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

Alice Brankin; Kerri Malone; Ivan Barilar; Simone Battaglia; Emanuele Borroni; Angela Pires Brandao; Andrea Maurizio Cabibbe; Joshua James Carter; Darren Chetty; Daniela Maria Cirillo; Pauline Claxton; David A Clifton; Ted Cohen; Jorge Coronel; Derrick W Crook; Viola Dreyer; Sarah G. Earle; Vincent Escuyer; Lucilaine Ferrazoli; George Fú Gāo; Jennifer Gardy; Saheer Gharbia; Kelen Teixeira Ghisi; Arash Ghodousi; Ana Gibertoni Cruz; Louis Grandjean; Clara Grazian; Ramona Groenheit; Jennifer Guthrie; Wencong He; Harald Hoffmann; Sarah J.; Martin Hunt; Nazir Ismail; Lisa Jarrett; Lavania Joseph; Ruwen Jou; Priti Kambli; Rukhsar Khot; Jeff Knaggs; Anastasia Koch; Donna Kohlerschmidt; Samaneh Kouchaki; Alexander Lachapelle; A Lalvani; Simon Grandjean Lapierre; Ian Laurenson; Brice Letcher; Wan-Hsuan Lin; Chunfa Liu; Dongxin Liu; Ayan Mandal; Mikael Mansjö; Daniela Matias; Graeme Meintjes; Flávia de Freitas Mendes; Matthias Merker; Marina Mihalic; James Millard; Paolo Miotto; Nerges Mistry; David Moore; Kimberlee A. Musser; Dumisani Ngcamu; Hoang Ngoc Nhung; Stefan Niemann; Kayzad Soli Nilgiriwala; Camus Nimmo; Max O'Donnell; Nana Okozi; Rosangela Siqueira Oliveira; Shaheed V. Omar; Nicholas Paton; Timothy E A Peto; Juliana Maira Watanabe Pinhata; Sara Plesnik; Zully Puyen; Marie Rabodoarivelo; Niaina Rakotosamimanana; Paola Rancoita; Priti Rathod; E. B. Robinson; Gillian Rodger; Camilla Rodrigues; Timothy C. Rodwell; Aysha Roohi; David Santos-Lazaro; Sanchi Shah; Thomas Andreas Kohl; Grace Smith; Walter Solano; Andrea Spitaleri; Philip Supply; Adrie Steyn; Utkarsha Surve; Sabira Tahseen; Nguyen Thuong; Guy Thwaites; Katharina Todt; Alberto Trovato

doi:10.1371/journal.pbio.3001721

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

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

Alice Brankin, Kerri Malone, Ivan Barilar, Simone Battaglia, Emanuele Borroni, Angela Pires Brandao, Andrea Maurizio Cabibbe, Joshua James Carter, Darren Chetty, Daniela Maria Cirillo, …

