eLife (Sep 2023)
Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes
- Megan E Carey,
- Zoe A Dyson,
- Danielle J Ingle,
- Afreenish Amir,
- Mabel K Aworh,
- Marie Anne Chattaway,
- Ka Lip Chew,
- John A Crump,
- Nicholas A Feasey,
- Benjamin P Howden,
- Karen H Keddy,
- Mailis Maes,
- Christopher M Parry,
- Sandra Van Puyvelde,
- Hattie E Webb,
- Ayorinde Oluwatobiloba Afolayan,
- Anna P Alexander,
- Shalini Anandan,
- Jason R Andrews,
- Philip M Ashton,
- Buddha Basnyat,
- Ashish Bavdekar,
- Isaac I Bogoch,
- John D Clemens,
- Kesia Esther da Silva,
- Anuradha De,
- Joep de Ligt,
- Paula Lucia Diaz Guevara,
- Christiane Dolecek,
- Shanta Dutta,
- Marthie M Ehlers,
- Louise Francois Watkins,
- Denise O Garrett,
- Gauri Godbole,
- Melita A Gordon,
- Andrew R Greenhill,
- Chelsey Griffin,
- Madhu Gupta,
- Rene S Hendriksen,
- Robert S Heyderman,
- Yogesh Hooda,
- Juan Carlos Hormazabal,
- Odion O Ikhimiukor,
- Junaid Iqbal,
- Jobin John Jacob,
- Claire Jenkins,
- Dasaratha Ramaiah Jinka,
- Jacob John,
- Gagandeep Kang,
- Abdoulie Kanteh,
- Arti Kapil,
- Abhilasha Karkey,
- Samuel Kariuki,
- Robert A Kingsley,
- Roshine Mary Koshy,
- AC Lauer,
- Myron M Levine,
- Ravikumar Kadahalli Lingegowda,
- Stephen P Luby,
- Grant Austin Mackenzie,
- Tapfumanei Mashe,
- Chisomo Msefula,
- Ankur Mutreja,
- Geetha Nagaraj,
- Savitha Nagaraj,
- Satheesh Nair,
- Take K Naseri,
- Susana Nimarota-Brown,
- Elisabeth Njamkepo,
- Iruka N Okeke,
- Sulochana Putli Bai Perumal,
- Andrew J Pollard,
- Agila Kumari Pragasam,
- Firdausi Qadri,
- Farah N Qamar,
- Sadia Isfat Ara Rahman,
- Savitra Devi Rambocus,
- David A Rasko,
- Pallab Ray,
- Roy Robins-Browne,
- Temsunaro Rongsen-Chandola,
- Jean Pierre Rutanga,
- Samir K Saha,
- Senjuti Saha,
- Karnika Saigal,
- Mohammad Saiful Islam Sajib,
- Jessica C Seidman,
- Jivan Shakya,
- Varun Shamanna,
- Jayanthi Shastri,
- Rajeev Shrestha,
- Sonia Sia,
- Michael J Sikorski,
- Ashita Singh,
- Anthony M Smith,
- Kaitlin A Tagg,
- Dipesh Tamrakar,
- Arif Mohammed Tanmoy,
- Maria Thomas,
- Mathew S Thomas,
- Robert Thomsen,
- Nicholas R Thomson,
- Siaosi Tupua,
- Krista Vaidya,
- Mary Valcanis,
- Balaji Veeraraghavan,
- François-Xavier Weill,
- Jackie Wright,
- Gordon Dougan,
- Silvia Argimón,
- Jacqueline A Keane,
- David M Aanensen,
- Stephen Baker,
- Kathryn E Holt,
- Global Typhoid Genomics Consortium Group Authorship
Affiliations
- Megan E Carey
- ORCiD
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom; IAVI, Chelsea & Westminster Hospital, London, United Kingdom
- Zoe A Dyson
- ORCiD
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Danielle J Ingle
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
- Afreenish Amir
- National Institute of Health, Islamabad, Pakistan
- Mabel K Aworh
- Nigeria Field Epidemiology and Laboratory Training Programme, Abuja, Nigeria; College of Veterinary Medicine, North Carolina State University, Raleigh, United States
- Marie Anne Chattaway
- United Kingdom Health Security Agency, London, United Kingdom
- Ka Lip Chew
- National University Hospital, Singapore, Singapore
- John A Crump
- ORCiD
- Centre for International Health, University of Otago, Dunedin, New Zealand
- Nicholas A Feasey
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom; Malawi-Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Benjamin P Howden
- ORCiD
- Centre for Pathogen Genomics, Department of Microbiology and Immunology, University of Melbourne at Doherty Institute for Infection and Immunity, Melbourne, Australia; Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Karen H Keddy
- Independent consultant, Johannesburg, South Africa
- Mailis Maes
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Christopher M Parry
- ORCiD
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Sandra Van Puyvelde
- ORCiD
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom; University of Antwerp, Antwerp, Belgium
- Hattie E Webb
- ORCiD
- Centers for Disease Control and Prevention, Atlanta, United States
- Ayorinde Oluwatobiloba Afolayan
- ORCiD
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
- Anna P Alexander
- Lady Willingdon Hospital, Manali, India
- Shalini Anandan
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
- Jason R Andrews
- ORCiD
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, United States
- Philip M Ashton
