Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges
Published 2019 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges
Authors
Keywords
-
Journal
Genome Medicine
Volume 11, Issue 1, Pages -
Publisher
Springer Science and Business Media LLC
Online
2019-07-25
DOI
10.1186/s13073-019-0660-8
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Social network analysis and whole genome sequencing in a cohort study to investigate TB transmission in an educational setting
- (2019) Simon Packer et al. BMC INFECTIOUS DISEASES
- Genomic prediction of tuberculosis drug-resistance: benchmarking existing databases and prediction algorithms
- (2019) Tra-My Ngo et al. BMC BIOINFORMATICS
- Whole-Genome Sequencing for Drug Resistance Profile Prediction in Mycobacterium tuberculosis
- (2019) Sebastian M. Gygli et al. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
- Extensive global movement of multidrug-resistant M. tuberculosis strains revealed by whole-genome analysis
- (2019) Keira A Cohen et al. THORAX
- GWAS for quantitative resistance phenotypes in Mycobacterium tuberculosis reveals resistance genes and regulatory regions
- (2019) Maha R. Farhat et al. Nature Communications
- Drug Penetration Gradients Associated with Acquired Drug Resistance in Tuberculosis Patients
- (2018) Keertan Dheda et al. AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
- Evaluation of whole genome sequencing and software tools for drug susceptibility testing of Mycobacterium tuberculosis
- (2018) J. van Beek et al. CLINICAL MICROBIOLOGY AND INFECTION
- The use of whole-genome sequencing in cluster investigation of a multidrug-resistant tuberculosis outbreak
- (2018) Maeve K. Lalor et al. EUROPEAN RESPIRATORY JOURNAL
- Direct whole genome sequencing of sputum accurately identifies drug resistant Mycobacterium tuberculosis faster than MGIT culture sequencing
- (2018) Ronan M. Doyle et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis
- (2018) Francesc Coll et al. NATURE GENETICS
- High-throughput metabolomic analysis predicts mode of action of uncharacterized antimicrobial compounds
- (2018) Mattia Zampieri et al. Science Translational Medicine
- A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination
- (2018) Caitlin Collins et al. PLoS Computational Biology
- Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data
- (2018) Benjamin Sobkowiak et al. BMC GENOMICS
- XDR tuberculosis in South Africa: genomic evidence supporting transmission in communities
- (2018) Sara C. Auld et al. EUROPEAN RESPIRATORY JOURNAL
- Whole Genome Sequencing of Mycobacterium tuberculosis
- (2018) Andrea M. Cabibbe et al. EUROPEAN RESPIRATORY JOURNAL
- Prevalence and characterization of heterogeneous VNTR clusters comprising drug susceptible and/or variable resistant Mycobacterium tuberculosis complex isolates in the Netherlands from 2004-2016
- (2018) Inge Roof et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Bacterial Factors That Predict Relapse after Tuberculosis Therapy
- (2018) Roberto Colangeli et al. NEW ENGLAND JOURNAL OF MEDICINE
- Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing
- (2018) NEW ENGLAND JOURNAL OF MEDICINE
- Clinically prevalent mutations in Mycobacterium tuberculosis alter propionate metabolism and mediate multidrug tolerance
- (2018) Nathan D. Hicks et al. Nature Microbiology
- Evaluation of the impact of a sequencing assay for detection of drug resistance on the clinical management of tuberculosis
- (2018) Phil Lowenthal et al. CLINICAL INFECTIOUS DISEASES
- A fast and agnostic method for bacterial genome-wide association studies: Bridging the gap between k-mers and genetic events
- (2018) Magali Jaillard et al. PLoS Genetics
- Compensatory evolution drives multidrug-resistant tuberculosis in Central Asia
- (2018) Matthias Merker et al. eLife
- A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis
- (2017) Paolo Miotto et al. EUROPEAN RESPIRATORY JOURNAL
- Identification of novel mutations associated with cycloserine resistance in Mycobacterium tuberculosis
- (2017) Jiazhen Chen et al. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
- Real-Time Sequencing of Mycobacterium tuberculosis: Are We There Yet?
- (2017) Robyn S. Lee et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Same-Day Diagnostic and Surveillance Data for Tuberculosis via Whole-Genome Sequencing of Direct Respiratory Samples
- (2017) Antonina A. Votintseva et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Highly Sensitive Detection of Isoniazid Heteroresistance in Mycobacterium tuberculosis by DeepMelt Assay
- (2017) Bin Liang et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Tuberculosis is changing
- (2017) Timothy M Walker et al. LANCET INFECTIOUS DISEASES
- Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance
- (2017) Abigail L Manson et al. NATURE GENETICS
- Transmission of Extensively Drug-Resistant Tuberculosis in South Africa
- (2017) N. Sarita Shah et al. NEW ENGLAND JOURNAL OF MEDICINE
- Evaluation of a Rapid Molecular Drug-Susceptibility Test for Tuberculosis
- (2017) Yingda L. Xie et al. NEW ENGLAND JOURNAL OF MEDICINE
- Mycobacterium tuberculosis resistance prediction and lineage classification from genome sequencing: comparison of automated analysis tools
- (2017) Viola Schleusener et al. Scientific Reports
- Mutations inpepQConfer Low-Level Resistance to Bedaquiline and Clofazimine in Mycobacterium tuberculosis
- (2016) Deepak Almeida et al. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
- Genomic Analysis of the Evolution of Fluoroquinolone Resistance in Mycobacterium tuberculosis Prior to Tuberculosis Diagnosis
- (2016) Danfeng Zhang et al. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
- Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages
- (2016) Jody E. Phelan et al. BMC GENOMICS
- Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review
- (2016) Hollie-Ann Hatherell et al. BMC Medicine
- Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing
- (2016) K. Schmidt et al. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
- Whole-Genome Sequencing of Mycobacterium tuberculosis Provides Insight into the Evolution and Genetic Composition of Drug-Resistant Tuberculosis in Belarus
- (2016) Kurt R. Wollenberg et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Rapid Drug Susceptibility Testing of Drug-Resistant Mycobacterium tuberculosis Isolates Directly from Clinical Samples by Use of Amplicon Sequencing: a Proof-of-Concept Study
- (2016) Rebecca E. Colman et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance
- (2016) Christopher A Desjardins et al. NATURE GENETICS
- Genomic diversity in autopsy samples reveals within-host dissemination of HIV-associated Mycobacterium tuberculosis
- (2016) Tami D Lieberman et al. NATURE MEDICINE
- Microbial genome-wide association studies: lessons from human GWAS
- (2016) Robert A. Power et al. NATURE REVIEWS GENETICS
- Whole genome sequencing of Mycobacterium tuberculosis for detection of recent transmission and tracing outbreaks: A systematic review
- (2016) Vlad Nikolayevskyy et al. TUBERCULOSIS
- Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes
- (2016) John A. Lees et al. Nature Communications
- Whole Genome Sequence Analysis of a Large Isoniazid-Resistant Tuberculosis Outbreak in London: A Retrospective Observational Study
- (2016) Nicola Casali et al. PLOS MEDICINE
- Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study
- (2016) Louise J Pankhurst et al. Lancet Respiratory Medicine
- Identifying lineage effects when controlling for population structure improves power in bacterial association studies
- (2016) Sarah G. Earle et al. Nature Microbiology
- Paradoxical Hypersusceptibility of Drug-resistant M ycobacterium tuberculosis to β-lactam Antibiotics
- (2016) Keira A. Cohen et al. EBioMedicine
- Tracing Mycobacterium tuberculosis transmission by whole genome sequencing in a high incidence setting: a retrospective population-based study in East Greenland
- (2016) K. Bjorn-Mortensen et al. Scientific Reports
- Mutations in Genes for the F420Biosynthetic Pathway and a Nitroreductase Enzyme Are the Primary Resistance Determinants in SpontaneousIn Vitro-Selected PA-824-Resistant Mutants of Mycobacterium tuberculosis
- (2015) Hana L. Haver et al. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
- Collaborative Effort for a Centralized Worldwide Tuberculosis Relational Sequencing Data Platform: Figure 1.
