Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes
Issued Date
2023-01-01
Resource Type
eISSN
2050084X
Scopus ID
2-s2.0-85175204073
Journal Title
eLife
Volume
12
Rights Holder(s)
SCOPUS
Bibliographic Citation
eLife Vol.12 (2023)
Suggested Citation
Carey M.E. Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes. eLife Vol.12 (2023). doi:10.7554/ELIFE.85867 Retrieved from: https://repository.li.mahidol.ac.th/handle/20.500.14594/90937
Title
Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes
Author(s)
Author's Affiliation
Kamuzu University of Health Sciences
UK Health Security Agency
Faculty of Health Sciences
KEM Hospital
Mahidol Oxford Tropical Medicine Research Unit
NIHR Oxford Biomedical Research Centre
Oxford University Clinical Research Unit
Université Paris Cité
The Peter Doherty Institute for Infection and Immunity
Dhulikel Hospital, Kathmandu
University of Rwanda
Malawi-Liverpool-Wellcome Trust Clinical Research Programme
Papua New Guinea Institute of Medical Research
Research Institute for Tropical Medicine
Kenya Medical Research Institute
Kanchi Kamakoti Childs Trust Hospital
International Vaccine Institute, Seoul
National Institute of Health Pakistan
Society for Applied Studies Kolkata
The Aga Khan University
Instituto Nacional de Salud
National Institute for Communicable Diseases
London School of Hygiene & Tropical Medicine
National University Hospital
UCLA Fielding School of Public Health
Organisation Mondiale de la Santé
Royal Children's Hospital, Melbourne
School of Clinical Medicine
BYL Nair Charitable Hospital & TN Medical College
National Health Laboratory Service
University College London
Centers for Disease Control and Prevention
Liverpool School of Tropical Medicine
University of Liverpool
Quadram Institute Bioscience
University of Otago
University of Toronto
University of Maryland School of Medicine
Universiteit Antwerpen
Faculty of Medicine, Nursing and Health Sciences
Stanford University
Technical University of Denmark
Federation University Australia
Instituto de Salud Publica de Chile
International Centre for Diarrhoeal Disease Research Bangladesh
All India Institute of Medical Sciences, New Delhi
Kempegowda Institute of Medical Sciences
Nuffield Department of Medicine
National Institute of Cholera and Enteric Diseases India
University of Ibadan
Christian Medical College & Hospital, Ludhiana
Wellcome Sanger Institute
Korea University
NC State University
St. John's Medical College Hospital
University of Oxford Medical Sciences Division
Chelsea and Westminster Hospital
College of Medical, Veterinary & Life Sciences
Christian Medical College, Vellore
Postgraduate Institute of Medical Education & Research, Chandigarh
Chinchpada Christian Hospital
Institute for Research in Science and Technology
Lady Willingdon Hospital
Independent consultant
Makunda Christian Leprosy and General Hospital
Duncan Hospital
Kasturba Hospital for Infectious Diseases
Rural Development Trust Hospital
Nigeria Field Epidemiology and Laboratory Training Programme
Child Health Research Foundation
Institute of Environmental Science and Research
Dhulikhel Hospital
National Microbiology Reference Laboratory
Chacha Nehru Bal Chikitsalaya
Ministry of Health
Sabin Vaccine Institute
UK Health Security Agency
Faculty of Health Sciences
KEM Hospital
Mahidol Oxford Tropical Medicine Research Unit
NIHR Oxford Biomedical Research Centre
Oxford University Clinical Research Unit
Université Paris Cité
The Peter Doherty Institute for Infection and Immunity
Dhulikel Hospital, Kathmandu
University of Rwanda
Malawi-Liverpool-Wellcome Trust Clinical Research Programme
Papua New Guinea Institute of Medical Research
Research Institute for Tropical Medicine
Kenya Medical Research Institute
Kanchi Kamakoti Childs Trust Hospital
International Vaccine Institute, Seoul
National Institute of Health Pakistan
Society for Applied Studies Kolkata
The Aga Khan University
Instituto Nacional de Salud
National Institute for Communicable Diseases
London School of Hygiene & Tropical Medicine
National University Hospital
UCLA Fielding School of Public Health
Organisation Mondiale de la Santé
Royal Children's Hospital, Melbourne
School of Clinical Medicine
BYL Nair Charitable Hospital & TN Medical College
National Health Laboratory Service
University College London
Centers for Disease Control and Prevention
Liverpool School of Tropical Medicine
University of Liverpool
Quadram Institute Bioscience
University of Otago
University of Toronto
University of Maryland School of Medicine
Universiteit Antwerpen
Faculty of Medicine, Nursing and Health Sciences
Stanford University
Technical University of Denmark
Federation University Australia
Instituto de Salud Publica de Chile
International Centre for Diarrhoeal Disease Research Bangladesh
All India Institute of Medical Sciences, New Delhi
Kempegowda Institute of Medical Sciences
Nuffield Department of Medicine
National Institute of Cholera and Enteric Diseases India
University of Ibadan
Christian Medical College & Hospital, Ludhiana
Wellcome Sanger Institute
Korea University
NC State University
St. John's Medical College Hospital
University of Oxford Medical Sciences Division
Chelsea and Westminster Hospital
College of Medical, Veterinary & Life Sciences
Christian Medical College, Vellore
Postgraduate Institute of Medical Education & Research, Chandigarh
Chinchpada Christian Hospital
Institute for Research in Science and Technology
Lady Willingdon Hospital
Independent consultant
Makunda Christian Leprosy and General Hospital
Duncan Hospital
Kasturba Hospital for Infectious Diseases
Rural Development Trust Hospital
Nigeria Field Epidemiology and Laboratory Training Programme
Child Health Research Foundation
Institute of Environmental Science and Research
Dhulikhel Hospital
National Microbiology Reference Laboratory
Chacha Nehru Bal Chikitsalaya
Ministry of Health
Sabin Vaccine Institute
Other Contributor(s)
Abstract
Background: The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000). 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 becomedominant 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.