Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing

Caroline Allix-Beguec; Irena Arandjelovic; Lijun Bi; Patrick Beckert; Maryline Bonnet; Phelim Bradley; Andrea M. Cabibbe; Irving Cancino-Munoz; Mark J. Caulfield; Angkana Chaiprasert; Daniela M. Cirillo; David Clifton; Inaki Comas; Derrick W. Crook; Maria R. De Filippo; Han de Neeling; Roland Diel; Francis A. Drobniewski; Kiatichai Faksri; Maha R. Farhat; Joy Fleming; Philip Fowler; Tom A. Fowler; Qian Gao; Jennifer Gardy; Deborah Gascoyne-Binzi; Ana-Luiza Gibertoni-Cruz; Ana Gil-Brusola; Tanya Golubchik; Ximena Gonzalo; Louis Grandjean; Guangxue He; Jennifer L. Guthrie; Sarah Hoosdally; Martin Hunt; Zamin Iqbal; Nazir Ismail; James Johnston; Faisal M. Khanzada; Chiea C. Khor; Thomas A. Kohl; Clare Kong; Sam Lipworth; Qingyun Liu; Gugu Maphalala; Elena Martinez; Vanessa Mathys; Matthias Merker; Paolo Miotto; Nerges Mistry; David A. J. Moore; Megan Murray; Stefan Niemann; Rick T-H Ong; Tim E. A. Peto; James E. Posey; Therdsak Prammananan; Alexander Pym; Camilla Rodrigues; Mabel Rodrigues; Timothy Rodwell; Gian M. Rossolini; Elisabeth Sanchez Padilla; Marco Schito; Xin Shen; Jay Shendure; Vitali Sintchenko; Alex Sloutsky; E. Grace Smith; Matthew Snyder; Karine Soetaert; Angela M. Starks; Philip Supply; Prapat Suriyapol; Sabira Tahseen; Patrick Tang; Yik-Ying Teo; Thuong N. T. Thuong; Guy Thwaites; Enrico Tortoli; Shaheed Omar; Dick van Soolingen; A. Sarah Walker; Timothy M. Walker; Mark Wilcox; Daniel J. Wilson; David Wyllie; Yang Yang; Hongtai Zhang; Yanlin Zhao; Baoli Zhu; CRyPTIC Consortium

doi:10.1056/NEJMoa1800474

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Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing

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Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing

Caroline Allix-Beguec, Irena Arandjelovic, Lijun Bi, Patrick Beckert, Maryline Bonnet, Phelim Bradley, Andrea M. Cabibbe, Irving Cancino-Munoz, Mark J. Caulfield, Angkana Chaiprasert, …

