A data compendium associating the genomes of 12,289 Mycobacterium tuberculosis isolates with quantitative resistance phenotypes to 13 antibiotics

Epidemiological cutoff values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing of M. tuberculosis

(2022)   EUROPEAN RESPIRATORY JOURNAL

Rifampicin mono-resistant tuberculosis is not the same as multidrug-resistant tuberculosis: a descriptive study from Khayelitsha, South Africa

(2021) Zubeida Salaam-Dreyer et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Population structure, biogeography and transmissibility of Mycobacterium tuberculosis

(2021) Luca Freschi et al.   Nature Communications

Prevalence and genetic profiles of isoniazid resistance in tuberculosis patients: A multicountry analysis of cross-sectional data

(2020) Anna S. Dean et al.   PLOS MEDICINE

In vitro Study of Bedaquiline Resistance in Mycobacterium tuberculosis Multi-Drug Resistant Clinical Isolates

(2020) Giulia Degiacomi et al.   Frontiers in Microbiology

MDR M. tuberculosis outbreak clone in Eswatini missed by Xpert has elevated bedaquiline resistance dated to the pre-treatment era

(2020) Patrick Beckert et al.   Genome Medicine

Evolving rifampicin and isoniazid mono-resistance in a high multidrug-resistant and extensively drug-resistant tuberculosis region: a retrospective data analysis

(2019) Nomonde Ritta Mvelase et al.   BMJ Open

In Vitro Susceptibility of Mycobacterium tuberculosis to Amikacin, Kanamycin, and Capreomycin

(2018) J. A. Dijkstra et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Hearing loss with kanamycin treatment for multidrug-resistant tuberculosis in Bangladesh

(2018) Scott K. Heysell et al.   EUROPEAN RESPIRATORY JOURNAL

Ecology and evolution of Mycobacterium tuberculosis

(2018) Sebastien Gagneux   NATURE REVIEWS MICROBIOLOGY

Prevalence and patterns of rifampicin and isoniazid resistance conferring mutations in Mycobacterium tuberculosis isolates from Uganda

(2018) Edgar Kigozi et al.   PLoS One

Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing

(2018)   NEW ENGLAND JOURNAL OF MEDICINE

Outbreak of multidrug-resistant tuberculosis in South Africa undetected by WHO-endorsed commercial tests: an observational study

(2018) Ndivhuho A Makhado et al.   LANCET INFECTIOUS DISEASES

A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis

(2017) Paolo Miotto et al.   EUROPEAN RESPIRATORY JOURNAL

Bedaquiline-based treatment regimen for multidrug-resistant tuberculosis

(2017) Ioana D. Olaru et al.   EUROPEAN RESPIRATORY JOURNAL

Are moxifloxacin and levofloxacin equally effective to treat XDR tuberculosis?

(2017) Thomas Maitre et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Treatment outcomes of rifampin-sparing treatment in patients with pulmonary tuberculosis with rifampin-mono-resistance or rifampin adverse events: A retrospective cohort analysis

(2017) Shinhee Park et al.   RESPIRATORY MEDICINE

Mutations inpepQConfer Low-Level Resistance to Bedaquiline and Clofazimine in Mycobacterium tuberculosis

(2016) Deepak Almeida et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Rifabutin and rifampin resistance levels and associated rpoB mutations in clinical isolates of Mycobacterium tuberculosis complex

(2016) Zenda L. Berrada et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study

(2016) Louise J Pankhurst et al.   Lancet Respiratory Medicine

Prevalence, Risk Factors, and Treatment Outcomes of Isoniazid- and Rifampicin- Mono-Resistant Pulmonary Tuberculosis in Lima, Peru

(2016) Leonela Villegas 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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Evaluation of the Cepheid Xpert MTB/RIF assay

(2014) Thomas M Shinnick et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

Fluoroquinolone resistance in non-multidrug-resistant tuberculosis—a surveillance study in New South Wales, Australia, and a review of global resistance rates

(2014) Jennifer Ho et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

Consequences of genomic diversity in Mycobacterium tuberculosis

(2014) Mireia Coscolla et al.   SEMINARS IN IMMUNOLOGY

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

Multidrug-Resistant Tuberculosis Drug Susceptibility and Molecular Diagnostic Testing

(2012) Ameeta S. Kalokhe et al.   AMERICAN JOURNAL OF THE MEDICAL SCIENCES

Study of the Rifampin Monoresistance Mechanism in Mycobacterium tuberculosis

(2012) Y. Pang et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Protecting the tuberculosis drug pipeline: stating the case for the rational use of fluoroquinolones

(2012) Giovanni Battista Migliori et al.   EUROPEAN RESPIRATORY JOURNAL

De novo assembly and genotyping of variants using colored de Bruijn graphs

(2012) Zamin Iqbal et al.   NATURE GENETICS

Feasibility, diagnostic accuracy, and effectiveness of decentralised use of the Xpert MTB/RIF test for diagnosis of tuberculosis and multidrug resistance: a multicentre implementation study

(2011) Catharina C Boehme et al.   LANCET

Rates and Mechanisms of Resistance Development in Mycobacterium tuberculosis to a Novel Diarylquinoline ATP Synthase Inhibitor

(2009) E. Huitric et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS