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Article Dans Une Revue PLoS Biology Année : 2022

A data compendium associating the genomes of 12,289 Mycobacterium tuberculosis isolates with quantitative resistance phenotypes to 13 antibiotics

Alice Brankin (1) , Kerri M. Malone (2) , Ivan Barilar (3) , Simone Battaglia (4) , Emanuele Borroni (4) , Angela Pires Brandao (5, 6) , Andrea Maurizio Cabibbe (4) , Joshua Carter (7) , Darren Chetty (8) , Daniela María Cirillo (4) , Pauline Claxton (9) , David A. Clifton (1) , Ted Cohen (10) , Jorge Coronel (11) , Derrick W. Crook (1) , Viola Dreyer (3) , Sarah G. Earle (1) , Vincent Escuyer (12) , Lucilaine Ferrazoli (6) , George Fú Gāo (13) , Jennifer Gardy (14) , Saheer Gharbia (15) , Kelen Teixeira Ghisi (6) , Arash Ghodousi (16, 4) , Ana Lúıza Gibertoni Cruz (1) , Louis Grandjean (17) , Clara Grazian (18) , Ramona Groenheit (19) , Jennifer L. Guthrie (20, 21) , Wencong He (13) , Harald Hoffmann (22) , Sarah Hoosdally J. (1) , Martin Hunt (2, 1) , Nazir Ahmed Ismail (23) , Lisa Jarrett (15) , Lavania Joseph (23) , Ruwen Jou (24) , Priti Kambli (25) , Rukhsar Khot (25) , Jeff Knaggs (2, 1) , Anastasia Koch (26) , Donna Kohlerschmidt (12) , Samaneh Kouchaki (1, 27) , Alexander S. Lachapelle (1) , Ajit Lalvani (28) , Simon Grandjean Lapierre (29) , Ian F. Laurenson (9) , Brice Letcher (2) , Wan-Hsuan Lin (24) , Chunfa Liu (13) , Dongxin Liu (13) , Ayan Mandal (30) , Mikael Mansjö (2) , Daniela Matias (15) , Graeme Meintjes (26) , Flávia de Freitas Mendes (6) , Matthias Merker (3) , Marina Mihalic (22) , James Millard (8) , Paolo Miotto (4) , Nerges Mistry (30) , David Moore (31, 11) , Kimberlee A. Musser (12) , Dumisani Ngcamu (23) , Hoang Ngoc Nhung (32) , Stefan Niemann (3, 33) , Kayzad Soli Nilgiriwala (30) , Camus Nimmo (17) , Max O'Donnell (34) , Nana Okozi (23) , Rosangela Siqueira Oliveira (6) , Shaheed Vally Omar (23) , Nicholas Paton (35) , Timothy Ea Peto (1) , Juliana Maira Watanabe Pinhata (6) , Sara Plesnik (22) , Zully M. Puyen (36) , Marie Sylvianne Rabodoarivelo (37) , Niaina Rakotosamimanana (37) , Paola M.V. Rancoita (16) , Priti Rathod (15) , Esther Robinson (15) , Gillian Rodger (1) , Camilla Rodrigues (25) , Timothy C. Rodwell (38, 39) , Aysha Roohi (1) , David Santos-Lazaro (36) , Sanchi Shah (30) , Thomas Andreas Kohl (3) , Grace A. Smith (15) , Walter Solano (40) , Andrea Spitaleri (4, 16) , Philip Supply (41) , Adrie J.C. Steyn (8) , Utkarsha Surve (25) , Sabira Tahseen (42) , Nguyen Thuy Thuong (32) , Guy Thwaites (32, 1) , Katharina Todt (22) , Alberto Trovato (4) , Christian Utpatel (3) , Annelies van Rie (43) , Srinivasan Vijay (9) , Timothy M. Walker (1, 32) , A. Sarah Walker (1) , Robin M. Warren (44) , Jim Werngren (19) , Maria Wijkander (19) , Robert J. Wilkinson (45, 46, 28) , Daniel J. Wilson (1) , Penelope Wintringer (2) , Yu-Xin Xiao (24) , Yang Yang (1, 47) , Yanlin Zhao (13) , Shen-Yuan Yao (23) , Baoli Zhu (48) , Philip W. Fowler (1) , Zamin Iqbal (2)
1 University of Oxford
2 EMBL-EBI - European Bioinformatics Institute [Hinxton]
3 Forschungszentrum Borstel - Research Center Borstel
4 IRCCS San Raffaele Scientific Institute [Milan, Italie]
5 COC - Casa de Oswaldo Cruz [Rio de Janeiro]
6 Instituto Adolfo Lutz [São Paulo, Brazil]
7 Stanford School of Medicine [Stanford]
8 AHRI - Africa Health Research Institute [Durban/Mtubatuba]
9 Edin. - University of Edinburgh
10 YSPH - Yale School of Public Health
11 UPC - Universidad Peruana de Ciencias Aplicadas (Lima)
12 Wadsworth Center
13 Chinese Center for Disease Control and Prevention
14 Bill & Melinda Gates Foundation [Seattle]
15 UKHSA - UK Health Security Agency [London]
16 UniSR - Universita Vita Salute San Raffaele = Vita-Salute San Raffaele University [Milan, Italie]
17 UCL - University College of London [London]
18 UNSW - University of New South Wales [Sydney]
19 Public Health Agency of Sweden
20 University of British Columbia [Vancouver]
21 Public Health Ontario - Santé publique Ontario
22 Synlab Academy, Synlab Holding Deutschland GmbH, Mannheim
23 NICD - National Institute for Communicable Diseases [Johannesburg]
24 Taipei Medical University
25 PD Hinduja Hospital & Research Institute, Mumbai
26 University of Cape Town
27 UNIS - University of Surrey
28 Imperial College London
29 UdeM - Université de Montréal
30 PRA Health sciences [Mumbai]
31 LSHTM - London School of Hygiene and Tropical Medicine
32 OUCRU - Oxford University Clinical Research Unit [Ho Chi Minh City]
33 DZIF - German Centre for Infection Research - partner site Hamburg-Lübeck-Borstel-Riems
34 CUIMC - Columbia University Irving Medical Center
35 NUS - National University of Singapore
36 Socios En Salud [Lima, Peru]
37 Institut Pasteur de Madagascar
38 FIND - Foundation for Innovative New Diagnostics
39 UC San Diego - University of California [San Diego]
40 UPCH - Universidad Peruana Cayetano Heredia
41 CIIL - Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204
42 National TB control Program [Islamabad, Pakistan]
43 UA - University of Antwerp
44 Stellenbosch University
45 Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, Department of Medicine, University of Cape Town
46 The Francis Crick Institute [London]
47 Shanghai Jiao Tong University School of Medicine
48 CAS - Chinese Academy of Sciences [Beijing]
Alice Brankin
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Vincent Escuyer
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Clara Grazian
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Ramona Groenheit
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Simon Grandjean Lapierre
Niaina Rakotosamimanana
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Aysha Roohi
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Annelies van Rie
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Zamin Iqbal
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Résumé

