Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal

A Novel Reporter Phage To Detect Tuberculosis and Rifampin Resistance in a High-HIV-Burden Population

(2015) Max R. O'Donnell et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage

(2015) Matthias Merker et al.   NATURE GENETICS

Four decades of transmission of a multidrug-resistant Mycobacterium tuberculosis outbreak strain

(2015) Vegard Eldholm et al.   Nature Communications

Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area

(2015) JA Guerra-Assunção et al.   eLife

Effects of introducing Xpert MTB/RIF test on multi-drug resistant tuberculosis diagnosis in KwaZulu-Natal South Africa

(2014) Nomonde R Dlamini-Mvelase et al.   BMC INFECTIOUS DISEASES

Adherence in the Treatment of Patients With Extensively Drug-Resistant Tuberculosis and HIV in South Africa

(2014) Max R. OʼDonnell et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES

Fitness costs of rifampicin resistance inMycobacterium tuberculosisare amplified under conditions of nutrient starvation and compensated by mutation in the β′ subunit of RNA polymerase

(2014) Taeksun Song et al.   MOLECULAR MICROBIOLOGY

Evolution and transmission of drug-resistant tuberculosis in a Russian population

(2014) Nicola Casali et al.   NATURE GENETICS

A Trial of Mass Isoniazid Preventive Therapy for Tuberculosis Control

(2014) Gavin J. Churchyard et al.   NEW ENGLAND JOURNAL OF MEDICINE

Do We Need to Detect Isoniazid Resistance in Addition to Rifampicin Resistance in Diagnostic Tests for Tuberculosis?

(2014) Claudia M. Denkinger et al.   PLoS One

High Rates of Potentially Infectious Tuberculosis and Multidrug-Resistant Tuberculosis (MDR-TB) among Hospital Inpatients in KwaZulu Natal, South Africa Indicate Risk of Nosocomial Transmission

(2014) Nonkqubela Bantubani et al.   PLoS One

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

(2014) Francesc Coll et al.   Nature Communications

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

Inferring patient to patient transmission of Mycobacterium tuberculosisfrom whole genome sequencing data

(2013) Josephine M Bryant et al.   BMC INFECTIOUS DISEASES

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

Programmatically Selected Multidrug-Resistant Strains Drive the Emergence of Extensively Drug-Resistant Tuberculosis in South Africa

(2013) Borna Müller 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

Putative Compensatory Mutations in the rpoC Gene of Rifampin-Resistant Mycobacterium tuberculosis Are Associated with Ongoing Transmission

(2012) M. de Vos et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

SITVITWEB – A publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology

(2012) Christophe Demay et al.   INFECTION GENETICS AND EVOLUTION

Nosocomial Transmission of Extensively Drug-Resistant Tuberculosis in a Rural Hospital in South Africa

(2012) Neel R. Gandhi 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

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative Analysis of Mycobacterium tuberculosis pe and ppe Genes Reveals High Sequence Variation and an Apparent Absence of Selective Constraints

(2012) Christopher R. E. McEvoy et al.   PLoS One

Population Structure of Multi- and Extensively Drug-Resistant Mycobacterium tuberculosis Strains in South Africa

(2011) V. N. Chihota et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

Spread of Extensively Drug-Resistant Tuberculosis in KwaZulu-Natal Province, South Africa

(2011) Prashini Moodley et al.   PLoS One

Global tuberculosis drug development pipeline: the need and the reality

(2010) Zhenkun Ma et al.   LANCET

Rapid Molecular Detection of Tuberculosis and Rifampin Resistance

(2010) Catharina C. Boehme et al.   NEW ENGLAND JOURNAL OF MEDICINE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Genome Analysis of Multi- and Extensively-Drug-Resistant Tuberculosis from KwaZulu-Natal, South Africa

(2009) Thomas R. Ioerger et al.   PLoS One

Clinical Characteristics and Treatment Outcomes of Patients with Isoniazid‐Monoresistant Tuberculosis

(2008) Adithya Cattamanchi et al.   CLINICAL INFECTIOUS DISEASES

Extensively drug-resistant tuberculosis

(2008) Mandeep Jassal et al.   LANCET INFECTIOUS DISEASES

High Functional Diversity in Mycobacterium tuberculosis Driven by Genetic Drift and Human Demography

(2008) Ruth Hershberg et al.   PLOS BIOLOGY