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

After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection

(2012) A. Namouchi et al.   GENOME RESEARCH

Microevolution of extensively drug-resistant tuberculosis in Russia

(2012) N. Casali et al.   GENOME RESEARCH

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

Transforming clinical microbiology with bacterial genome sequencing

(2012) Xavier Didelot et al.   NATURE REVIEWS GENETICS

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

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

First Worldwide Proficiency Study on Variable-Number Tandem-Repeat Typing of Mycobacterium tuberculosis Complex Strains

(2011) J. L. de Beer et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Evidence for several waves of global transmission in the seventh cholera pandemic

(2011) Ankur Mutreja et al.   NATURE

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

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

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

Mycobacterium tuberculosis Lineage Influences Innate Immune Response and Virulence and Is Associated with Distinct Cell Envelope Lipid Profiles

(2011) Nitya Krishnan et al.   PLoS One

Rapid Pneumococcal Evolution in Response to Clinical Interventions

(2011) N. J. Croucher et al.   SCIENCE

High-Resolution Typing by Integration of Genome Sequencing Data in a Large Tuberculosis Cluster

(2010) A. C. Schurch et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The tempo and mode of molecular evolution of Mycobacterium tuberculosis at patient-to-patient scale

(2009) Anita C. Schürch et al.   INFECTION GENETICS AND EVOLUTION

Genomic Diversity among Drug Sensitive and Multidrug Resistant Isolates of Mycobacterium tuberculosis with Identical DNA Fingerprints

(2009) Stefan Niemann et al.   PLoS One