Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes - Archive ouverte HAL
Article Dans Une Revue eLife Année : 2023

Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes

Megan Carey (1, 2, 3) , Zoe Dyson (2, 4, 5) , Danielle Ingle (6) , Afreenish Amir (7) , Mabel Aworh (8, 9) , Marie Anne Chattaway (10) , Ka Lip Chew (11) , John Crump (12) , Nicholas Feasey (13, 14) , Benjamin Howden (6) , Karen Keddy (15) , Mailis Maes (1) , Christopher Parry (13) , Sandra van Puyvelde (1, 16) , Hattie Webb (17) , Ayorinde Oluwatobiloba Afolayan (18) , Anna Alexander (19) , Shalini Anandan (20) , Jason Andrews (21) , Philip Ashton (22, 23) , Buddha Basnyat (24) , Ashish Bavdekar (25) , Isaac Bogoch (26) , John Clemens (27, 28, 29, 30) , Kesia Esther da Silva (21) , Anuradha De (31) , Joep de Ligt (32) , Paula Lucia Diaz Guevara (33) , Christiane Dolecek (34, 35) , Shanta Dutta (36) , Marthie Ehlers (37, 38) , Louise Francois Watkins (17) , Denise Garrett (39) , Gauri Godbole (10) , Melita Gordon (23) , Andrew Greenhill (40, 41) , Chelsey Griffin (17) , Madhu Gupta (42) , Rene Hendriksen (43) , Robert Heyderman (44) , Yogesh Hooda (45) , Juan Carlos Hormazabal (46) , Odion Ikhimiukor (18) , Junaid Iqbal (47) , Jobin John Jacob (20) , Claire Jenkins (10) , Dasaratha Ramaiah Jinka (48) , Jacob John (20) , Gagandeep Kang (20) , Abdoulie Kanteh (49) , Arti Kapil (50) , Abhilasha Karkey (24) , Samuel Kariuki (51) , Robert Kingsley (52) , Roshine Mary Koshy (53) , Ac Lauer (17) , Myron Levine (54) , Ravikumar Kadahalli Lingegowda (55) , Stephen Luby (21) , Grant Austin Mackenzie (49) , Tapfumanei Mashe (56, 57) , Chisomo Msefula (14) , Ankur Mutreja (1) , Geetha Nagaraj (55) , Savitha Nagaraj (58) , Satheesh Nair (10) , Take Naseri (59) , Susana Nimarota-Brown (59) , Elisabeth Njamkepo (60) , Iruka Okeke (18) , Sulochana Putli Bai Perumal (61) , Andrew Pollard (34) , Agila Kumari Pragasam (62) , Firdausi Qadri (28) , Farah Qamar (47) , Sadia Isfat Ara Rahman (28) , Savitra Devi Rambocus (6) , David Rasko (54) , Pallab Ray (42) , Roy Robins-Browne (6, 63) , Temsunaro Rongsen-Chandola (64) , Jean Pierre Rutanga (65) , Samir Saha (45) , Senjuti Saha (45) , Karnika Saigal (66) , Mohammad Saiful Islam Sajib (45, 67) , Jessica Seidman (39) , Jivan Shakya (68) , Varun Shamanna (55) , Jayanthi Shastri (31, 69) , Rajeev Shrestha (70, 71) , Sonia Sia (72) , Michael Sikorski (54) , Ashita Singh (73) , Anthony Smith (74) , Kaitlin Tagg (17) , Dipesh Tamrakar (70, 71) , Arif Mohammed Tanmoy (45) , Maria Thomas (75) , Mathew Thomas (76) , Robert Thomsen (59) , Nicholas Thomson (5) , Siaosi Tupua (59) , Krista Vaidya (77) , Mary Valcanis (6) , Balaji Veeraraghavan (20) , François-Xavier Weill (60) , Jackie Wright (32) , Gordon Dougan (1) , Silvia Argimón (34) , Jacqueline Keane (1) , David Aanensen (34) , Stephen Baker (1, 3) , Kathryn Holt (2, 4)
1 CAM - University of Cambridge [UK]
2 LSHTM - London School of Hygiene and Tropical Medicine
3 Chelsea and Westminster Hospital
4 Monash university
5 The Wellcome Trust Sanger Institute [Cambridge]
6 University of Melbourne
7 National Institute of Health [Islamabad, Pakistan]
8 NCDC - Nigeria Centre for Disease Control [Abuja, Nigeria]
9 NC State - North Carolina State University [Raleigh]
10 UKHSA - UK Health Security Agency [London]
11 NUH - National University Hospital [Singapore]
12 University of Otago Wellington
13 LSTM - Liverpool School of Tropical Medicine
14 KUHeS - Kamuzu University of Health Sciences
15 Auteur indépendant
16 UA - University of Antwerp
17 CDC - Centers for Disease Control and Prevention [Atlanta]
18 University of Ibadan
19 Lady Willingdon Manali Hospital [Manali, India]
