SynthesiseLife2023
Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000
Open access · goldAbstract readMeta-Analysis
In one paragraph
Synthesis in eLife, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 papers.
0numbers the graph read from it
0cells of the map it votes in
80citing papers in PubMed
21.3field-weighted citation impact, top 1% of its field
What it found
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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.
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Who cites it
80 citing papers in PubMed, 106 citations in OpenAlex.
- Prolonged fever in ESBL-producingRadiology case reports · 2026Article
- Emergence of Genotype 2.3.1 Multidrug-Resistant Salmonella enterica Serovar Typhi Strain, West Africa, 2021-2025.Emerging infectious diseases · 2026Article
- Azithromycin-resistantJAC-antimicrobial resistance · 2026Article
- Presence of globally prominent multidrug-resistant genotypes ofMicrobial genomics · 2026Article
- Integrated genomic analysis of Salmonella Typhi from Pakistan: Antimicrobial resistance determinants, pangenome structure, and reverse vaccinology-driven vaccine target discovery.Functional & integrative genomics · 2026Article
- Global genomic surveillance uncovers emergence and spatiotemporal patterns of World Health Organization priority antibiotic resistance in invasive Salmonella.Nature communications · 2026Article
- OmpW-mediated sensing of MUC2 GalNAc contributes to the ileal tropism of Salmonella Typhi.Cell reports · 2026Article
- Exploring the Clinical Landscape of Long Non-coding RNAs in Cancer Diagnosis and Therapy.Biochemical genetics · 2026Review
- Azithromycin minimum inhibitory concentration (MIC) creep and clinical-microbiological profile of typhoidal and nontyphoidal Salmonella isolates from blood specimens at a tertiary care hospital in Pune, India.The Indian journal of medical research · 2026Article
- Performance of mechanically sheared DNA in multiplexed Oxford Nanopore sequencing forMicrobial genomics · 2026Article
- Mind the governance gap: a one health scoping review of national AMR performance indicators.npj antimicrobials and resistance · 2026Article
- Genomic analysis ofMicrobial genomics · 2026Article
- Review
- Review
- Article
- A mouse model for studying chronicmBio · 2026Article
- Evolution and rise of antimicrobial resistance in key public health bacteria within and across the One Health sectors.Future microbiology · 2026Review
- Exploring barriers to and motivations for vaccine uptake in a typhoid vaccine trial in Vellore, South India: a qualitative study.BMC public health · 2026Article
- Exploring and enhancing community awareness on antimicrobial resistance: perspectives from world antimicrobial resistance awareness week celebration in Ghana.BMC public health · 2026Article
- AMRnet: a data visualization platform to interactively explore pathogen variants and antimicrobial resistance.Nucleic acids research · 2026Article
20 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
115 authors at 20 institutions in 31 countries.
Megan E CareyCambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom.ORCID 0000-0002-7797-9080
Zoe A DysonDepartment of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom.ORCID 0000-0002-8887-3492
Danielle J IngleDepartment of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia.
Afreenish AmirNational Institute of Health, Islamabad, Pakistan.
Mabel K AworhNigeria Field Epidemiology and Laboratory Training Programme, Abuja, Nigeria.
Marie Anne ChattawayUnited Kingdom Health Security Agency, London, United Kingdom.
Ka Lip ChewNational University Hospital, Singapore, Singapore.
John A CrumpCentre for International Health, University of Otago, Dunedin, New Zealand.ORCID 0000-0002-4529-102X
Nicholas A FeaseyDepartment of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom.
Benjamin P HowdenCentre for Pathogen Genomics, Department of Microbiology and Immunology, University of Melbourne at Doherty Institute for Infection and Immunity, Melbourne, Australia.ORCID 0000-0003-0237-1473
Karen H KeddyIndependent consultant, Johannesburg, South Africa.
Mailis MaesCambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom.