- Malawi-Liverpool Wellcome Programme, Blantyre, Malawi; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Buddha Basnyat
- Oxford University Clinical Research Unit Nepal, Kathmandu, Nepal
- Ashish Bavdekar
- KEM Hospital Research Centre, Pune, India
- Isaac I Bogoch
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, Canada
- John D Clemens
- International Vaccine Institute, Seoul, Republic of Korea; International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh; UCLA Fielding School of Public Health, Los Angeles, United States; Korea University, Seoul, Republic of Korea
- Kesia Esther da Silva
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, United States
- Anuradha De
- ORCiD
- Topiwala National Medical College, Mumbai, India
- Joep de Ligt
- ESR, Institute of Environmental Science and Research Ltd., Porirua, Wellington, New Zealand
- Paula Lucia Diaz Guevara
- ORCiD
- Grupo de Microbiologia, Instituto Nacional de Salud, Bogota, Colombia
- Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Shanta Dutta
- ICMR - National Institute of Cholera & Enteric Diseases, Kolkata, India
- Marthie M Ehlers
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa; Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Pretoria, South Africa
- Louise Francois Watkins
- ORCiD
- Centers for Disease Control and Prevention, Atlanta, United States
- Denise O Garrett
- Sabin Vaccine Institute, Washington DC, United States
- Gauri Godbole
- United Kingdom Health Security Agency, London, United Kingdom
- Melita A Gordon
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Andrew R Greenhill
- Federation University Australia, Churchill, Australia; Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
- Chelsey Griffin
- Centers for Disease Control and Prevention, Atlanta, United States
- Madhu Gupta
- Post Graduate Institute of Medical Education and Research, Chandigarh, India
- Rene S Hendriksen
- Technical University of Denmark, Copenhagen, Denmark
- Robert S Heyderman
- Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
- Yogesh Hooda
- Child Health Research Foundation, Dhaka, Bangladesh
- Juan Carlos Hormazabal
- Bacteriologia, Subdepartamento de Enfermedades Infecciosas, Departamento de Laboratorio Biomedico, Instituto de Salud Publica de Chile (ISP), Santiago, Chile
- Odion O Ikhimiukor
- ORCiD
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
- Junaid Iqbal
- ORCiD
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
- Jobin John Jacob
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
- Claire Jenkins
- United Kingdom Health Security Agency, London, United Kingdom
- Dasaratha Ramaiah Jinka
- ORCiD
- Rural Development Trust Hospital, Anantapur, India
- Jacob John
- Department of Community Health, Christian Medical College, Vellore, India
- Gagandeep Kang
- ORCiD
- Department of Community Health, Christian Medical College, Vellore, India
- Abdoulie Kanteh
- Medical Research Council Unit The Gambia at London School Hygiene & Tropical Medicine, Fajara, Gambia
- Arti Kapil
- All India Institute of Medical Sciences, Delhi, India
- Abhilasha Karkey
- Oxford University Clinical Research Unit Nepal, Kathmandu, Nepal
- Samuel Kariuki
- ORCiD
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
- Robert A Kingsley
- Quadram Institute Bioscience, Norwich, United Kingdom
- Roshine Mary Koshy
- Makunda Christian Hospital, Assam, India
- AC Lauer
- Centers for Disease Control and Prevention, Atlanta, United States
- Myron M Levine
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, USA, Baltimore, United States
- Ravikumar Kadahalli Lingegowda
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
- Stephen P Luby
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, United States
- Grant Austin Mackenzie
- Medical Research Council Unit The Gambia at London School Hygiene & Tropical Medicine, Fajara, Gambia
- Tapfumanei Mashe
- National Microbiology Reference Laboratory, Harare, Zimbabwe; World Health Organization, Harare, Zimbabwe
- Chisomo Msefula
- ORCiD
- Kamuzu University of Health Sciences, Blantyre, Malawi
- Ankur Mutreja
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Geetha Nagaraj
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
- Savitha Nagaraj
- Saint Johns Medical College and Hospital, Bengaluru, India
- Satheesh Nair
- ORCiD
- United Kingdom Health Security Agency, London, United Kingdom
- Take K Naseri
- Ministry of Health, Government of Samoa, Apia, Samoa