20 Christian Medical College [Vellore, India]
21 Stanford University
22 MLW - Malawi Liverpool Wellcome Trust Clinical Research Programme
23 University of Liverpool
24 Oxford University Clinical Research Unit [Kathmandu]
25 KEM Hospital Research Center [Pune, India]
26 University of Toronto
27 IVI - International Vaccine Institute
28 ICDDR,B - International Centre for Diarrhoeal Disease Research, Bangladesh
29 UCLA - University of California [Los Angeles]
30 Korea University [Seoul]
31 Topiwala National Medical College & BYL Nair Charitable Hospital [Mumbai, India]
32 ESR - Institute of Environmental Science and Research
33 Instituto Nacional de Salud [Bogota]
34 University of Oxford
35 Mahidol University [Bangkok]
36 National Institute of Cholera and Enteric Diseases
37 University of Pretoria [South Africa]
38 NHLS - National Health Laboratory Service [Johannesburg, South Africa]
39 Sabin vaccine institute [Washington DC, USA]
40 Federation University [Churchill, Australia]
41 PNG-IMR - Papua New Guinea Institute of Medical Research
42 Post Graduate Institute of Medical Education & Research [Chandigarh, India]
43 DTU - Danmarks Tekniske Universitet = Technical University of Denmark
44 UCL - University College of London [London]
45 CHRF - Child Health Research Foundation
46 ISP - Instituto de Salud Pública de Chile
47 The Aga Khan University
48 Rural Development Trust [Anantapur, India]
49 London School of Hygiene & Tropical Medicine [Fajara, The Gambia]
50 All India Institute of Medical Sciences [New Delhi]
51 KEMRI - Kenya Medical Research Institute
52 QIB - Quadram Institute Bioscience [Norwich, U.K.]
53 MCLGH - Makunda Christian Leprosy and General Hospital [Assam, India]
54 University of Maryland [Baltimore]
55 Kempegowda Institute of Medical Sciences [Bengaluru, India]
56 National Microbiology Reference Laboratory [Harare, Zimbabwe]
57 OMS / WHO - Organisation Mondiale de la Santé / World Health Organization Office [Genève, Suisse]
58 Saint John's Medical College [Bengaluru, India]
59 Ministry of Health [Samoa]
60 IP - Institut Pasteur [Paris]
61 Kanchi Kamakoti CHILDS Trust Hospital [Chennai, India]
62 NIHR Oxford Biomedical Research Centre [Oxford, UK]
63 MCRI - Murdoch Children's Research Institute
64 SAS - Society for Applied Studies [New Delhi, India]
65 Université libre de Kigali
66 Chacha Nehru Bal Chikitsalaya [New Delhi, India]
67 University of Glasgow
68 Tribhuvan University
69 Kasturba Hospital [New Delhi, India]
70 Dhulikhel Hospital [Dhulikhel, Nepal]
71 Kathmandu University
72 Research Institute for Tropical Medicine [Muntinlupa City, Philippines]
73 Chinchpada Christian Hospital [Navapur, India]
74 NICD - National Institute for Communicable Diseases [Johannesburg]
75 CMCHL - Christian Medical College and Hospital Ludhiana [Punjab, India]
76 Duncan Hospital [Raxaul, India]
77 UC Davis - University of California [Davis]
John Crump
Benjamin Howden
Karen Keddy
  • Fonction : Auteur
Christopher Parry
Ayorinde Oluwatobiloba Afolayan
Jason Andrews
Odion Ikhimiukor
Junaid Iqbal
Samuel Kariuki
Stephen Luby
  • Fonction : Auteur
Chisomo Msefula
Satheesh Nair
Elisabeth Njamkepo
Iruka Okeke
Samir Saha
Senjuti Saha
François-Xavier Weill
David Aanensen

Résumé

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]).
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Dates et versions

hal-04855967 , version 1 (02-01-2025)

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Megan Carey, Zoe Dyson, Danielle Ingle, Afreenish Amir, Mabel Aworh, et al.. Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes. eLife, 2023, 12, pp.e85867. ⟨10.7554/eLife.85867⟩. ⟨hal-04855967⟩

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