Culture-independent detection and characterisation ofMycobacterium tuberculosisandM. africanumin sputum samples using shotgun metagenomics on a benchtop sequencer

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Mixed Mycobacterium tuberculosis Complex Infections and False-Negative Results for Rifampin Resistance by GeneXpert MTB/RIF Are Associated with Poor Clinical Outcomes

(2014) N. M. Zetola et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Whole-Genome-Based Mycobacterium tuberculosis Surveillance: a Standardized, Portable, and Expandable Approach

(2014) T. A. Kohl et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing

(2014) Michael R. Wilson et al.   NEW ENGLAND JOURNAL OF MEDICINE

Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections

(2014) M. J. PALLEN   PARASITOLOGY

Evolutionary history of tuberculosis shaped by conserved mutations in the PhoPR virulence regulator

(2014) J. Gonzalo-Asensio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Whole-genome sequencing to control antimicrobial resistance

(2014) Claudio U. Köser et al.   TRENDS IN GENETICS

PolyTB: A genomic variation map for Mycobacterium tuberculosis

(2014) Francesc Coll et al.   TUBERCULOSIS

Recovery of a Medieval Brucella melitensis Genome Using Shotgun Metagenomics

(2014) G. L. Kay et al.   mBio

Current Methods in the Molecular Typing ofMycobacterium tuberculosisand Other Mycobacteria

(2014) Tomasz Jagielski et al.   Biomed Research International

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

The re-emergence of tuberculosis: what have we learnt from molecular epidemiology?

(2013) M.W. Borgdorff et al.   CLINICAL MICROBIOLOGY AND INFECTION

A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4

(2013) Nicholas J. Loman et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Mycobacterium canettii is intrinsically resistant to both pyrazinamide and pyrazinoic acid

(2013) S. Feuerriegel et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Multidrug-Resistant Tuberculosis in Panama Is Driven by Clonal Expansion of a Multidrug-Resistant Mycobacterium tuberculosis Strain Related to the KZN Extensively Drug-Resistant M. tuberculosis Strain from South Africa

(2013) F. Lanzas et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Whole-Genome Sequencing for Rapid Susceptibility Testing of M. tuberculosis

(2013) Claudio U. Köser et al.   NEW ENGLAND JOURNAL OF MEDICINE

Metagenomic Analysis of Tuberculosis in a Mummy

(2013) Jacqueline Z.-M. Chan et al.   NEW ENGLAND JOURNAL OF MEDICINE

Genome-Wide Comparison of Medieval and Modern Mycobacterium leprae

(2013) V. J. Schuenemann et al.   SCIENCE

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

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Diagnosis of tuberculosis and drug resistance: what can new tools bring us? [State of the art series. New tools. Number 1 in the series]

(2012) F. Drobniewski et al.   INTERNATIONAL JOURNAL OF TUBERCULOSIS AND LUNG DISEASE

Metagenomics and metatranscriptomics: Windows on CF-associated viral and microbial communities

(2012) Yan Wei Lim et al.   Journal of Cystic Fibrosis

Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study

(2012) Timothy M Walker et al.   LANCET INFECTIOUS DISEASES

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity

(2012) Nicholas J. Loman et al.   NATURE REVIEWS MICROBIOLOGY

Characterization of the Viral Microbiome in Patients with Severe Lower Respiratory Tract Infections, Using Metagenomic Sequencing

(2012) Fredrik Lysholm et al.   PLoS One

Failure to Recognize Nontuberculous Mycobacteria Leads to Misdiagnosis of Chronic Pulmonary Tuberculosis

(2012) Mamoudou Maiga et al.   PLoS One

Genotype of a historic strain of Mycobacterium tuberculosis

(2012) A. S. Bouwman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing

(2012) Andreas Keller et al.   Nature Communications

Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology

(2012) Claudio U. Köser et al.   PLoS Pathogens

Impact offgd1andddnDiversity in Mycobacterium tuberculosis Complex onIn VitroSusceptibility to PA-824

(2011) Silke Feuerriegel et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Whole-Genome Sequencing and Social-Network Analysis of a Tuberculosis Outbreak

(2011) Jennifer L. Gardy et al.   NEW ENGLAND JOURNAL OF MEDICINE

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

Mixed infection with Beijing and non-Beijing strains in pulmonary tuberculosis in Taiwan: prevalence, risk factors, and dominant strain

(2010) J.-Y. Wang et al.   CLINICAL MICROBIOLOGY AND INFECTION

Importance of identifying Mycobacterium bovis as a causative agent of human tuberculosis

(2010) C. Allix-Beguec et al.   EUROPEAN RESPIRATORY JOURNAL

Molecular characteristics of “Mycobacterium canettii” the smooth Mycobacterium tuberculosis bacilli

(2010) Michel Fabre et al.   INFECTION GENETICS AND EVOLUTION

Genomic Signatures of the Haarlem Lineage of Mycobacterium tuberculosis: Implications of Strain Genetic Variation in Drug and Vaccine Development

(2010) A. Cubillos-Ruiz et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Mixed-Strain Mycobacterium tuberculosis Infections among Patients Dying in a Hospital in KwaZulu-Natal, South Africa

(2010) T. Cohen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved

(2010) Iñaki Comas et al.   NATURE GENETICS

Mycobacterium africanum—Review of an Important Cause of Human Tuberculosis in West Africa

(2010) Bouke C. de Jong et al.   PLoS Neglected Tropical Diseases

Differences between tuberculosis cases infected withMycobacterium africanum, West African type 2, relative to Euro-AmericanMycobacterium tuberculosis: an update

(2009) Bouke C. de Jong et al.   FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY

Rapid Detection ofMycobacterium tuberculosisand Rifampin Resistance by Use of On-Demand, Near-Patient Technology

(2009) Danica Helb et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Use of Spoligotyping and Large Sequence Polymorphisms To Study the Population Structure of the Mycobacterium tuberculosis Complex in a Cohort Study of Consecutive Smear-Positive Tuberculosis Cases in The Gambia

(2009) B. C. de Jong et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Predictors for Identifying the Most Infectious Pulmonary Tuberculosis Patient

(2008) Chuan-Sheng Wang et al.   JOURNAL OF THE FORMOSAN MEDICAL ASSOCIATION

The clinical consequences of strain diversity in Mycobacterium tuberculosis

(2008) Mark P. Nicol et al.   TRANSACTIONS OF THE ROYAL SOCIETY OF TROPICAL MEDICINE AND HYGIENE