The New England journal of medicine, Vol.379(15), pp.1403-1415

11/10/2018

DOI: https://doi.org/10.1056/NEJMoa1800474

PMID: 30280646

Résumé

General & Internal Medicine

Life Sciences & Biomedicine

Medicine, General & Internal

Science & Technology

BACKGROUND The World Health Organization recommends drug-susceptibility testing of Mycobacterium tuberculosis complex for all patients with tuberculosis to guide treatment decisions and improve outcomes. Whether DNA sequencing can be used to accurately predict profiles of susceptibility to first-line antituberculosis drugs has not been clear. METHODS We obtained whole-genome sequences and associated phenotypes of resistance or susceptibility to the first-line antituberculosis drugs isoniazid, rifampin, ethambutol, and pyrazinamide for isolates from 16 countries across six continents. For each isolate, mutations associated with drug resistance and drug susceptibility were identified across nine genes, and individual phenotypes were predicted unless mutations of unknown association were also present. To identify how whole-genome sequencing might direct first-line drug therapy, complete susceptibility profiles were predicted. These profiles were predicted to be susceptible to all four drugs (i.e., pansusceptible) if they were predicted to be susceptible to isoniazid and to the other drugs or if they contained mutations of unknown association in genes that affect susceptibility to the other drugs. We simulated the way in which the negative predictive value changed with the prevalence of drug resistance. RESULTS A total of 10,209 isolates were analyzed. The largest proportion of phenotypes was predicted for rifampin (9660 [95.4%] of 10,130) and the smallest was predicted for ethambutol (8794 [89.8%] of 9794). Resistance to isoniazid, rifampin, ethambutol, and pyrazinamide was correctly predicted with 97.1%, 97.5%, 94.6%, and 91.3% sensitivity, respectively, and susceptibility to these drugs was correctly predicted with 99.0%, 98.8%, 93.6%, and 96.8% specificity. Of the 7516 isolates with complete phenotypic drug-susceptibility profiles, 5865 (78.0%) had complete genotypic predictions, among which 5250 profiles (89.5%) were correctly predicted. Among the 4037 phenotypic profiles that were predicted to be pansusceptible, 3952 (97.9%) were correctly predicted. CONCLUSIONS Genotypic predictions of the susceptibility of M. tuberculosis to first-line drugs were found to be correlated with phenotypic susceptibility to these drugs. (Funded by the Bill and Melinda Gates Foundation and others.)

