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

Whole-genome sequencing to detect recent transmission of Mycobacterium tuberculosis in settings with a high burden of tuberculosis

(2014) Tao Luo et al.   TUBERCULOSIS

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

Association between Mycobacterium tuberculosis lineage and time to sputum culture conversion

(2013) E. S. Click et al.   INTERNATIONAL JOURNAL OF TUBERCULOSIS AND LUNG DISEASE

Whole Genome Sequencing Analysis of Intrapatient Microevolution in Mycobacterium tuberculosis: Potential Impact on the Inference of Tuberculosis Transmission

(2013) Laura Pérez-Lago et al.   JOURNAL OF INFECTIOUS DISEASES

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

Use of Whole Genome Sequencing to Determine the Microevolution of Mycobacterium tuberculosis during an Outbreak

(2013) Midori Kato-Maeda et al.   PLoS One

Control of (Multi)Drug Resistance and Tuberculosis Incidence over 23 Years in the Context of a Well-Supported Tuberculosis Programme in Rural Malawi

(2013) Sebastian M. Mboma et al.   PLoS One

Clade-Specific Virulence Patterns of Mycobacterium tuberculosis Complex Strains in Human Primary Macrophages and Aerogenically Infected Mice

(2013) N. Reiling et al.   mBio

SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences

(2012) Francesc Coll et al.   BIOINFORMATICS

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

Epidemiologic Consequences of Microvariation in Mycobacterium tuberculosis

(2012) Barun Mathema 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

Host-pathogen coevolution in human tuberculosis

(2012) S. Gagneux   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ethnicity and mycobacterial lineage as determinants of tuberculosis disease phenotype

(2012) Manish Pareek et al.   THORAX

Relationship Between Mycobacterium tuberculosis Phylogenetic Lineage and Clinical Site of Tuberculosis

(2011) E. S. Click et al.   CLINICAL INFECTIOUS DISEASES

Human Macrophage Responses to Clinical Isolates from the Mycobacterium tuberculosis Complex Discriminate between Ancient and Modern Lineages

(2011) Damien Portevin et al.   PLoS Pathogens

Reconstructing disease outbreaks from genetic data: a graph approach

(2010) T Jombart et al.   HEREDITY

Molecular Detection of Mixed Infections ofMycobacterium tuberculosisStrains in Sputum Samples from Patients in Karonga District, Malawi

(2010) Kim Mallard et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Possible underlying mechanisms for successful emergence of the Mycobacterium tuberculosis Beijing genotype strains

(2010) Ida Parwati et al.   LANCET INFECTIOUS DISEASES

Changes in Mycobacterium tuberculosis Genotype Families Over 20 Years in a Population-Based Study in Northern Malawi

(2010) Judith R. Glynn et al.   PLoS One

Functional Genetic Diversity among Mycobacterium tuberculosis Complex Clinical Isolates: Delineation of Conserved Core and Lineage-Specific Transcriptomes during Intracellular Survival

(2010) Susanne Homolka et al.   PLoS Pathogens

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Major Mycobacterium tuberculosis Lineages Associate with Patient Country of Origin

(2009) M. B. Reed et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Genotyping of Genetically Monomorphic Bacteria: DNA Sequencing in Mycobacterium tuberculosis Highlights the Limitations of Current Methodologies

(2009) Iñaki Comas et al.   PLoS One

HIV and the risk of tuberculosis due to recent transmission over 12 years in Karonga District, Malawi

(2009) Rein M.G.J. Houben et al.   TRANSACTIONS OF THE ROYAL SOCIETY OF TROPICAL MEDICINE AND HYGIENE

Relationship between Mycobacterium tuberculosis Genotype and the Clinical Phenotype of Pulmonary and Meningeal Tuberculosis

(2008) G. Thwaites et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Progression to Active Tuberculosis, but Not Transmission, Varies byMycobacterium tuberculosisLineage in The Gambia

(2008) Bouke C. de Jong et al.   JOURNAL OF INFECTIOUS DISEASES

Genomic interrogation of ancestral Mycobacterium tuberculosis from south India

(2007) Sujatha Narayanan et al.   INFECTION GENETICS AND EVOLUTION