- (2015) Angela M. Starks et al. CLINICAL INFECTIOUS DISEASES
- The complex evolution of antibiotic resistance in Mycobacterium tuberculosis
- (2015) J.D. Fonseca et al. INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
- Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes
- (2015) Kim Judge et al. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
- Rapid Whole-Genome Sequencing of Mycobacterium tuberculosis Isolates Directly from Clinical Samples
- (2015) Amanda C. Brown et al. JOURNAL OF CLINICAL MICROBIOLOGY
- PhyResSE: a Web Tool Delineating Mycobacterium tuberculosis Antibiotic Resistance and Lineage from Whole-Genome Sequencing Data
- (2015) Silke Feuerriegel et al. JOURNAL OF CLINICAL MICROBIOLOGY
- CASTB (the comprehensive analysis server for the Mycobacterium tuberculosis complex): A publicly accessible web server for epidemiological analyses, drug-resistance prediction and phylogenetic comparison of clinical isolates
- (2015) Hiroki Iwai et al. TUBERCULOSIS
- Four decades of transmission of a multidrug-resistant Mycobacterium tuberculosis outbreak strain
- (2015) Vegard Eldholm et al. Nature Communications
- Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis
- (2015) Phelim Bradley et al. Nature Communications
- Within patient microevolution of Mycobacterium tuberculosis correlates with heterogeneous responses to treatment
- (2015) Qingyun Liu et al. Scientific Reports
- Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences
- (2015) Francesc Coll et al. Genome Medicine
- Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal
- (2015) Keira A. Cohen et al. PLOS MEDICINE
- Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area
- (2015) JA Guerra-Assunção et al. eLife
- TGS-TB: Total Genotyping Solution for Mycobacterium tuberculosis Using Short-Read Whole-Genome Sequencing
- (2015) Tsuyoshi Sekizuka et al. PLoS One
- Cross-Resistance between Clofazimine and Bedaquiline through Upregulation of MmpL5 in Mycobacterium tuberculosis
- (2014) R. C. Hartkoorn et al. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
- Genetic Determinants Involved inp-Aminosalicylic Acid Resistance in Clinical Isolates from Tuberculosis Patients in Northern China from 2006 to 2012
- (2014) Xiaobing Zhang et al. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
- KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes
- (2014) Andreas Steiner et al. BMC GENOMICS
- Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting
- (2014) João Perdigão et al. BMC GENOMICS
- Dissecting Vancomycin-Intermediate Resistance in Staphylococcus aureus Using Genome-Wide Association
- (2014) Md Tauqeer Alam et al. Genome Biology and Evolution
- Recurrence due to Relapse or Reinfection WithMycobacterium tuberculosis: A Whole-Genome Sequencing Approach in a Large, Population-Based Cohort With a High HIV Infection Prevalence and Active Follow-up
- (2014) José Afonso Guerra-Assunção et al. JOURNAL OF INFECTIOUS DISEASES
- Evolution and transmission of drug-resistant tuberculosis in a Russian population
- (2014) Nicola Casali et al. NATURE GENETICS
- Multidrug-Resistant Tuberculosis and Culture Conversion with Bedaquiline
- (2014) Andreas H. Diacon et al. NEW ENGLAND JOURNAL OF MEDICINE
- Acquired Resistance of Mycobacterium tuberculosis to Bedaquiline
- (2014) Koen Andries et al. PLoS One
- A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens
- (2014) Maha R Farhat et al. Genome Medicine
- Assessment of Mycobacterium tuberculosis transmission in Oxfordshire, UK, 2007–12, with whole pathogen genome sequences: an observational study
- (2014) Timothy M Walker et al. Lancet Respiratory Medicine
- Culture-independent detection and characterisation ofMycobacterium tuberculosisandM. africanumin sputum samples using shotgun metagenomics on a benchtop sequencer
- (2014) Emma L. Doughty et al. PeerJ
- Inferring patient to patient transmission of Mycobacterium tuberculosisfrom whole genome sequencing data
- (2013) Josephine M Bryant et al. BMC INFECTIOUS DISEASES
- para-Aminosalicylic Acid Is a Prodrug Targeting Dihydrofolate Reductase inMycobacterium tuberculosis
- (2013) Jun Zheng et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- Rifampin Heteroresistance in Mycobacterium tuberculosis Cultures as Detected by Phenotypic and Genotypic Drug Susceptibility Test Methods
- (2013) D. B. Folkvardsen et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis
- (2013) Maha R Farhat et al. NATURE GENETICS
- Evolution of high-level ethambutol-resistant tuberculosis through interacting mutations in decaprenylphosphoryl-β-D-arabinose biosynthetic and utilization pathway genes
- (2013) Hassan Safi et al. NATURE GENETICS
- Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance
- (2013) Hongtai Zhang et al. NATURE GENETICS
- Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis
- (2013) Christopher B Ford et al. NATURE GENETICS
- Whole-Genome Sequencing for Rapid Susceptibility Testing of M. tuberculosis
- (2013) Claudio U. Köser et al. NEW ENGLAND JOURNAL OF MEDICINE
- Whole Genome Sequencing Reveals Complex Evolution Patterns of Multidrug-Resistant Mycobacterium tuberculosis Beijing Strains in Patients
- (2013) Matthias Merker et al. PLoS One
- Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study
- (2013) Andreas Roetzer et al. PLOS MEDICINE
- Mutations in panD encoding aspartate decarboxylase are associated with pyrazinamide resistance in Mycobacterium tuberculosis
- (2013) Shuo Zhang et al. Emerging Microbes & Infections
- Randomized Pilot Trial of Eight Weeks of Bedaquiline (TMC207) Treatment for Multidrug-Resistant Tuberculosis: Long-Term Outcome, Tolerability, and Effect on Emergence of Drug Resistance
- (2012) A. H. Diacon et al. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
- rplCT460C Identified as a Dominant Mutation in Linezolid-Resistant Mycobacterium tuberculosis Strains
- (2012) Patrick Beckert et al. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
- Mixed-Strain Mycobacterium tuberculosis Infections and the Implications for Tuberculosis Treatment and Control
- (2012) T. Cohen et al. CLINICAL MICROBIOLOGY REVIEWS
- Microevolution of extensively drug-resistant tuberculosis in Russia
- (2012) N. Casali et al. GENOME RESEARCH
- A systematic review of gyrase mutations associated with fluoroquinolone-resistant Mycobacterium tuberculosis and a proposed gyrase numbering system
- (2012) Fernanda Maruri et al. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
- Dynamic Population Changes in Mycobacterium tuberculosis During Acquisition and Fixation of Drug Resistance in Patients
- (2012) Gang Sun et al. JOURNAL OF INFECTIOUS DISEASES
- Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study
- (2012) Timothy M Walker et al. LANCET INFECTIOUS DISEASES
- Delamanid for Multidrug-Resistant Pulmonary Tuberculosis
- (2012) Maria Tarcela Gler et al. NEW ENGLAND JOURNAL OF MEDICINE
- A Point Mutation in cycA Partially Contributes to the D-cycloserine Resistance Trait of Mycobacterium bovis BCG Vaccine Strains
- (2012) Jeffrey M. Chen et al. PLoS One
- Mycobacterium tuberculosis – Heterogeneity revealed through whole genome sequencing
- (2012) Chris Ford et al. TUBERCULOSIS
- Single nucleotide polymorphisms in Mycobacterium tuberculosis and the need for a curated database
- (2012) David Stucki et al. TUBERCULOSIS
- Mutations ingidBConfer Low-Level Streptomycin Resistance in Mycobacterium tuberculosis
- (2011) Sharon Y. Wong et al. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
- The PE/PPE multigene family codes for virulence factors and is a possible source of mycobacterial antigenic variation: Perhaps more?
- (2011) Yusuf Akhter et al. BIOCHIMIE
- PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species
- (2011) Joseph J. Gillespie et al. INFECTION AND IMMUNITY
- Population Structure of Multi- and Extensively Drug-Resistant Mycobacterium tuberculosis Strains in South Africa
- (2011) V. N. Chihota et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Validation of pncA Gene Sequencing in Combination with the Mycobacterial Growth Indicator Tube Method To Test Susceptibility of Mycobacterium tuberculosis to Pyrazinamide
- (2011) S. O. Simons et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Mycobacterium tuberculosis thymidylate synthase gene thyX is essential and potentially bifunctional, while thyA deletion confers resistance to p-aminosalicylic acid
- (2011) A. S. Fivian-Hughes et al. MICROBIOLOGY-SGM
- Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection
- (2011) Christopher B Ford et al. NATURE GENETICS
- Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes
- (2011) Iñaki Comas et al. NATURE GENETICS
- Dynamics of Antibiotic Resistant Mycobacterium tuberculosis during Long-Term Infection and Antibiotic Treatment
- (2011) Solomon H. Mariam et al. PLoS One
- Pyrazinamide Inhibits Trans-Translation in Mycobacterium tuberculosis
- (2011) W. Shi et al. SCIENCE
- The non-clonality of drug resistance in Beijing-genotype isolates of Mycobacterium tuberculosis from the Western Cape of South Africa
- (2010) Thomas R Ioerger et al. BMC GENOMICS
- MIRU-VNTRplus: a web tool for polyphasic genotyping of Mycobacterium tuberculosis complex bacteria
- (2010) T. Weniger et al. NUCLEIC ACIDS RESEARCH
- Molecular Genetics of para-Aminosalicylic Acid Resistance in Clinical Isolates and Spontaneous Mutants of Mycobacterium tuberculosis
- (2009) V. Mathys et al. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
- Resistant mutants of Mycobacterium tuberculosis selected in vitro do not reflect the in vivo mechanism of isoniazid resistance
- (2009) Indra L. Bergval et al. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
- Rapid Detection ofMycobacterium tuberculosisand Rifampin Resistance by Use of On-Demand, Near-Patient Technology
- (2009) Danica Helb et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Overexpression of the chromosomally encoded aminoglycoside acetyltransferase eis confers kanamycin resistance in Mycobacterium tuberculosis
- (2009) M. A. Zaunbrecher et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Tuberculosis Drug Resistance Mutation Database
- (2009) Andreas Sandgren et al. PLOS MEDICINE
- TB database: an integrated platform for tuberculosis research
- (2008) T. B. K. Reddy et al. NUCLEIC ACIDS RESEARCH
Discover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversationAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now