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Titre: Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing
Créateurs - sans rôle: Caroline Allix-Beguec - Genoscreen, Lille, France
Irena Arandjelovic - Univ Belgrade, Fac Med, Inst Microbiol & Immunol, Belgrade, Serbia
Lijun Bi - Chinese Acad Sci, Inst Biophys, Key Lab RNA Biol, Beijing 100101 2, Peoples R China
Patrick Beckert - Forschungszentrum Borstel, Leibniz Lungenzentrum, Borstel, Germany
Maryline Bonnet - Epictr, Paris, France
Phelim Bradley - European Bioinformat Inst Hinxton, Cambridge, England
Andrea M. Cabibbe - IRCCS, Emerging Bacterial Pathogens Unit, San Raffaele Sci Inst, WHO Collaborating Ctr & TB Supranational Referenc, Milan, Italy
Irving Cancino-Munoz - CSIC, IBV, Calle Jaime Roig, Valencia, Spain
Mark J. Caulfield - Genom England, London, England
Angkana Chaiprasert - Mahidol Univ, Fac Med, Siriraj Hosp, Salaya, Nakhon Pathom, Thailand
Daniela M. Cirillo - IRCCS, Emerging Bacterial Pathogens Unit, San Raffaele Sci Inst, WHO Collaborating Ctr & TB Supranational Referenc, Milan, Italy
David Clifton - Univ Oxford, Inst Biomed Engn, Dept Engn Sci, Oxford, England
Inaki Comas - CSIC, IBV, Calle Jaime Roig, Valencia, Spain
Derrick W. Crook - University of Oxford
Maria R. De Filippo - IRCCS, Emerging Bacterial Pathogens Unit, San Raffaele Sci Inst, WHO Collaborating Ctr & TB Supranational Referenc, Milan, Italy
Han de Neeling - Natl Inst Publ Hlth & Environm RIVM, Bilthoven, Netherlands
Roland Diel - Univ Med Hosp Schleswig Holstein, ARCN, Inst Epidemiol, Kiel, Germany
Francis A. Drobniewski - Imperial Coll, London, England
Kiatichai Faksri - Khon Kaen Univ, Fac Med, Dept Microbiol, Khon Kaen, Thailand
Maha R. Farhat - Harvard Med Sch, Boston, MA USA
Joy Fleming - Chinese Acad Sci, Inst Biophys, Key Lab RNA Biol, Beijing 100101 2, Peoples R China
Philip Fowler - Univ Oxford, John Radcliffe Hosp, Nuffield Dept Med, Oxford, England
Tom A. Fowler - Genom England, London, England
Qian Gao - Fudan Univ, Shanghai Med Coll, Shanghai, Peoples R China
Jennifer Gardy - British Columbia Ctr Dis Control, Vancouver, BC, Canada
Deborah Gascoyne-Binzi - Leeds Teaching Hosp NHS Trust, Leeds, W Yorkshire, England
Ana-Luiza Gibertoni-Cruz - Univ Oxford, John Radcliffe Hosp, Nuffield Dept Med, Oxford, England
Ana Gil-Brusola - Hosp Univ & Politecn La Fe, Avinguda Fernando Abril Martorell, Valencia, Spain
Tanya Golubchik - Univ Oxford, Big Data Inst, Old Rd Campus, Oxford, England
Ximena Gonzalo - Imperial Coll, London, England
Louis Grandjean - Imperial Coll London, Dept Med, Sect Paediat, London, England
Guangxue He - Chinese Ctr Dis Control & Prevent, Beijing 2, Peoples R China
Jennifer L. Guthrie - British Columbia Ctr Dis Control, Vancouver, BC, Canada
Sarah Hoosdally - Univ Oxford, John Radcliffe Hosp, Nuffield Dept Med, Oxford, England
Martin Hunt - European Bioinformat Inst Hinxton, Cambridge, England
Zamin Iqbal - European Bioinformat Inst Hinxton, Cambridge, England
Nazir Ismail - NICD, Johannesburg, South Africa
James Johnston - British Columbia Ctr Dis Control, Vancouver, BC, Canada
Faisal M. Khanzada - Natl TB Reference Lab, Natl TB Control Program, Islamabad, Pakistan
Chiea C. Khor - Genome Institute of Singapore
Thomas A. Kohl - Forschungszentrum Borstel, Leibniz Lungenzentrum, Borstel, Germany
Clare Kong - British Columbia Ctr Dis Control, Vancouver, BC, Canada
Sam Lipworth - Univ Oxford, John Radcliffe Hosp, Nuffield Dept Med, Oxford, England
Qingyun Liu - Fudan Univ, Key Lab Med Mol Virol, Sch Basic Med, Shanghai, Peoples R China
Gugu Maphalala - Minist Hlth, NRL, Mbabane, Switzerland
Elena Martinez - Westmead Hosp, Ctr Infect Dis & Microbiol, Wentworthville New South Wales, Wentworthville, NSW, Australia
Vanessa Mathys - Sci Inst Publ Hlth WIV ISP, Bacterial Dis Serv, Operat Direct Communicable & Infect Dis, Brussels, Belgium
Matthias Merker - Forschungszentrum Borstel, Leibniz Lungenzentrum, Borstel, Germany
