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

Conor J Meehan; Galo A Goig; Thomas A Kohl; Lennert Verboven; Anzaan Dippenaar; Matthew Ezewudo; 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; Bouke C de Jong; Margaretha de Vos; Fabrizio Menardo; Sebastien Gagneux; Qian Gao; Tim H Heupink; Qingyun Liu; Chloé Loiseau; Leen Rigouts; Timothy C Rodwell; Elisa Tagliani; Timothy M Walker; Robin M Warren; Yanlin Zhao; Matteo Zignol; Marco Schito; Jennifer Gardy; Daniela M Cirillo; Stefan Niemann; Inaki Comas; Annelies Van Rie

doi:10.1038/s41579-019-0214-5

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

Conor J Meehan, Galo A Goig, Thomas A Kohl, Lennert Verboven, Anzaan Dippenaar, Matthew Ezewudo, 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 CabibbeBouke C de Jong, Margaretha de Vos, Fabrizio Menardo, Sebastien Gagneux, Qian Gao, Tim H Heupink, Qingyun Liu, Chloé Loiseau, Leen Rigouts, Timothy C Rodwell, Elisa Tagliani, Timothy M Walker, Robin M Warren, Yanlin Zhao, Matteo Zignol, Marco Schito, Jennifer Gardy, Daniela M Cirillo, Stefan Niemann, Inaki Comas, Annelies Van Rie

Mycobacteriology

Research output: Contribution to journal › A1: Web of Science-article › peer-review

Abstract

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.

Original language	English
Journal	Nature Reviews Microbiology
Volume	17
Issue number	9
Pages (from-to)	533-545
Number of pages	13
ISSN	1740-1526
DOIs	https://doi.org/10.1038/s41579-019-0214-5
Publication status	Published - 2019

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Meehan, C. J., Goig, G. A., Kohl, T. A., Verboven, L., Dippenaar, A., Ezewudo, M., Farhat, M. R., Guthrie, J. L., Laukens, K., Miotto, P., Ofori-Anyinam, B., Dreyer, V., Supply, P., Suresh, A., Utpatel, C., van Soolingen, D., Zhou, Y., Ashton, P. M., Brites, D., ... Van Rie, A. (2019). Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues. Nature Reviews Microbiology, 17(9), 533-545. https://doi.org/10.1038/s41579-019-0214-5

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title = "Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues",

abstract = "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.",

author = "Meehan, {Conor J} and Goig, {Galo A} and Kohl, {Thomas A} and Lennert Verboven and Anzaan Dippenaar and Matthew Ezewudo and Farhat, {Maha R} and Guthrie, {Jennifer L} and Kris Laukens and Paolo Miotto and Boatema Ofori-Anyinam and Viola Dreyer and Philip Supply and Anita Suresh and Christian Utpatel and {van Soolingen}, Dick and Yang Zhou and Ashton, {Philip M} and Daniela Brites and Cabibbe, {Andrea M} and {de Jong}, {Bouke C} and {de Vos}, Margaretha and Fabrizio Menardo and Sebastien Gagneux and Qian Gao and Heupink, {Tim H} and Qingyun Liu and Chlo{\'e} Loiseau and Leen Rigouts and Rodwell, {Timothy C} and Elisa Tagliani and Walker, {Timothy M} and Warren, {Robin M} and Yanlin Zhao and Matteo Zignol and Marco Schito and Jennifer Gardy and Cirillo, {Daniela M} and Stefan Niemann and Inaki Comas and {Van Rie}, Annelies",

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Meehan, CJ, Goig, GA, Kohl, TA, Verboven, L, Dippenaar, A, Ezewudo, M, Farhat, MR, Guthrie, JL, Laukens, K, Miotto, P, Ofori-Anyinam, B, Dreyer, V, Supply, P, Suresh, A, Utpatel, C, van Soolingen, D, Zhou, Y, Ashton, PM, Brites, D, Cabibbe, AM, de Jong, BC, de Vos, M, Menardo, F, Gagneux, S, Gao, Q, Heupink, TH, Liu, Q, Loiseau, C, Rigouts, L, Rodwell, TC, Tagliani, E, Walker, TM, Warren, RM, Zhao, Y, Zignol, M, Schito, M, Gardy, J, Cirillo, DM, Niemann, S, Comas, I & Van Rie, A 2019, 'Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues', Nature Reviews Microbiology, vol. 17, no. 9, pp. 533-545. https://doi.org/10.1038/s41579-019-0214-5

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T1 - Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues

AU - Meehan, Conor J

AU - Goig, Galo A

AU - Kohl, Thomas A

AU - Verboven, Lennert

AU - Dippenaar, Anzaan

AU - Ezewudo, Matthew

AU - Farhat, Maha R

AU - Guthrie, Jennifer L

AU - Laukens, Kris

AU - Miotto, Paolo

AU - Ofori-Anyinam, Boatema

AU - Dreyer, Viola

AU - Supply, Philip

AU - Suresh, Anita

AU - Utpatel, Christian

AU - van Soolingen, Dick

AU - Zhou, Yang

AU - Ashton, Philip M

AU - Brites, Daniela

AU - Cabibbe, Andrea M

AU - de Jong, Bouke C

AU - de Vos, Margaretha

AU - Menardo, Fabrizio

AU - Gagneux, Sebastien

AU - Gao, Qian

AU - Heupink, Tim H

AU - Liu, Qingyun

AU - Loiseau, Chloé

AU - Rigouts, Leen

AU - Rodwell, Timothy C

AU - Tagliani, Elisa

AU - Walker, Timothy M

AU - Warren, Robin M

AU - Zhao, Yanlin

AU - Zignol, Matteo

AU - Schito, Marco

AU - Gardy, Jennifer

AU - Cirillo, Daniela M

AU - Niemann, Stefan

AU - Comas, Inaki

AU - Van Rie, Annelies

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PY - 2019

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N2 - 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.

AB - 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.

U2 - 10.1038/s41579-019-0214-5

DO - 10.1038/s41579-019-0214-5

M3 - A1: Web of Science-article

C2 - 31209399

SN - 1740-1526

VL - 17

SP - 533

EP - 545

JO - Nature Reviews Microbiology

JF - Nature Reviews Microbiology

IS - 9

ER -

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

Abstract

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