The Comprehensive Resistance Prediction for Tuberculosis: an International Consortium (CRyPTIC) presents here a data compendium of 12,289 Mycobacterium tuberculosis global clinical isolates, all of which have undergone whole-genome sequencing and have had their minimum inhibitory concentrations to 13 antitubercular drugs measured in a single assay. It is the largest matched phenotypic and genotypic dataset for M . tuberculosis to date. Here, we provide a summary detailing the breadth of data collected, along with a description of how the isolates were selected, collected, and uniformly processed in CRyPTIC partner laboratories across 23 countries. The compendium contains 6,814 isolates resistant to at least 1 drug, including 2,129 samples that fully satisfy the clinical definitions of rifampicin resistant (RR), multidrug resistant (MDR), pre-extensively drug resistant (pre-XDR), or extensively drug resistant (XDR). The data are enriched for rare resistance-associated variants, and the current limits of genotypic prediction of resistance status (sensitive/resistant) are presented by using a genetic mutation catalogue, along with the presence of suspected resistance-conferring mutations for isolates resistant to the newly introduced drugs bedaquiline, clofazimine, delamanid, and linezolid. Finally, a case study of rifampicin monoresistance demonstrates how this compendium could be used to advance our genetic understanding of rare resistance phenotypes. The data compendium is fully open source and it is hoped that it will facilitate and inspire future research for years to come.
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Dates et versions

hal-03837104 , version 1 (03-11-2022)

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Alice Brankin, Kerri M. Malone, Ivan Barilar, Simone Battaglia, Emanuele Borroni, et al.. A data compendium associating the genomes of 12,289 Mycobacterium tuberculosis isolates with quantitative resistance phenotypes to 13 antibiotics. PLoS Biology, 2022, 20 (8), pp.e3001721. ⟨10.1371/journal.pbio.3001721⟩. ⟨hal-03837104⟩
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