Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions

When are pathogen genome sequences informative of transmission events?

(2018) Finlay Campbell et al.   PLoS Pathogens

Transmission of multidrug-resistant Mycobacterium tuberculosis in Shanghai, China: a retrospective observational study using whole-genome sequencing and epidemiological investigation

(2017) Chongguang Yang et al.   LANCET INFECTIOUS DISEASES

Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review

(2016) Hollie-Ann Hatherell et al.   BMC Medicine

Whole genome analysis of Mycobacterium tuberculosis isolates from recurrent episodes of tuberculosis, Finland, 1995–2013

(2016) V. Korhonen et al.   CLINICAL MICROBIOLOGY AND INFECTION

Substantial molecular evolution and mutation rates in prolonged latent Mycobacterium tuberculosis infection in humans

(2016) Troels Lillebaek et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Monitoring the spread of meticillin-resistant Staphylococcus aureus in The Netherlands from a reference laboratory perspective

(2016) T. Donker et al.   JOURNAL OF HOSPITAL INFECTION

Genomic Epidemiology of Methicillin-Resistant Staphylococcus aureus in a Neonatal Intensive Care Unit

(2016) Taj Azarian et al.   PLoS One

Using genomics data to reconstruct transmission trees during disease outbreaks

(2016) M.D. HALL et al.   REVUE SCIENTIFIQUE ET TECHNIQUE-OFFICE INTERNATIONAL DES EPIZOOTIES

Whole Genome Sequence Analysis of a Large Isoniazid-Resistant Tuberculosis Outbreak in London: A Retrospective Observational Study

(2016) Nicola Casali et al.   PLOS MEDICINE

Delineating Community Outbreaks of Salmonella enterica Serovar Typhimurium by Use of Whole-Genome Sequencing: Insights into Genomic Variability within an Outbreak

(2015) Sophie Octavia et al.   JOURNAL OF CLINICAL MICROBIOLOGY

PhyResSE: a Web Tool Delineating Mycobacterium tuberculosis Antibiotic Resistance and Lineage from Whole-Genome Sequencing Data

(2015) Silke Feuerriegel et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Reemergence and Amplification of Tuberculosis in the Canadian Arctic

(2015) Robyn S. Lee et al.   JOURNAL OF INFECTIOUS DISEASES

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

Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis

(2015) Phelim Bradley et al.   Nature Communications

Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set

(2015) Matthew Hall et al.   PLoS Computational Biology

Recurrence due to Relapse or Reinfection WithMycobacterium tuberculosis: A Whole-Genome Sequencing Approach in a Large, Population-Based Cohort With a High HIV Infection Prevalence and Active Follow-up

(2014) José Afonso Guerra-Assunção et al.   JOURNAL OF INFECTIOUS DISEASES

Bayesian Inference of Infectious Disease Transmission from Whole-Genome Sequence Data

(2014) Xavier Didelot et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2014) Nicola Casali et al.   NATURE GENETICS

Whole Genome Sequencing of Mycobacterium tuberculosis Reveals Slow Growth and Low Mutation Rates during Latent Infections in Humans

(2014) Roberto Colangeli et al.   PLoS One

Omics approaches in food safety: fulfilling the promise?

(2014) Teresa M. Bergholz et al.   TRENDS IN MICROBIOLOGY

Within-Host Bacterial Diversity Hinders Accurate Reconstruction of Transmission Networks from Genomic Distance Data

(2014) Colin J. Worby et al.   PLoS Computational Biology

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

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

Genome dynamics during experimental evolution

(2013) Jeffrey E. Barrick et al.   NATURE REVIEWS GENETICS

Finding Evidence for Local Transmission of Contagious Disease in Molecular Epidemiological Datasets

(2013) Rolf J. F. Ypma et al.   PLoS One

Elucidating Emergence and Transmission of Multidrug-Resistant Tuberculosis in Treatment Experienced Patients by Whole Genome Sequencing

(2013) Taane G. Clark et al.   PLoS One

Evolutionary Dynamics of Vibrio cholerae O1 following a Single-Source Introduction to Haiti

(2013) L. S. Katz et al.   mBio

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

Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: a retrospective observational study

(2013) Josephine M Bryant et al.   Lancet Respiratory Medicine

Using statistical methods and genotyping to detect tuberculosis outbreaks

(2013) J Steve Kammerer et al.   International Journal of Health Geographics

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

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

Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection

(2011) Christopher B Ford et al.   NATURE GENETICS

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria

(2009) Chih-Horng Kuo et al.   Biology Direct

Resolving the impact of waiting time distributions on the persistence of measles

(2009) A. J. K. Conlan et al.   Journal of the Royal Society Interface