Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues
Por:
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 and Van Rie A
Publicada:
1 sep 2019
Resumen:
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.
Filiaciones:
Meehan CJ:
Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
:
Institute of Biomedicine of Valencia, CSIC, Valencia, Spain
Kohl TA:
Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Borstel, Germany
German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
Verboven L:
Tuberculosis Omics Research Consortium, Department of Epidemiology and Social Medicine, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
Dippenaar A:
DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
Ezewudo M:
Critical Path Institute, Tucson, AZ, USA
Farhat MR:
Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA
Guthrie JL:
University of British Columbia, Vancouver, Canada
Laukens K:
Adrem Data Laboratory, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
Miotto P:
Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
Ofori-Anyinam B:
Center for Global Health Security and Diplomacy, Ottawa, Canada
Food and Drugs Authority, Accra, Ghana
Dreyer V:
Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Borstel, Germany
German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
Supply P:
University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, Lille, France
U1019 - UMR 8204, Center for Infection and Immunity of Lille, Lille, France
Suresh A:
Foundation for Innovative New Diagnostics, Geneva, Switzerland
Utpatel C:
Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Borstel, Germany
German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
van Soolingen D:
National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
Zhou Y:
National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
Ashton PM:
Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
Brites D:
Swiss Tropical and Public Health Institute, Basel, Switzerland
University of Basel, Basel, Switzerland
Cabibbe AM:
Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
de Jong BC:
Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
de Vos M:
Tuberculosis Omics Research Consortium, Department of Epidemiology and Social Medicine, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
Menardo F:
Swiss Tropical and Public Health Institute, Basel, Switzerland
University of Basel, Basel, Switzerland
Gagneux S:
Swiss Tropical and Public Health Institute, Basel, Switzerland
University of Basel, Basel, Switzerland
Gao Q:
Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, China
Heupink TH:
Tuberculosis Omics Research Consortium, Department of Epidemiology and Social Medicine, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
Liu Q:
Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, China
Loiseau C:
Swiss Tropical and Public Health Institute, Basel, Switzerland
University of Basel, Basel, Switzerland
Rigouts L:
Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
Rodwell TC:
Foundation for Innovative New Diagnostics, Geneva, Switzerland
Tagliani E:
Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
Walker TM:
Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
Warren RM:
DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
Zhao Y:
National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
Zignol M:
Global Tuberculosis Programme, World Health Organization, Geneva, Switzerland
Schito M:
Critical Path Institute, Tucson, AZ, USA
Gardy J:
University of British Columbia, Vancouver, Canada
Cirillo DM:
Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
Niemann S:
Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Borstel, Germany
German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
:
Institute of Biomedicine of Valencia, CSIC, Valencia, Spain.
Van Rie A:
Tuberculosis Omics Research Consortium, Department of Epidemiology and Social Medicine, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.
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