PLoS biology, Vol.20(8), e3001721

01/08/2022

DOI: https://doi.org/10.1371/journal.pbio.3001721

PMID: 35944069

Abstract

Biochemistry, Molecular Biology

Microbiology and Parasitology

Bacteriology

Genomics

Life Sciences

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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Title: A data compendium associating the genomes of 12,289 Mycobacterium tuberculosis isolates with quantitative resistance phenotypes to 13 antibiotics
Creators: Alice Brankin - University of Oxford [Oxford]
Kerri Malone - European Bioinformatics Institute [Hinxton]
Ivan Barilar - Forschungszentrum Borstel - Research Center Borstel
Simone Battaglia - IRCCS San Raffaele Scientific Institute [Milan, Italie]
Emanuele Borroni - IRCCS San Raffaele Scientific Institute [Milan, Italie]
Angela Pires Brandao - Casa de Oswaldo Cruz [Rio de Janeiro]
Andrea Maurizio Cabibbe - IRCCS San Raffaele Scientific Institute [Milan, Italie]
Joshua James Carter - Stanford School of Medicine [Stanford]
Darren Chetty - Africa Health Research Institute [Durban/Mtubatuba]
Daniela Maria Cirillo - IRCCS San Raffaele Scientific Institute [Milan, Italie]
Pauline Claxton - University of Edinburgh
David A Clifton - University of Oxford [Oxford]
Ted Cohen - Yale School of Public Health
Jorge Coronel - Universidad Peruana de Ciencias Aplicadas (Lima)
Derrick W Crook - University of Oxford [Oxford]
Viola Dreyer - Forschungszentrum Borstel - Research Center Borstel
Sarah G. Earle - University of Oxford [Oxford]
Vincent Escuyer - Wadsworth Center
Lucilaine Ferrazoli - Instituto Adolfo Lutz [São Paulo, Brazil]
George Fú Gāo - Chinese Center for Disease Control and Prevention
Jennifer Gardy - Bill & Melinda Gates Foundation [Seattle]
Saheer Gharbia - UK Health Security Agency
Kelen Teixeira Ghisi - Instituto Adolfo Lutz [São Paulo, Brazil]
Arash Ghodousi - Universita Vita Salute San Raffaele = Vita-Salute San Raffaele University [Milan, Italie]
Ana Gibertoni Cruz - University of Oxford [Oxford]
Louis Grandjean - University College of London [London]
Clara Grazian - University of New South Wales [Sydney]
Ramona Groenheit - Public Health Agency of Sweden
Jennifer Guthrie - University of British Columbia [Vancouver]
Wencong He - Chinese Center for Disease Control and Prevention
Harald Hoffmann - Synlab Academy, Synlab Holding Deutschland GmbH, Mannheim
Sarah J. - University of Oxford [Oxford]
Martin Hunt - European Bioinformatics Institute [Hinxton]
Nazir Ismail - National Institute for Communicable Diseases [Johannesburg]
Lisa Jarrett - UK Health Security Agency
Lavania Joseph - National Institute for Communicable Diseases [Johannesburg]
Ruwen Jou - Taipei Medical University
Priti Kambli - PD Hinduja Hospital & Research Institute, Mumbai
Rukhsar Khot - PD Hinduja Hospital & Research Institute, Mumbai
Jeff Knaggs - European Bioinformatics Institute [Hinxton]
Anastasia Koch - University of Cape Town
Donna Kohlerschmidt - Wadsworth Center
Samaneh Kouchaki
Alexander Lachapelle - University of Oxford [Oxford]
A Lalvani - Imperial College London
Simon Grandjean Lapierre - Université de Montréal
Ian Laurenson - University of Edinburgh
Brice Letcher - European Bioinformatics Institute [Hinxton]
Wan-Hsuan Lin - Taipei Medical University
Chunfa Liu - Chinese Center for Disease Control and Prevention
Dongxin Liu - Chinese Center for Disease Control and Prevention
Ayan Mandal - PRA Health sciences [Mumbai]
Mikael Mansjö - European Bioinformatics Institute [Hinxton]
Daniela Matias - UK Health Security Agency
Graeme Meintjes - University of Cape Town
Flávia de Freitas Mendes - Instituto Adolfo Lutz [São Paulo, Brazil]
Matthias Merker - Forschungszentrum Borstel - Research Center Borstel
Marina Mihalic - Synlab Academy, Synlab Holding Deutschland GmbH, Mannheim
James Millard - Africa Health Research Institute [Durban/Mtubatuba]
Paolo Miotto - IRCCS San Raffaele Scientific Institute [Milan, Italie]
Nerges Mistry - PRA Health sciences [Mumbai]
David Moore - London School of Hygiene and Tropical Medicine
Kimberlee A. Musser - Wadsworth Center
Dumisani Ngcamu - National Institute for Communicable Diseases [Johannesburg]
Hoang Ngoc Nhung - Oxford University Clinical Research Unit [Ho Chi Minh City]
Stefan Niemann - Forschungszentrum Borstel - Research Center Borstel
Kayzad Soli Nilgiriwala - PRA Health sciences [Mumbai]
Camus Nimmo - University College of London [London]
Max O'Donnell - Columbia University Irving Medical Center
Nana Okozi - National Institute for Communicable Diseases [Johannesburg]
Rosangela Siqueira Oliveira - Instituto Adolfo Lutz [São Paulo, Brazil]
Shaheed V. Omar - National Institute for Communicable Diseases [Johannesburg]
Nicholas Paton - National University of Singapore
Timothy E A Peto - University of Oxford [Oxford]
Juliana Maira Watanabe Pinhata - Instituto Adolfo Lutz [São Paulo, Brazil]
Sara Plesnik - Synlab Academy, Synlab Holding Deutschland GmbH, Mannheim
Zully Puyen - Socios En Salud [Lima, Peru]
Marie Rabodoarivelo - Institut Pasteur de Madagascar
Niaina Rakotosamimanana - Institut Pasteur de Madagascar
Paola Rancoita - Universita Vita Salute San Raffaele = Vita-Salute San Raffaele University [Milan, Italie]
Priti Rathod - UK Health Security Agency
E. B. Robinson - UK Health Security Agency
Gillian Rodger - University of Oxford [Oxford]
Camilla Rodrigues - PD Hinduja Hospital & Research Institute, Mumbai
Timothy C. Rodwell - Foundation for Innovative New Diagnostics
Aysha Roohi - University of Oxford [Oxford]
David Santos-Lazaro - Socios En Salud [Lima, Peru]
Sanchi Shah - PRA Health sciences [Mumbai]
Thomas Andreas Kohl - Forschungszentrum Borstel - Research Center Borstel
Grace Smith - UK Health Security Agency
Walter Solano - Universidad Peruana Cayetano Heredia
Andrea Spitaleri - IRCCS San Raffaele Scientific Institute [Milan, Italie]
Philip Supply - Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204
Adrie Steyn - Africa Health Research Institute [Durban/Mtubatuba]
Utkarsha Surve - PD Hinduja Hospital & Research Institute, Mumbai
Sabira Tahseen - National TB control Program [Islamabad, Pakistan]
Nguyen Thuong - Oxford University Clinical Research Unit [Ho Chi Minh City]
Guy Thwaites - Oxford University Clinical Research Unit [Ho Chi Minh City]
Katharina Todt - Synlab Academy, Synlab Holding Deutschland GmbH, Mannheim
Alberto Trovato - IRCCS San Raffaele Scientific Institute [Milan, Italie]
Publication Details: PLoS biology, Vol.20(8), e3001721
Date published: 01/08/2022
Date accepted: 21/06/2022
Grant note: This work was supported by Wellcome Trust/Newton Fund-MRC Collaborative Award (200205/Z/15/Z); and Bill & Melinda Gates Foundation Trust (OPP1133541). Oxford CRyPTIC consortium members are funded/supported by the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC), the views expressed are those of the authors and not necessarily those of the NHS, the NIHR or the Department of Health, and the National Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, a partnership between Public Health England and the University of Oxford, the views expressed are those of the authors and not necessarily those of the NIHR, Public Health England or the Department of Health and Social Care. J.M. is supported by the Wellcome Trust (203919/Z/16/Z). Z.Y. is supported by the National Science and Technology Major Project, China Grant No. 2018ZX10103001. K.M.M. is supported by EMBL’s EIPOD3 programme funded by the European Union’s Horizon 2020 research and innovation programme under Marie Sklodowska Curie Actions. T.C.R. is funded in part by funding from Unitaid Grant No. 2019-32-FIND MDR. R.S.O. is supported by FAPESP Grant No. 17/16082-7. L.F. received financial support from FAPESP Grant No. 2012/51756-5. B.Z. is supported by the National Natural Science Foundation of China (81991534) and the Beijing Municipal Science & Technology Commission (Z201100005520041). N.T.T.T. is supported by the Wellcome Trust International Intermediate Fellowship (206724/Z/17/Z). G.T. is funded by the Wellcome Trust. R.W. is supported by the South African Medical Research Council. J.C. is supported by the Rhodes Trust and Stanford Medical Scientist Training Program (T32 GM007365). A.L. is supported by the National Institute for Health Research (NIHR) Health Protection Research Unit in Respiratory Infections at Imperial College London. S.G.L. is supported by the Fonds de Recherche en Santé du Québec. C.N. is funded by Wellcome Trust Grant No. 203583/Z/16/Z. A.V.R. is supported by Research Foundation Flanders (FWO) under Grant No. G0F8316N (FWO Odysseus). G.M. was supported by the Wellcome Trust (098316, 214321/Z/18/Z, and 203135/Z/16/Z), and the South African Research Chairs Initiative of the Department of Science and Technology and National Research Foundation (NRF) of South Africa (Grant No. 64787). The funders had no role in the study design, data collection, data analysis, data interpretation, or writing of this report. The opinions, findings and conclusions expressed in this manuscript reflect those of the authors alone. L.G. was supported by the Wellcome Trust (201470/Z/16/Z), the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under award number 1R01AI146338, the GOSH Charity (VC0921) and the GOSH/ICH Biomedical Research Centre (www.nihr.ac.uk). A.B. is funded by the NDM Prize Studentship from the Oxford Medical Research Council Doctoral Training Partnership and the Nuffield Department of Clinical Medicine. D.J.W. is supported by a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (Grant No. 101237/Z/13/B) and by the Robertson Foundation. A.S.W. is an NIHR Senior Investigator. T.M.W. is a Wellcome Trust Clinical Career Development Fellow (214560/Z/18/Z). A.S.L. is supported by the Rhodes Trust. R.J.W. receives funding from the Francis Crick Institute which is supported by Wellcome Trust, (FC0010218), UKRI (FC0010218), and CRUK (FC0010218). T.C. has received grant funding and salary support from US NIH, CDC, USAID and Bill and Melinda Gates Foundation. The computational aspects of this research were supported by the Wellcome Trust Core Award Grant Number 203141/Z/16/Z and the NIHR Oxford BRC (BRC-1215-20008). Parts of the work were funded by the German Center of Infection Research (DZIF). The Scottish Mycobacteria Reference Laboratory is funded through National Services Scotland. The Wadsworth Center contributions were supported in part by Cooperative Agreement No. U60OE000103 funded by the Centers for Disease Control and Prevention through the Association of Public Health Laboratories and NIH/NIAID grant AI-117312.
Identifiers: 99777766102346
Academic Unit: School of Computer Science and Electronic Engineering
Language: English
Resource Type: Journal article

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

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