Genomic perspectives on the evolution and spread of bacterial pathogens

Ten years of pan-genome analyses

(2015) George Vernikos et al.   CURRENT OPINION IN MICROBIOLOGY

Time-Scaled Evolutionary Analysis of the Transmission and Antibiotic Resistance Dynamics of Staphylococcus aureus Clonal Complex 398

(2014) M. J. Ward et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Variable recombination dynamics during the emergence, transmission and ‘disarming’ of a multidrug-resistant pneumococcal clone

(2014) Nicholas J Croucher et al.   BMC BIOLOGY

An Outbreak of Respiratory Tularemia Caused by Diverse Clones of Francisella tularensis

(2014) Anders Johansson et al.   CLINICAL INFECTIOUS DISEASES

Evidence for Soft Selective Sweeps in the Evolution of Pneumococcal Multidrug Resistance and Vaccine Escape

(2014) Nicholas J. Croucher et al.   Genome Biology and Evolution

Genome sequencing defines phylogeny and spread of methicillin-resistantStaphylococcus aureusin a high transmission setting

(2014) Steven Y.C. Tong et al.   GENOME RESEARCH

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

Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis

(2014) Kirsten I. Bos et al.   NATURE

MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island

(2014) Philip M Ashton et al.   NATURE BIOTECHNOLOGY

Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution

(2014) Astrid von Mentzer et al.   NATURE GENETICS

Epistasis and Allele Specificity in the Emergence of a Stable Polymorphism in Escherichia coli

(2014) J. Plucain et al.   SCIENCE

Phylodynamic Analysis of Clinical and Environmental Vibrio cholerae Isolates from Haiti Reveals Diversification Driven by Positive Selection

(2014) Taj Azarian et al.   mBio

Genomic Epidemiology of the Haitian Cholera Outbreak: a Single Introduction Followed by Rapid, Extensive, and Continued Spread Characterized the Onset of the Epidemic

(2014) Mark Eppinger et al.   mBio

A random six-phase switch regulates pneumococcal virulence via global epigenetic changes

(2014) Ana Sousa Manso et al.   Nature Communications

Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant Acinetobacter baumanniiin Birmingham, England

(2014) Mihail R Halachev et al.   Genome Medicine

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

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

Comprehensive Identification of Single Nucleotide Polymorphisms Associated with Beta-lactam Resistance within Pneumococcal Mosaic Genes

(2014) Claire Chewapreecha et al.   PLoS Genetics

A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic

(2013) M. T. G. Holden et al.   GENOME RESEARCH

Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study

(2013) Josephine M Bryant et al.   LANCET

Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans

(2013) Iñaki Comas et al.   NATURE GENETICS

Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis

(2013) Maha R Farhat et al.   NATURE GENETICS

Diverse Sources of C. difficile Infection Identified on Whole-Genome Sequencing

(2013) David W. Eyre et al.   NEW ENGLAND JOURNAL OF MEDICINE

Within-Host Evolution of Staphylococcus aureus during Asymptomatic Carriage

(2013) Tanya Golubchik et al.   PLoS One

Evolutionary genomics of epidemic and nonepidemic strains of Pseudomonas aeruginosa

(2013) J. R. Dettman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter

(2013) S. K. Sheppard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative Genomics of Recent Shiga Toxin-Producing Escherichia coli O104:H4: Short-Term Evolution of an Emerging Pathogen

(2013) Y. H. Grad et al.   mBio

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

(2013) L. S. Katz et al.   mBio

Dominant Role of Nucleotide Substitution in the Diversification of Serotype 3 Pneumococci over Decades and during a Single Infection

(2013) Nicholas J. Croucher et al.   PLoS Genetics

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

Nepalese origin of cholera epidemic in Haiti

(2012) R.R. Frerichs et al.   CLINICAL MICROBIOLOGY AND INFECTION

Pseudomonas aeruginosa population structure revisited under environmental focus: impact of water quality and phage pressure

(2012) Katherina Selezska et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study

(2012) Simon R Harris et al.   LANCET INFECTIOUS DISEASES

Transforming clinical microbiology with bacterial genome sequencing

(2012) Xavier Didelot et al.   NATURE REVIEWS GENETICS

Molecular tracing of the emergence, adaptation, and transmission of hospital-associated methicillin-resistant Staphylococcus aureus

(2012) P. R. McAdam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tracking a Hospital Outbreak of Carbapenem-Resistant Klebsiella pneumoniae with Whole-Genome Sequencing

(2012) E. S. Snitkin et al.   Science Translational Medicine

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

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

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

(2011) Ankur Mutreja et al.   NATURE

Identification of a Salmonellosis Outbreak by Means of Molecular Sequencing

(2011) E. Kurt Lienau et al.   NEW ENGLAND JOURNAL OF MEDICINE

Open-Source Genomic Analysis of Shiga-Toxin–ProducingE. coliO104:H4

(2011) Holger Rohde et al.   NEW ENGLAND JOURNAL OF MEDICINE

Epidemic Profile of Shiga-Toxin–ProducingEscherichia coliO104:H4 Outbreak in Germany

(2011) Christina Frank et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

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

Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation

(2011) D. A. Rasko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid Pneumococcal Evolution in Response to Clinical Interventions

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

Population Genetics of Vibrio cholerae from Nepal in 2010: Evidence on the Origin of the Haitian Outbreak

(2011) R. S. Hendriksen et al.   mBio

Burkholderia cenocepacia in cystic fibrosis: epidemiology and molecular mechanisms of virulence

(2010) P. Drevinek et al.   CLINICAL MICROBIOLOGY AND INFECTION

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

A Recalibrated Molecular Clock and Independent Origins for the Cholera Pandemic Clones

(2008) Lu Feng et al.   PLoS One