Christopher M ParryDepartment of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom.ORCID 0000-0001-7563-7282
Sandra Van PuyveldeCambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom.ORCID 0000-0001-8434-5732
Hattie E WebbCenters for Disease Control and Prevention, Atlanta, United States.ORCID 0000-0002-1190-7930
Ayorinde Oluwatobiloba AfolayanGlobal Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria.ORCID 0000-0003-1405-2365
Anna P AlexanderLady Willingdon Hospital, Manali, India.
Shalini AnandanDepartment of Clinical Microbiology, Christian Medical College, Vellore, India.
Jason R AndrewsDivision of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, United States.ORCID 0000-0002-5967-251X
Philip M AshtonMalawi-Liverpool Wellcome Programme, Blantyre, Malawi.
Buddha BasnyatOxford University Clinical Research Unit Nepal, Kathmandu, Nepal.
Ashish BavdekarKEM Hospital Research Centre, Pune, India.
Isaac I BogochDepartment of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, Canada.
John D ClemensInternational Vaccine Institute, Seoul, Republic of Korea.
Kesia Esther da SilvaDivision of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, United States.
Anuradha DeTopiwala National Medical College, Mumbai, India.ORCID 0000-0002-8701-4100
Joep de LigtESR, Institute of Environmental Science and Research Ltd., Porirua, Wellington, New Zealand.
Paula Lucia Diaz GuevaraGrupo de Microbiologia, Instituto Nacional de Salud, Bogota, Colombia.ORCID 0000-0002-8252-5622
Christiane DolecekCentre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
Shanta DuttaICMR - National Institute of Cholera & Enteric Diseases, Kolkata, India.
Marthie M EhlersDepartment of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.
Louise Francois WatkinsCenters for Disease Control and Prevention, Atlanta, United States.ORCID 0000-0002-1165-1162
Denise O GarrettSabin Vaccine Institute, Washington DC, United States.
Gauri GodboleUnited Kingdom Health Security Agency, London, United Kingdom.
Melita A GordonInstitute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.
Andrew R GreenhillFederation University Australia, Churchill, Australia.
Chelsey GriffinCenters for Disease Control and Prevention, Atlanta, United States.
Madhu GuptaPost Graduate Institute of Medical Education and Research, Chandigarh, India.
Rene S HendriksenTechnical University of Denmark, Copenhagen, Denmark.
Robert S HeydermanResearch Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom.
Yogesh HoodaChild Health Research Foundation, Dhaka, Bangladesh.
Juan Carlos HormazabalBacteriologia, Subdepartamento de Enfermedades Infecciosas, Departamento de Laboratorio Biomedico, Instituto de Salud Publica de Chile (ISP), Santiago, Chile.
Odion O IkhimiukorGlobal Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria.ORCID 0000-0002-3738-4584
Junaid IqbalDepartment of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan.ORCID 0000-0002-5014-2176
Jobin John JacobDepartment of Clinical Microbiology, Christian Medical College, Vellore, India.
Claire JenkinsUnited Kingdom Health Security Agency, London, United Kingdom.
Dasaratha Ramaiah JinkaRural Development Trust Hospital, Anantapur, India.ORCID 0000-0002-8184-279X
Jacob JohnDepartment of Community Health, Christian Medical College, Vellore, India.
Gagandeep KangDepartment of Community Health, Christian Medical College, Vellore, India.ORCID 0000-0002-3656-564X
Abdoulie KantehMedical Research Council Unit The Gambia at London School Hygiene & Tropical Medicine, Fajara, Gambia.
Arti KapilAll India Institute of Medical Sciences, Delhi, India.
Abhilasha KarkeyOxford University Clinical Research Unit Nepal, Kathmandu, Nepal.
Samuel KariukiCentre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya.ORCID 0000-0003-3209-9503
Robert A KingsleyQuadram Institute Bioscience, Norwich, United Kingdom.
Roshine Mary KoshyMakunda Christian Hospital, Assam, India.
A C LauerCenters for Disease Control and Prevention, Atlanta, United States.
Myron M LevineCenter for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, USA, Baltimore, United States.
Ravikumar Kadahalli LingegowdaCentral Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India.
