Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues

被引：235

作者：

Meehan, Conor J. ^{[1
]}

Goig, Galo A. ^{[2
]}

Kohl, Thomas A. ^{[3
,4
]}

Verboven, Lennert ^{[5
]}

Dippenaar, Anzaan ^{[6
]}

Ezewudo, Matthew ^{[7
]}

Farhat, Maha R. ^{[8
,9
]}

Guthrie, Jennifer L. ^{[10
]}

Laukens, Kris ^{[11
]}

Miotto, Paolo ^{[12
]}

Ofori-Anyinam, Boatema ^{[13
,14
]}

Dreyer, Viola ^{[3
,4
]}

Supply, Philip ^{[15
,16
]}

Suresh, Anita ^{[17
]}

Utpatel, Christian ^{[3
,4
]}

van Soolingen, Dick ^{[18
]}

Zhou, Yang ^{[19
]}

Ashton, Philip M. ^{[20
]}

Brites, Daniela ^{[21
,22
]}

Cabibbe, Andrea M. ^{[12
]}

de Jong, Bouke C. ^{[1
]}

de Vos, Margaretha ^{[5
]}

Menardo, Fabrizio ^{[21
,22
]}

Gagneux, Sebastien ^{[21
,22
]}

Gao, Qian ^{[23
]}

Heupink, Tim H. ^{[5
]}

Liu, Qingyun ^{[23
]}

Loiseau, Chloe ^{[21
,22
]}

Rigouts, Leen ^{[1
]}

Rodwell, Timothy C. ^{[17
]}

Tagliani, Elisa ^{[12
]}

Walker, Timothy M. ^{[17
,24
]}

Warren, Robin M. ^{[6
]}

Zhao, Yanlin ^{[19
]}

Zignol, Matteo ^{[25
]}

Schito, Marco ^{[7
]}

Gardy, Jennifer ^{[10
]}

Cirillo, Daniela M. ^{[12
]}

Niemann, Stefan ^{[3
,4
]}

Comas, Inaki ^{[2
]}

Van Rie, Annelies ^{[5
]}

机构：

[1] Inst Trop Med, Dept Biomed Sci, Unit Mycobacteriol, Antwerp, Belgium

[2] CSIC, Inst Biomed Valencia, Valencia, Spain

[3] Res Ctr Borstel, Prior Area Infect, Mol & Expt Mycobacteriol, Borstel, Germany

[4] German Ctr Infect Res, Partner Site Hamburg Lubeck Borstel Riems, Borstel, Germany

[5] Univ Antwerp, Fac Med & Hlth Sci, Dept Epidemiol & Social Med, TB Omics Res Consortium,Inst Global Hlth, Antwerp, Belgium

[6] Stellenbosch Univ, DST NRF Ctr Excellence Biomed TB Res, Div Mol Biol & Human Genet,Fac Med & Hlth Sci, South African Med Res Council,Ctr TB Res, Cape Town, South Africa

[7] Crit Path Inst, Tucson, AZ USA

[8] Harvard Med Sch, Dept Biomed Informat, Boston, MA 02115 USA

[9] Massachusetts Gen Hosp, Pulm & Crit Care Med, Boston, MA 02114 USA

[10] Univ British Columbia, Vancouver, BC, Canada

[11] Univ Antwerp, Dept Math & Comp Sci, Adrem Data Lab, Antwerp, Belgium

[12] IRCCS, San Raffaele Sci Inst, Div Immunol Transplantat & Infect Dis, Emerging Bacterial Pathogens Unit, Milan, Italy

[13] Ctr Global Hlth Secur & Diplomacy, Ottawa, ON, Canada

[14] Food & Drugs Author, Accra, Ghana

[15] Univ Lille, CHU Lille, INSERM, CNRS,Inst Pasteur Lille, Lille, France

[16] Ctr Infect & Immun Lille, UMR 8204, U1019, Lille, France

[17] Fdn Innovat New Diagnost, Geneva, Switzerland

[18] Natl Inst Publ Hlth & Environm RIVM, Ctr Infect Dis Control, Natl TB Reference Lab, Bilthoven, Netherlands

[19] Chinese Ctr Dis Control & Prevent, Natl Ctr TB Control & Prevent, Beijing, Peoples R China

[20] Univ Oxford, Nuffield Dept Med, Ctr Trop Med & Global Hlth, Oxford, England

[21] Swiss Trop & Publ Hlth Inst, Basel, Switzerland

[22] Univ Basel, Basel, Switzerland

[23] Fudan Univ, Sch Basic Med Sci, Key Lab Med Mol Virol, Minist Educ & Hlth, Shanghai, Peoples R China

[24] Univ Oxford, John Radcliffe Hosp, Nuffield Dept Med, Oxford, England

[25] WHO, Global TB Programme, Geneva, Switzerland

来源：

NATURE REVIEWS MICROBIOLOGY | 2019年 / 17卷 / 09期

基金：

欧洲研究理事会; 美国国家卫生研究院;

关键词：

GENOTYPE MTBDRSL ASSAY; DRUG-RESISTANCE; MOLECULAR EPIDEMIOLOGY; MUTATION-RATE; ONLINE TOOLS; SUSCEPTIBILITY; SURVEILLANCE; TRANSMISSION; RIFAMPIN; REINFECTION;

D O I：

10.1038/s41579-019-0214-5

中图分类号：

Q93 [微生物学];

学科分类号：

071005 ; 100705 ;

摘要：

Whole genome sequencing (WGS) of Mycobacterium tuberculosis has rapidly progressed from a research tool to a clinical application for the diagnosis and management of tuberculosis and in public health surveillance. This development has been facilitated by drastic drops in cost, advances in technology and concerted efforts to translate sequencing data into actionable information. There is, however, a risk that, in the absence of a consensus and international standards, the widespread use of WGS technology may result in data and processes that lack harmonization, comparability and validation. In this Review, we outline the current landscape of WGS pipelines and applications, and set out best practices for M. tuberculosis WGS, including standards for bioinformatics pipelines, curated repositories of resistance-causing variants, phylogenetic analyses, quality control and standardized reporting.

引用

页码：533 / 545

页数：13

共 50 条

[1] Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues
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Thomas A. Kohl
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Maha R. Farhat
Jennifer L. Guthrie
Kris Laukens
Paolo Miotto
Boatema Ofori-Anyinam
Viola Dreyer
Philip Supply
Anita Suresh
Christian Utpatel
Dick van Soolingen
Yang Zhou
Philip M. Ashton
Daniela Brites
Andrea M. Cabibbe
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Margaretha de Vos
Fabrizio Menardo
Sebastien Gagneux
Qian Gao
Tim H. Heupink
Qingyun Liu
Chloé Loiseau
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Timothy C. Rodwell
Elisa Tagliani
Timothy M. Walker
Robin M. Warren
Yanlin Zhao
Matteo Zignol
Marco Schito
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Stefan Niemann
Inaki Comas
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