Evidence map›Paper›PMID 25961941›Full record

ArticleNature genetics2015

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

Vanessa K Wong, Stephen Baker, Derek J Pickard, Julian Parkhill, Andrew J Page, Nicholas A Feasey, Robert A Kingsley, Nicholas R Thomson, Jacqueline A Keane, François-Xavier Weill and 64 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 267 papers, 6 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
267citing papers in PubMed, 6 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

267 citing papers in PubMed, 6 syntheses or guidelines pooled it.

  1. Pooled it
  2. A Systematic Review on Antimicrobial Resistance amongThe American journal of tropical medicine and hygiene · 2020
    Pooled it
  3. Pooled it
  4. Pooled it
  5. A systematic review of antimicrobial resistance of typhoidalThe Indian journal of medical research · 2019
    Pooled it
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  10. Safety and immunogenicity of Vi-typhoid conjugate vaccine co-administration with routine 9-month vaccination in Burkina Faso: A randomized controlled phase 2 trial.International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases · 2021
    Trial
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  13. IgA and IgG1 Specific to Vi Polysaccharide ofFrontiers in immunology · 2019
    Trial
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207 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

74 authors.

Vanessa K Wong1] Wellcome Trust Sanger Institute, Hinxton, UK. [2] Department of Microbiology, Addenbrooke's Hospital, Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge, UK.
Stephen Baker1] Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK. [3] Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
Derek J PickardWellcome Trust Sanger Institute, Hinxton, UK.
Julian ParkhillWellcome Trust Sanger Institute, Hinxton, UK.ORCID 0000000270695958
Andrew J PageWellcome Trust Sanger Institute, Hinxton, UK.
Nicholas A FeaseyLiverpool School of Tropical Medicine, Liverpool, UK.
Robert A Kingsley1] Wellcome Trust Sanger Institute, Hinxton, UK. [2] Institute of Food Research, Norwich Research Park, Norwich, UK.
Nicholas R Thomson1] Wellcome Trust Sanger Institute, Hinxton, UK. [2] Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
Jacqueline A KeaneWellcome Trust Sanger Institute, Hinxton, UK.
François-Xavier WeillInstitut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, France.
David J EdwardsDepartment of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia.
Jane Hawkey1] Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia. [2] Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria, Australia.
Simon R HarrisWellcome Trust Sanger Institute, Hinxton, UK.ORCID 0000000315126194
Alison E MatherWellcome Trust Sanger Institute, Hinxton, UK.
Amy K CainWellcome Trust Sanger Institute, Hinxton, UK.
James HadfieldWellcome Trust Sanger Institute, Hinxton, UK.
Peter J HartInstitute of Biomedical Research, School of Immunity and Infection, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, UK.
Nga Tran Vu ThieuHospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.
Elizabeth J KlemmWellcome Trust Sanger Institute, Hinxton, UK.
Dafni A GlinosWellcome Trust Sanger Institute, Hinxton, UK.
Robert F Breiman1] Kenya Medical Research Institute (KEMRI), Nairobi, Kenya. [2] Centers for Disease Control and Prevention, Atlanta, Georgia, USA. [3] Emory Global Health Institute, Atlanta, Georgia, USA.
Conall H WatsonCentre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.
Samuel Kariuki1] Wellcome Trust Sanger Institute, Hinxton, UK. [2] Kenya Medical Research Institute (KEMRI), Nairobi, Kenya.
Melita A GordonInstitute of Infection and Global Health, University of Liverpool, Liverpool, UK.
Robert S HeydermanMalawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi.
Chinyere OkoroWellcome Trust Sanger Institute, Hinxton, UK.
Jan Jacobs1] Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium. [2] Department of Microbiology and Immunology, Katholieke Universiteit (KU) Leuven, University of Leuven, Leuven, Belgium.
Octavie Lunguya1] National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo. [2] University Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo.
W John EdmundsCentre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.
Chisomo Msefula1] Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi. [2] Microbiology Department, College of Medicine, University of Malawi, Blantyre, Malawi.
Jose A ChabalgoityDepartamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Montevideo, Uruguay.
Mike KamaMinistry of Health, Suva, Fiji.
Kylie JenkinsFiji Health Sector Support Program, Suva, Fiji.
Shanta DuttaNational Institute of Cholera and Enteric Diseases, Kolkata, India.
Florian MarksInternational Vaccine Institute, Department of Epidemiology, Seoul, Republic of Korea.
Josefina CamposEnteropathogen Division, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) Carlos G. Malbran Institute, Buenos Aires, Argentina.
Corinne Thompson1] Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK.
Stephen Obaro1] Division of Pediatric Infectious Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA. [2] University of Abuja Teaching Hospital, Abuja, Nigeria. [3] Bingham University, Karu, Nigeria.
Calman A MacLennan1] Wellcome Trust Sanger Institute, Hinxton, UK. [2] Institute of Biomedical Research, School of Immunity and Infection, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, UK. [3] Novartis Vaccines Institute for Global Health, Siena, Italy.
Christiane DolecekCentre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK.
Karen H KeddyCentre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service, University of the Witwatersrand, Johannesburg, South Africa.
Anthony M SmithCentre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service, University of the Witwatersrand, Johannesburg, South Africa.
Christopher M Parry1] Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK. [2] Graduate School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan.
Abhilasha KarkeyPatan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal.
E Kim Mulholland1] Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK. [2] Murdoch Childrens Research Institute, Melbourne, Victoria, Australia.
James I Campbell1] Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK.
Sabina DongolPatan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal.
Buddha BasnyatPatan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal.
Muriel DufourEnteric and Leptospira Reference Laboratory, Institute of Environmental Science and Research, Ltd. (ESR), Porirua, New Zealand.
Don BandaranayakeNational Centre for Biosecurity and Infectious Disease, Institute of Environmental Science and Research, Porirua, New Zealand.
Take Toleafoa NaseriSamoa Ministry of Health, Apia, Samoa.
Shalini Pravin SinghNational Influenza Center, World Health Organization, Center for Communicable Disease Control, Suva, Fiji.
Mochammad HattaDepartment of Microbiology, Hasanuddin University, Makassar, Indonesia.
Paul Newton1] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK. [2] Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos.
Robert S OnsareKenya Medical Research Institute (KEMRI), Nairobi, Kenya.
Lupeoletalalei IsaiaNational Health Services, Tupua Tamasese Meaole Hospital, Apia, Samoa.
David Dance1] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK. [2] Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos.
Viengmon DavongLao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos.
Guy Thwaites1] Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK.
Lalith Wijedoru1] Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. [2] Paediatric Emergency Medicine, Chelsea and Westminster Hospital, London, UK.
John A CrumpCentre for International Health and Otago International Health Research Network, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand.ORCID 000000024529102X
Elizabeth De PinnaSalmonella Reference Service, Public Health England, Colindale, London, UK.
Satheesh NairSalmonella Reference Service, Public Health England, Colindale, London, UK.
Eric J NillesEmerging Disease Surveillance and Response, Division of Pacific Technical Support, World Health Organization, Suva, Fiji.
Duy Pham ThanhHospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.
Paul Turner1] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK. [2] Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. [3] Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia.ORCID 0000000210137815
Sona SoengCambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia.
Mary ValcanisMicrobiological 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.
Joan PowlingMicrobiological 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.
Karolina DimovskiMicrobiological 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.
Geoff HoggMicrobiological 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.
Jeremy Farrar1] Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK.
Kathryn E HoltDepartment of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia.ORCID 0000000339492471
Gordon DouganWellcome Trust Sanger Institute, Hinxton, UK.