Paolo Miotto - IRCCS, Emerging Bacterial Pathogens Unit, San Raffaele Sci Inst, WHO Collaborating Ctr & TB Supranational Referenc, Milan, Italy
Nerges Mistry - Fdn Med Res, Bombay, Maharashtra, India
David A. J. Moore - London Sch Hyg & Trop Med, TB Ctr, London, England
Megan Murray - Harvard Med Sch, Boston, MA USA
Stefan Niemann - Forschungszentrum Borstel, Leibniz Lungenzentrum, Borstel, Germany
Rick T-H Ong - Natl Univ Singapore, Saw Swee Hock Sch Publ Hlth, Singapore, Singapore
Tim E. A. Peto - Univ Oxford, John Radcliffe Hosp, Nuffield Dept Med, Oxford, England
James E. Posey - Ctr Dis Control & Prevent, Atlanta, GA USA
Therdsak Prammananan - Natl Sci & Technol Dev Agcy, Biotec, Biotec, Thailand
Alexander Pym - UKZN, AHRI, Nelson Mandela Sch Med, Durban, South Africa
Camilla Rodrigues - Hinduja Hosp, Dept Microbiol, Bombay, Maharashtra, India
Mabel Rodrigues - British Columbia Ctr Dis Control, Vancouver, BC, Canada
Timothy Rodwell - Univ Calif San Diego, La Jolla, CA 92093 USA
Gian M. Rossolini - Florence Careggi Univ Hosp, Clin Microbiol & Virol Unit, Florence, Italy
Elisabeth Sanchez Padilla - Epictr, Paris, France
Marco Schito - Crit Path Inst, Tucson, AZ 85718 USA
Xin Shen - Shenzhen Ctr Chron Dis Control, Shenzhen, Peoples R China
Jay Shendure - University of Washington
Vitali Sintchenko - The University of Sydney
Alex Sloutsky - Univ Massachusetts, Sch Med, Worcester, MA 01655 USA
E. Grace Smith - Natl Mycobacterial Reference Serv, Publ Hlth England, Publ Hlth Lab Birmingham, Birmingham, W Midlands, England
Matthew Snyder - Univ Washington, Seattle, WA 98195 USA
Karine Soetaert - Sci Inst Publ Hlth WIV ISP, Bacterial Dis Serv, Operat Direct Communicable & Infect Dis, Brussels, Belgium
Angela M. Starks - Ctr Dis Control & Prevent, Atlanta, GA USA
Philip Supply - Univ Lille, CNRS, INSERM, CHU Lille,Inst Pasteur Lille,U1019,UMR 8204,CIIL, F-59000 Lille, France
Prapat Suriyapol - Mahidol Univ, Fac Med, Siriraj Hosp, Salaya, Nakhon Pathom, Thailand
Sabira Tahseen - Natl TB Reference Lab, Natl TB Control Program, Islamabad, Pakistan
Patrick Tang - British Columbia Ctr Dis Control, Vancouver, BC, Canada
Yik-Ying Teo - Genome Inst Singapore, Agcy Sci Technol & Res, Singapore, Singapore
Thuong N. T. Thuong - Univ Oxford, Clin Res Unit, Hosp Trop Dis, Ho Chi Minh City, Vietnam
Guy Thwaites - Univ Oxford, Clin Res Unit, Hosp Trop Dis, Ho Chi Minh City, Vietnam
Enrico Tortoli - IRCCS, Emerging Bacterial Pathogens Unit, San Raffaele Sci Inst, WHO Collaborating Ctr & TB Supranational Referenc, Milan, Italy
Shaheed Omar - NICD, Johannesburg, South Africa
Dick van Soolingen - Natl Inst Publ Hlth & Environm RIVM, Bilthoven, Netherlands
A. Sarah Walker - Univ Oxford, John Radcliffe Hosp, Nuffield Dept Med, Oxford, England
Timothy M. Walker - Univ Oxford, John Radcliffe Hosp, Nuffield Dept Med, Oxford, England
Mark Wilcox - Leeds Teaching Hosp NHS Trust, Leeds, W Yorkshire, England
Daniel J. Wilson - University of Oxford
David Wyllie - Univ Oxford, John Radcliffe Hosp, Nuffield Dept Med, Oxford, England
Yang Yang - Univ Oxford, Inst Biomed Engn, Dept Engn Sci, Oxford, England
Hongtai Zhang - Chinese Acad Sci, Inst Biophys, Key Lab RNA Biol, Beijing 100101 2, Peoples R China
Yanlin Zhao - Chinese Ctr Dis Control & Prevent, Natl TB Reference Lab, Beijing 2, Peoples R China
Baoli Zhu - Chinese Acad Sci, Microbial Genome Res Ctr, Beijing 2, Peoples R China
CRyPTIC Consortium
Détails de publication: The New England journal of medicine, Vol.379(15), pp.1403-1415
Éditeur: Massachusetts Medical Soc
Nombre de pages: 13
Note de subvention: Bill and Melinda Gates Foundation; Bill & Melinda Gates Foundation MC_PC_16027 / MRC; UK Research & Innovation (UKRI); Medical Research Council UK (MRC)
Identifiants: 99158674709311
Unité académique: Recherches translationnelles sur le VIH et les Maladies Infect. Endém. émerg. - TransVIHMI
Langue: English
Type de ressource: Journal article