- Susana Nimarota-Brown
- Ministry of Health, Government of Samoa, Apia, Samoa
- Elisabeth Njamkepo
- Institut Pasteur, Université Paris Cité, Paris, France
- Iruka N Okeke
- ORCiD
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
- Sulochana Putli Bai Perumal
- Kanchi Kamakoti CHILDS Trust Hospital, Chennai, India
- Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom; The NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
- Agila Kumari Pragasam
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
- Firdausi Qadri
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
- Farah N Qamar
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
- Sadia Isfat Ara Rahman
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
- Savitra Devi Rambocus
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- David A Rasko
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, United States; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, United States
- Pallab Ray
- Post Graduate Institute of Medical Education and Research, Chandigarh, India
- Roy Robins-Browne
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia; Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Australia
- Temsunaro Rongsen-Chandola
- Centre for Health Research and Development, Society for Applied Studies, Delhi, India
- Jean Pierre Rutanga
- University of Rwanda, College of Science and Technology, Kigali, Rwanda
- Samir K Saha
- ORCiD
- Child Health Research Foundation, Dhaka, Bangladesh
- Senjuti Saha
- ORCiD
- Child Health Research Foundation, Dhaka, Bangladesh
- Karnika Saigal
- Chacha Nehru Bal Chikitsalaya, Delhi, India
- Mohammad Saiful Islam Sajib
- Child Health Research Foundation, Dhaka, Bangladesh; Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
- Jessica C Seidman
- Sabin Vaccine Institute, Washington DC, United States
- Jivan Shakya
- Dhulikhel Hospital, Dhulikhel, Nepal; Institute for Research in Science and Technology, Kathmandu, Nepal
- Varun Shamanna
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
- Jayanthi Shastri
- Topiwala National Medical College, Mumbai, India; Kasturba Hospital for Infectious Diseases, Mumbai, India
- Rajeev Shrestha
- Center for Infectious Disease Research & Surveillance, Dhulikhel Hospital, Kathmandu University Hospital, Dhulikhel, Nepal
- Sonia Sia
- Research Institute for Tropical Medicine, Department of Health, Muntinlupa City, Philippines
- Michael J Sikorski
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, USA, Baltimore, United States; Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, United States; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, United States
- Ashita Singh
- Chinchpada Christian Hospital, Navapur, India
- Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa
- Kaitlin A Tagg
- Centers for Disease Control and Prevention, Atlanta, United States
- Dipesh Tamrakar
- Center for Infectious Disease Research & Surveillance, Dhulikhel Hospital, Kathmandu University Hospital, Dhulikhel, Nepal
- Arif Mohammed Tanmoy
- Child Health Research Foundation, Dhaka, Bangladesh
- Maria Thomas
- Christian Medical College, Ludhiana, Ludhiana, India
- Mathew S Thomas
- Duncan Hospital, Raxaul, India
- Robert Thomsen
- Ministry of Health, Government of Samoa, Apia, Samoa
- Nicholas R Thomson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Siaosi Tupua
- Ministry of Health, Government of Samoa, Apia, Samoa
- Krista Vaidya
- University of California Davis, Davis, United States
- Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
- François-Xavier Weill
- Institut Pasteur, Université Paris Cité, Paris, France
- Jackie Wright
- ESR, Institute of Environmental Science and Research Ltd., Porirua, Wellington, New Zealand
- Gordon Dougan
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
- Jacqueline A Keane
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
- David M Aanensen
- ORCiD
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
- Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom; IAVI, Chelsea & Westminster Hospital, London, United Kingdom
- Kathryn E Holt
- ORCiD
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia
- Global Typhoid Genomics Consortium Group Authorship
- DOI
- https://doi.org/10.7554/eLife.85867
- Journal volume & issue
-
Vol. 12
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 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]).
Keywords