Within-host evolution of bacterial pathogens

Identification of antimicrobial resistance genes in multidrug-resistant clinical Bacteroides fragilis isolates by whole genome shotgun sequencing

(2015) Thomas Vognbjerg Sydenham et al.   ANAEROBE

Klebsiella pneumoniae Carbapenemase (KPC)-Producing K. pneumoniae at a Single Institution: Insights into Endemicity from Whole-Genome Sequencing

(2015) Amy J. Mathers et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The application of genomics to tracing bacterial pathogen transmission

(2015) Nicholas J Croucher et al.   CURRENT OPINION IN MICROBIOLOGY

Within-host diversity of MRSA antimicrobial resistances

(2015) Kinga I. Stanczak-Mrozek et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Whole-genome sequencing improves discrimination of relapse from reinfection and identifies transmission events among patients with recurrent Clostridium difficile infections

(2015) M. Mac Aogáin et al.   JOURNAL OF HOSPITAL INFECTION

Long-term social dynamics drive loss of function in pathogenic bacteria

(2015) Sandra Breum Andersen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Measurably evolving pathogens in the genomic era

(2015) Roman Biek et al.   TRENDS IN ECOLOGY & EVOLUTION

Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission

(2015) Gavin K. Paterson et al.   Nature Communications

Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis

(2015) Lucy A. Weinert et al.   Nature Communications

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

(2015) Xavier Didelot et al.   PLoS Computational Biology

Genome Sequencing of an Extended Series of NDM-Producing Klebsiella pneumoniae Isolates from Neonatal Infections in a Nepali Hospital Characterizes the Extent of Community- versus Hospital-Associated Transmission in an Endemic Setting

(2014) N. Stoesser et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

In VivoEvolution to Colistin Resistance by PmrB Sensor Kinase Mutation in KPC-Producing Klebsiella pneumoniae Is Associated with Low-Dosage Colistin Treatment

(2014) Antonio Cannatelli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

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

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

Progressive genomic convergence of twoHelicobacter pyloristrains during mixed infection of a patient with chronic gastritis

(2014) Qizhi Cao et al.   GUT

Phase Variation Mediates Reductions in Expression of Surface Proteins during Persistent Meningococcal Carriage

(2014) M. Alamro et al.   INFECTION AND IMMUNITY

Bidirectional genomic exchange between Helicobacter pylori strains from a family in Coventry, United Kingdom

(2014) Juliane Krebes et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Prediction of Staphylococcus aureus Antimicrobial Resistance by Whole-Genome Sequencing

(2014) N. C. Gordon et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Multiple-Strain Colonization in Nasal Carriers of Staphylococcus aureus

(2014) A. A. Votintseva et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis

(2014) Rasmus Lykke Marvig et al.   NATURE GENETICS

Targeting virulence: can we make evolution-proof drugs?

(2014) Richard C. Allen et al.   NATURE REVIEWS MICROBIOLOGY

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

(2014) Nicholas J. Croucher et al.   NUCLEIC ACIDS RESEARCH

Human and Helicobacter pylori coevolution shapes the risk of gastric disease

(2014) N. Kodaman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Alternating antibiotic treatments constrain evolutionary paths to multidrug resistance

(2014) Seungsoo Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Virulence and Pathogenesis of HIV-1 Infection: An Evolutionary Perspective

(2014) C. Fraser et al.   SCIENCE

The changing face of the molecular evolutionary clock

(2014) Simon Y.W. Ho   TRENDS IN ECOLOGY & EVOLUTION

Environmental Heterogeneity Drives Within-Host Diversification and Evolution of Pseudomonas aeruginosa

(2014) T. Markussen et al.   mBio

Within-Host Evolution of Pseudomonas aeruginosa Reveals Adaptation toward Iron Acquisition from Hemoglobin

(2014) R. L. Marvig et al.   mBio

Novel Determinants of Antibiotic Resistance: Identification of Mutated Loci in Highly Methicillin-Resistant Subpopulations of Methicillin-Resistant Staphylococcus aureus

