ReviewNature reviews. Microbiology2019
Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues.
Abstract readReview
In one paragraph
Review in Nature reviews. Microbiology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 248 papers, 2 of them syntheses that pooled it.
0numbers the graph read from it
0cells of the map it votes in
248citing papers in PubMed, 2 pooled it
–field-weighted citation impact
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
248 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Targeted next-generation sequencing to diagnose drug-resistant tuberculosis: a systematic review and meta-analysis.The Lancet. Infectious diseases · 2024Pooled it
- Nanopore Sequencing for Mycobacterium tuberculosis: a Critical Review of the Literature, New Developments, and Future Opportunities.Journal of clinical microbiology · 2022Pooled it
- Molecular Diagnostics for WHO Priority Bacterial Pathogens: A Bibliometric Mapping of Diagnostic Platforms, Resistance Markers, and Antimicrobial Resistance Research Trends.MicrobiologyOpen · 2026Review
- Variation in multiple classes of simple sequence repeats can alter drug susceptibility inbioRxiv : the preprint server for biology · 2026Article
- Diagnosis of Mycobacteriosis in Cultured Hybrid Tilapia (Oreochromis spp.) in Trinidad and Tobago.Journal of fish diseases · 2026Article
- Optimizing culture-free approaches to recover high-qualityMicrobial genomics · 2026Article
- Performance of next-generation sequencing technologies for detecting drug-resistant tuberculosis in people with pulmonary tuberculosis.The Cochrane database of systematic reviews · 2026Article
- Current Landscape of Molecular Diagnostic Tests and Emerging Tools for Tuberculosis and Drug Resistance.Diagnostics (Basel, Switzerland) · 2026Review
- Evaluating the Performance of Sputum-Based Targeted Sequencing Against Mycobacterial Whole-Genome Sequencing in Predicting Tuberculosis Drug Resistance.International journal of molecular sciences · 2026Article
- Mycobacteria Amplicon Sequencing Tool: automated resistance prediction and lineage classification forMicrobiology resource announcements · 2026Article
- Complete genomes reveal a refined map of Mycobacterium tuberculosis genetic diversity across evolutionary scales.Nature communications · 2026Article
- Hybrid sequencing reveals incompleteness of the H37Rv reference genome and highlights lineage-specific genomic divergence inMicrobial genomics · 2026Article
- Reference-free clustering as an epidemiological tool forMicrobial genomics · 2026Article
- Zoonotic tuberculosis: When diagnostic and surveillance systems are not designed to detect it.One health (Amsterdam, Netherlands) · 2026Article
- Resistance to Linezolid and Pretomanid in the Era of Modern Drug-Resistant Tuberculosis Treatment in South Africa: A Systematic Review and Meta-Analysis.Antibiotics (Basel, Switzerland) · 2026Review
- Evaluation of DNA extraction methods from clinical Mycobacterium tuberculosis primary liquid culture for whole-genome sequencing.BMC genomics · 2026Article
- Pervasive genome structure heterogeneity iniScience · 2026Article
- Detection of drug resistance mutations and spoligotype mapping in Mycobacterium tuberculosis using deeplex sequencing, including novel and uncharacterized spoligotypes.Archives of microbiology · 2026Article
- Nosocomial tuberculosis: the blind spot in global tuberculosis prevention and care.Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases · 2026Article
- The Impact of Adopting Whole-Genome Sequencing for Tuberculosis Diagnosis in China: A Cost-Effectiveness Analysis.Open forum infectious diseases · 2026Article
188 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
41 authors.
Conor J MeehanUnit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.ORCID http://orcid.org/0000-0003-0724-8343
Galo A GoigInstitute of Biomedicine of Valencia, CSIC, Valencia, Spain.
Thomas A KohlMolecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Borstel, Germany.
Lennert VerbovenTuberculosis Omics Research Consortium, Department of Epidemiology and Social Medicine, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.ORCID http://orcid.org/0000-0002-5647-5852
Anzaan DippenaarDST-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.
Matthew EzewudoCritical Path Institute, Tucson, AZ, USA.
Maha R FarhatDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0002-3871-5760
Jennifer L GuthrieUniversity of British Columbia, Vancouver, Canada.ORCID http://orcid.org/0000-0001-8565-203X
Kris LaukensAdrem Data Laboratory, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium.
Paolo MiottoEmerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy.
Boatema Ofori-AnyinamCenter for Global Health Security and Diplomacy, Ottawa, Canada.
Viola DreyerMolecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Borstel, Germany.
Philip SupplyUniversity of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, Lille, France.
Anita SureshFoundation for Innovative New Diagnostics, Geneva, Switzerland.
Christian UtpatelMolecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Borstel, Germany.
Dick van SoolingenNational Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands.
Yang ZhouNational Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
Philip M AshtonCentre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0002-1545-9661
Daniela BritesSwiss Tropical and Public Health Institute, Basel, Switzerland.ORCID http://orcid.org/0000-0002-8090-2287
Andrea M CabibbeEmerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy.ORCID http://orcid.org/0000-0001-9727-6465
Bouke C de JongUnit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
Margaretha de VosTuberculosis Omics Research Consortium, Department of Epidemiology and Social Medicine, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.
Fabrizio MenardoSwiss Tropical and Public Health Institute, Basel, Switzerland.
Sebastien GagneuxSwiss Tropical and Public Health Institute, Basel, Switzerland.
Qian GaoKey Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, China.
Tim H HeupinkTuberculosis Omics Research Consortium, Department of Epidemiology and Social Medicine, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.ORCID http://orcid.org/0000-0001-6237-3898
Qingyun LiuKey Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, China.
Chloé LoiseauSwiss Tropical and Public Health Institute, Basel, Switzerland.
Leen RigoutsUnit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.ORCID http://orcid.org/0000-0003-3301-9480
Timothy C RodwellFoundation for Innovative New Diagnostics, Geneva, Switzerland.
Elisa TaglianiEmerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy.
Timothy M WalkerNuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
Robin M WarrenDST-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.
Yanlin ZhaoNational Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.ORCID http://orcid.org/0000-0002-7890-4312
Matteo ZignolGlobal Tuberculosis Programme, World Health Organization, Geneva, Switzerland.
Marco SchitoCritical Path Institute, Tucson, AZ, USA.
Jennifer GardyUniversity of British Columbia, Vancouver, Canada.ORCID http://orcid.org/0000-0001-7255-7631
Daniela M CirilloEmerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy.
Stefan NiemannMolecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Borstel, Germany.
Inaki ComasInstitute of Biomedicine of Valencia, CSIC, Valencia, Spain. icomas@ibv.csic.es.ORCID http://orcid.org/0000-0001-5504-9408
Annelies Van RieTuberculosis Omics Research Consortium, Department of Epidemiology and Social Medicine, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium. annelies.vanrie@uantwerpen.be.
Funding
New Tools for the interpretation of Pathogen Genomic Data with a focus on Mycobacterium tuberculosisK01ES026835 · NIEHS · MASSACHUSETTS GENERAL HOSPITAL · PI FARHAT, MAHA · 2015 to 2019
$1.1MFDA HHS U18 FD005320NIEHS NIH HHS K01 ES026835World Health Organization 001
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.
Indexed as
Computational BiologyDrug Resistance, BacterialHumansMolecular Diagnostic TechniquesMolecular EpidemiologyMycobacterium tuberculosisPhylogenyPractice Guidelines as TopicTuberculosisWhole Genome Sequencing
Identifiers
PMID
31209399What OpenQuestion holds
Textmetadata
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Registered trials
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.