Funding

International Clinical Trials UnitU01AI062563 · NIAID · DUKE UNIVERSITY · PI BARTLETT, JOHN A · 2004 to 2007
$4.0M
The Impact and Society Ecology of Bacterial Zoonoses in Northern Tanzania: UnderR01TW009237 · FIC · DUKE UNIVERSITY · PI CRUMP, JOHN ANDREW · 2011 to 2014
$1.7M
Global Genomic and Proteomic Profiling of African Children with Typhoid FeverR01AI097493 · NIAID · UNIVERSITY OF NEBRASKA MEDICAL CENTER · PI OBARO, STEPHEN · 2012 to 2015
$1.6M
Integrating geographical and genetic mapping of salmonella disease in an endemicR01AI099525 · NIAID · KENYA MEDICAL RESEARCH INSTITUTE (KEMRI) · PI GUNN, JOHN S, KARIUKI, SAMUEL M · 2013 to 2024
$1.3M
Biotechnology and Biological Sciences Research Council BB/J010367/1Biotechnology and Biological Sciences Research Council BB/L017679Biotechnology and Biological Sciences Research Council BB/L018845Biotechnology and Biological Sciences Research Council BB/L018845/1Biotechnology and Biological Sciences Research Council BB/L018926Biotechnology and Biological Sciences Research Council BB/L018926/1FIC NIH HHS R01 TW009237Medical Research Council G1100100Medical Research Council G1100100/1Medical Research Council G9818340Medical Research Council MR/J003999/1NIAID NIH HHS R01 AI097493NIAID NIH HHS R01 AI099525NIAID NIH HHS R01 AI099525-02NIAID NIH HHS U01 AI062563Wellcome Trust 089275/H/09/ZWellcome Trust 089276Wellcome Trust 098051Wellcome Trust 100087Wellcome Trust 100087/Z/12/ZWellcome Trust 100891Wellcome Trust 101113/Z/13/ZWellcome Trust WT092152MAWorld Health Organization 001
6 · The paper itself

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.

Indexed as

Anti-Bacterial AgentsDrug Resistance, Multiple, BacterialGenome, BacterialHumansMolecular Sequence DataPhylogenyPhylogeographyQuinolinesSalmonella typhiSequence Analysis, DNATyphoid FeverAnti-Bacterial AgentsquinolineQuinolines

Identifiers

PMID25961941
PMCPMC4921243

What OpenQuestion holds

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.