(2014) J. Dordel et al.   mBio

A mutation burst during the acute phase of Helicobacter pylori infection in humans and rhesus macaques

(2014) Bodo Linz et al.   Nature Communications

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

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

Coexistence and Within-Host Evolution of Diversified Lineages of Hypermutable Pseudomonas aeruginosa in Long-term Cystic Fibrosis Infections

(2014) Sofía Feliziani et al.   PLoS Genetics

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

Relating Phylogenetic Trees to Transmission Trees of Infectious Disease Outbreaks

(2013) Rolf J. F. Ypma et al.   GENETICS

Evolutionary History of the Clostridium difficile Pathogenicity Locus

(2013) Kate E. Dingle et al.   Genome Biology and Evolution

Novel mutations in penicillin-binding protein genes in clinical Staphylococcus aureus isolates that are methicillin resistant on susceptibility testing, but lack the mec gene

(2013) X. Ba et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

In vivo evolution of antimicrobial resistance in a series of Staphylococcus aureus patient isolates: the entire picture or a cautionary tale?

(2013) S. J. van Hal et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Whole-Genome Sequencing Demonstrates That Fidaxomicin Is Superior to Vancomycin for Preventing Reinfection and Relapse of Infection With Clostridium difficile

(2013) David W. Eyre et al.   JOURNAL OF INFECTIOUS DISEASES

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

Population genomics of post-vaccine changes in pneumococcal epidemiology

(2013) Nicholas J Croucher et al.   NATURE GENETICS

Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures

(2013) Tami D Lieberman 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

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

Understanding, predicting and manipulating the genotypic evolution of antibiotic resistance

(2013) Adam C. Palmer et al.   NATURE REVIEWS GENETICS

Sequence assembly demystified

(2013) Niranjan Nagarajan et al.   NATURE REVIEWS GENETICS

Adhesion, invasion and evasion: the many functions of the surface proteins of Staphylococcus aureus

(2013) Timothy J. Foster et al.   NATURE REVIEWS MICROBIOLOGY

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

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

Whole Genome Sequence Analysis of the First Australian OXA-48-Producing Outbreak-Associated Klebsiella pneumoniae Isolates: The Resistome and In Vivo Evolution

(2013) Björn A. Espedido et al.   PLoS One

Within-Host Evolution of Staphylococcus aureus during Asymptomatic Carriage

(2013) Tanya Golubchik et al.   PLoS One

Evolutionary remodeling of global regulatory networks during long-term bacterial adaptation to human hosts

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

Genomic evolution and transmission ofHelicobacter pyloriin two South African families

(2013) Xavier Didelot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection of Mixed Infection from Bacterial Whole Genome Sequence Data Allows Assessment of Its Role in Clostridium difficile Transmission

(2013) David W. Eyre et al.   PLoS Computational Biology

Genome Analysis of a Transmissible Lineage of Pseudomonas aeruginosa Reveals Pathoadaptive Mutations and Distinct Evolutionary Paths of Hypermutators

(2013) Rasmus Lykke Marvig et al.   PLoS Genetics

Rapid Bacterial Whole-Genome Sequencing to Enhance Diagnostic and Public Health Microbiology

(2013) Sandra Reuter et al.   JAMA Internal 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

Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli

(2012) Xavier Didelot et al.   BMC GENOMICS

High-Resolution Single Nucleotide Polymorphism Analysis Distinguishes Recrudescence and Reinfection in Recurrent Invasive Nontyphoidal Salmonella Typhimurium Disease

(2012) Chinyere K. Okoro et al.   CLINICAL INFECTIOUS DISEASES

Deletion and acquisition of genomic content during early stage adaptation of Pseudomonas aeruginosa to a human host environment

(2012) Martin H. Rau et al.   ENVIRONMENTAL MICROBIOLOGY

The WalKR System Controls Major Staphylococcal Virulence Genes and Is Involved in Triggering the Host Inflammatory Response