Stephen P LubyDivision of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, United States.
Grant Austin MackenzieMedical Research Council Unit The Gambia at London School Hygiene & Tropical Medicine, Fajara, Gambia.
Tapfumanei MasheNational Microbiology Reference Laboratory, Harare, Zimbabwe.
Chisomo MsefulaKamuzu University of Health Sciences, Blantyre, Malawi.ORCID 0000-0003-2304-886X
Ankur MutrejaCambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom.
Geetha NagarajCentral Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India.
Savitha NagarajSaint Johns Medical College and Hospital, Bengaluru, India.
Satheesh NairUnited Kingdom Health Security Agency, London, United Kingdom.ORCID 0000-0002-7297-1485
Take K NaseriMinistry of Health, Government of Samoa, Apia, Samoa.
Susana Nimarota-BrownMinistry of Health, Government of Samoa, Apia, Samoa.
Elisabeth NjamkepoInstitut Pasteur, Université Paris Cité, Paris, France.
Iruka N OkekeGlobal Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria.ORCID 0000-0002-1694-7587
Sulochana Putli Bai PerumalKanchi Kamakoti CHILDS Trust Hospital, Chennai, India.
Andrew J PollardOxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom.
Agila Kumari PragasamDepartment of Clinical Microbiology, Christian Medical College, Vellore, India.
Firdausi QadriInternational Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh.
Farah N QamarDepartment of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan.
Sadia Isfat Ara RahmanInternational Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh.
Savitra Devi RambocusMicrobiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
David A RaskoDepartment of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, United States.
Pallab RayPost Graduate Institute of Medical Education and Research, Chandigarh, India.
Roy Robins-BrowneDepartment of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia.
Temsunaro Rongsen-ChandolaCentre for Health Research and Development, Society for Applied Studies, Delhi, India.
Jean Pierre RutangaUniversity of Rwanda, College of Science and Technology, Kigali, Rwanda.
Samir K SahaChild Health Research Foundation, Dhaka, Bangladesh.ORCID 0000-0003-3820-0748
Senjuti SahaChild Health Research Foundation, Dhaka, Bangladesh.ORCID 0000-0001-6087-6766
Karnika SaigalChacha Nehru Bal Chikitsalaya, Delhi, India.
Mohammad Saiful Islam SajibChild Health Research Foundation, Dhaka, Bangladesh.
Jessica C SeidmanSabin Vaccine Institute, Washington DC, United States.
Jivan ShakyaDhulikhel Hospital, Dhulikhel, Nepal.
Varun ShamannaCentral Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India.
Jayanthi ShastriTopiwala National Medical College, Mumbai, India.
Rajeev ShresthaCenter for Infectious Disease Research & Surveillance, Dhulikhel Hospital, Kathmandu University Hospital, Dhulikhel, Nepal.
Sonia SiaResearch Institute for Tropical Medicine, Department of Health, Muntinlupa City, Philippines.
Michael J SikorskiCenter for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, USA, Baltimore, United States.
Ashita SinghChinchpada Christian Hospital, Navapur, India.
Anthony M SmithCentre for Enteric Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa.
Kaitlin A TaggCenters for Disease Control and Prevention, Atlanta, United States.
Dipesh TamrakarCenter for Infectious Disease Research & Surveillance, Dhulikhel Hospital, Kathmandu University Hospital, Dhulikhel, Nepal.
Arif Mohammed TanmoyChild Health Research Foundation, Dhaka, Bangladesh.
Maria ThomasChristian Medical College, Ludhiana, Ludhiana, India.
Mathew S ThomasDuncan Hospital, Raxaul, India.
Robert ThomsenMinistry of Health, Government of Samoa, Apia, Samoa.
Nicholas R ThomsonWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom.
Siaosi TupuaMinistry of Health, Government of Samoa, Apia, Samoa.
Krista VaidyaUniversity of California Davis, Davis, United States.
Mary ValcanisMicrobiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
Balaji VeeraraghavanDepartment of Clinical Microbiology, Christian Medical College, Vellore, India.
