<region type="état">Victoria (État)</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Dougan, Gordon" sort="Dougan, Gordon" uniqKey="Dougan G" first="Gordon" last="Dougan">Gordon Dougan</name>
<affiliation wicri:level="1"><nlm:aff id="A1">Wellcome Trust Sanger Institute, Hinxton, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton</wicri:regionArea>
<wicri:noRegion>Hinxton</wicri:noRegion>
</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>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Anti-Bacterial Agents (pharmacology)</term>
<term>Anti-Bacterial Agents (therapeutic use)</term>
<term>Drug Resistance, Multiple, Bacterial</term>
<term>Genome, Bacterial</term>
<term>Humans</term>
<term>Molecular Sequence Data</term>
<term>Phylogeny</term>
<term>Phylogeography</term>
<term>Quinolines (pharmacology)</term>
<term>Quinolines (therapeutic use)</term>
<term>Salmonella typhi (genetics)</term>
<term>Sequence Analysis, DNA</term>
<term>Typhoid Fever (drug therapy)</term>
<term>Typhoid Fever (microbiology)</term>
<term>Typhoid Fever (transmission)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN</term>
<term>Antibactériens (pharmacologie)</term>
<term>Antibactériens (usage thérapeutique)</term>
<term>Données de séquences moléculaires</term>
<term>Fièvre typhoïde (microbiologie)</term>
<term>Fièvre typhoïde (traitement médicamenteux)</term>
<term>Fièvre typhoïde (transmission)</term>
<term>Génome bactérien</term>
<term>Humains</term>
<term>Multirésistance bactérienne aux médicaments</term>
<term>Phylogénie</term>
<term>Phylogéographie</term>
<term>Quinoléines (pharmacologie)</term>
<term>Quinoléines (usage thérapeutique)</term>
<term>Salmonella typhi (génétique)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="pharmacology" xml:lang="en"><term>Anti-Bacterial Agents</term>
<term>Quinolines</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="therapeutic use" xml:lang="en"><term>Anti-Bacterial Agents</term>
<term>Quinolines</term>
</keywords>
<keywords scheme="MESH" qualifier="drug therapy" xml:lang="en"><term>Typhoid Fever</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Salmonella typhi</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Salmonella typhi</term>
</keywords>
<keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Fièvre typhoïde</term>
</keywords>
<keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Typhoid Fever</term>
</keywords>
<keywords scheme="MESH" qualifier="pharmacologie" xml:lang="fr"><term>Antibactériens</term>
<term>Quinoléines</term>
</keywords>
<keywords scheme="MESH" qualifier="traitement médicamenteux" xml:lang="fr"><term>Fièvre typhoïde</term>
</keywords>
<keywords scheme="MESH" qualifier="transmission" xml:lang="en"><term>Typhoid Fever</term>
</keywords>
<keywords scheme="MESH" qualifier="usage thérapeutique" xml:lang="fr"><term>Antibactériens</term>
<term>Fièvre typhoïde</term>
<term>Quinoléines</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Drug Resistance, Multiple, Bacterial</term>
<term>Genome, Bacterial</term>
<term>Humans</term>
<term>Molecular Sequence Data</term>
<term>Phylogeny</term>
<term>Phylogeography</term>
<term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term>
<term>Données de séquences moléculaires</term>
<term>Génome bactérien</term>
<term>Humains</term>
<term>Multirésistance bactérienne aux médicaments</term>
<term>Phylogénie</term>
<term>Phylogéographie</term>
</keywords>
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<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>
<affiliations><list><country><li>Afrique du Sud</li>
<li>Argentine</li>
<li>Australie</li>
<li>Belgique</li>
<li>Cambodge</li>
<li>Corée du Sud</li>
<li>Fidji</li>
<li>France</li>
<li>Inde</li>
<li>Indonésie</li>
<li>Italie</li>
<li>Japon</li>
<li>Kenya</li>
<li>Laos</li>
<li>Malawi</li>
<li>Nigeria</li>
<li>Nouvelle-Zélande</li>
<li>Népal</li>
<li>Royaume-Uni</li>
<li>Samoa</li>
<li>Thaïlande</li>
<li>Uruguay</li>
<li>Viêt Nam</li>
<li>États-Unis</li>
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<li>Gauteng</li>
<li>Grand Londres</li>
<li>Géorgie (États-Unis)</li>
<li>Midlands de l'Ouest</li>
<li>Nebraska</li>
<li>Oxfordshire</li>
<li>Région capitale de Séoul</li>
<li>Victoria (État)</li>
<li>Île-de-France</li>
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<settlement><li>Birmingham</li>
<li>Johannesbourg</li>
<li>Londres</li>
<li>Melbourne</li>
<li>Oxford</li>
<li>Paris</li>
<li>Séoul</li>
</settlement>
<orgName><li>Université de Birmingham</li>
<li>Université de Melbourne</li>
<li>Université du Witwatersrand</li>
</orgName>
</list>
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<name sortKey="Turner, Paul" sort="Turner, Paul" uniqKey="Turner P" first="Paul" last="Turner">Paul Turner</name>
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</record>

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

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

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