Title :

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

Author(s) :

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

Journal title :

Plos Biology

Pages :

e3001721

Publication date :

2022

ISSN :

1545-7885

HAL domain(s) :

Sciences du Vivant [q-bio]/Microbiologie et Parasitologie/Bactériologie
Sciences du Vivant [q-bio]/Biochimie, Biologie Moléculaire/Génomique, Transcriptomique et Protéomique [q-bio.GN]

English abstract : [en]

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 ...
Show more >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.Show less >

Language :

Anglais

Peer reviewed article :

Oui

Audience :

Internationale

Popular science :

Non

Collections :

• Centre d'Infection et d'Immunité de Lille (CIIL) - U1019 - UMR 9017

Source :

Harvested from HAL