François-Xavier WeillInstitut Pasteur, Université Paris Cité, Paris, France.
Jackie WrightESR, Institute of Environmental Science and Research Ltd., Porirua, Wellington, New Zealand.
Gordon DouganCambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom.
Silvia ArgimónCentre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom.
Jacqueline A KeaneCambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom.
David M AanensenCentre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom.ORCID 0000-0001-6688-0854
Stephen BakerCambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom.
Kathryn E HoltDepartment of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom.ORCID 0000-0003-3949-2471
Global Typhoid Genomics Consortium Group Authorship
Christian Medical College, Vellore · INUniversity of Cambridge · GBCenters for Disease Control and Prevention · USChild Health Research Foundation · BDNational University of Samoa · WSUK Health Security Agency · GBDhulikhel Hospital · NPKempegowda Institute of Medical Sciences · INPeter Doherty Institute · AUStanford University · USUniversity of Ibadan · NGUniversity of Liverpool · GBUniversity of Maryland, Baltimore · USUniversity of Oxford · GBAga Khan University · PKInstitute of Post Graduate Medical Education and Research · INInstitut Pasteur · FRInternational Centre for Diarrhoeal Disease Research · BDMRC Unit the Gambia · GMNew Zealand Institute for Public Health and Forensic Science · NZ
Funding
Technology CoreU19AI110820 · NIAID · UNIVERSITY OF MARYLAND BALTIMORE · PI RASKO, DAVID A · 2014 to 2023
$36.5MInternational Clinical Trials UnitU01AI062563 · NIAID · DUKE UNIVERSITY · PI BARTLETT, JOHN A · 2004 to 2007
$4.0MInvestigating Febrile Deaths in Tanzania (INDITe)R01AI121378 · NIAID · DUKE UNIVERSITY · PI RUBACH, MATTHEW P · 2016 to 2020
$2.7MThe Impact and Society Ecology of Bacterial Zoonoses in Northern Tanzania: UnderR01TW009237 · FIC · DUKE UNIVERSITY · PI CRUMP, JOHN ANDREW · 2011 to 2014
$1.7MIntegrating 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
$1.3MGenomics of Salmonella Typhi in Samoa: Population structure and genomic epidemiologyF30AI156973 · NIAID · UNIVERSITY OF MARYLAND BALTIMORE · PI SIKORSKI, MICHAEL JOSEPH · 2021 to 2024
$158kBiotechnology and Biological Sciences Research Council BB/R012504/1Biotechnology and Biological Sciences Research Council BBS/E/F/00PR10348FIC NIH HHS R01 TW009237Medical Research Council MR/L00464X/Medical Research Council MR/TOO5033/1NIAID NIH HHS F30 AI156973NIAID NIH HHS R01 AI099525NIAID NIH HHS R01 AI121378NIAID NIH HHS U01 AI062563NIAID NIH HHS U19 AI110820Wellcome TrustWellcome Trust 106158/7/14/ZWellcome Trust 206194Wellcome Trust 206545/7/17/ZWorld Health Organization 001
Abstract
Background: The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Methods: This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch. Results: Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal 'sentinel' surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (≥3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has become dominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes. Conclusions: The consortium's aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies. Funding: No specific funding was awarded for this meta-analysis. Coordinators were supported by fellowships from the European Union (ZAD received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 845681), the Wellcome Trust (SB, Wellcome Trust Senior Fellowship), and the National Health and Medical Research Council (DJI is supported by an NHMRC Investigator Grant [GNT1195210]).
Indexed as
Salmonella typhiTyphoid FeverAnti-Bacterial AgentsCiprofloxacinDrug Resistance, BacterialHumansTravelAnti-Bacterial AgentsCiprofloxacinantimicrobial resistanceepidemiologygenomicsglobal healthinfectious diseasemicrobiologyS. enterica serovar typhityphoid conjugate vaccinetyphoid fever
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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 Socratic graph.