(2012) Aurélia Delauné et al.   INFECTION AND IMMUNITY

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

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

Progressive genome-wide introgression in agriculturalCampylobacter coli

(2012) Samuel K. Sheppard et al.   MOLECULAR ECOLOGY

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

Emergence and global spread of epidemic healthcare-associated Clostridium difficile

(2012) Miao He et al.   NATURE GENETICS

Transforming clinical microbiology with bacterial genome sequencing

(2012) Xavier Didelot et al.   NATURE REVIEWS GENETICS

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

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

Whole Genome Characterization of the Mechanisms of Daptomycin Resistance in Clinical and Laboratory Derived Isolates of Staphylococcus aureus

(2012) Anton Y. Peleg et al.   PLoS One

Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease

(2012) B. C. Young 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

On the evolution of virulence duringStaphylococcus aureusnasal carriage

(2012) Bernadette C. Young et al.   Virulence

A pilot study of rapid benchtop sequencing ofStaphylococcus aureusandClostridium difficilefor outbreak detection and surveillance

(2012) David W Eyre et al.   BMJ Open

Insights from Genomics into Bacterial Pathogen Populations

(2012) Daniel J. Wilson   PLoS Pathogens

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

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

Microevolutionary analysis of Clostridium difficile genomes to investigate transmission

(2012) Xavier Didelot et al.   GENOME BIOLOGY

Deep resequencing of serial sputum isolates of Mycobacterium tuberculosis during therapeutic failure due to poor compliance reveals stepwise mutation of key resistance genes on an otherwise stable genetic background

(2011) Nigel J. Saunders et al.   JOURNAL OF INFECTION

Parallel evolution and local differentiation in quinolone resistance in Pseudomonas aeruginosa

(2011) A. Wong et al.   MICROBIOLOGY-SGM

Identification of the in vitro target of an iron-responsive AraC-like protein from Neisseria meningitidis that is in a regulatory cascade with Fur

(2011) L. Fantappie et al.   MICROBIOLOGY-SGM

Time-dependent rates of molecular evolution

(2011) SIMON Y. W. HO et al.   MOLECULAR ECOLOGY

Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes

(2011) Tami D Lieberman et al.   NATURE GENETICS

Evolutionary paths to antibiotic resistance under dynamically sustained drug selection

(2011) Erdal Toprak et al.   NATURE GENETICS

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

Genetic Basis for In Vivo Daptomycin Resistance in Enterococci

(2011) Cesar A. Arias 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

Rates of Mutation and Host Transmission for an Escherichia coli Clone over 3 Years

(2011) Peter R. Reeves et al.   PLoS One

Helicobacter pylori genome evolution during human infection

(2011) L. Kennemann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary dynamics of bacteria in a human host environment

(2011) L. Yang 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

Control of bacterial virulence by AraC-like regulators that respond to chemical signals

(2011) Ji Yang et al.   TRENDS IN MICROBIOLOGY

Evolution of Multidrug Resistance during Staphylococcus aureus Infection Involves Mutation of the Essential Two Component Regulator WalKR

(2011) Benjamin P. Howden et al.   PLoS Pathogens

What traits are carried on mobile genetic elements and why?

(2010) D J Rankin et al.   HEREDITY

Simultaneous carriage of multiple genotypes of Staphylococcus aureus in children

(2010) K. Mongkolrattanothai et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Microevolution of Helicobacter pylori during Prolonged Infection of Single Hosts and within Families

(2010) Giovanna Morelli et al.   PLoS Genetics

Two Novel Point Mutations in Clinical Staphylococcus aureus Reduce Linezolid Susceptibility and Switch on the Stringent Response to Promote Persistent Infection

(2010) Wei Gao et al.   PLoS Pathogens

Host Imprints on Bacterial Genomes—Rapid, Divergent Evolution in Individual Patients

(2010) Jaroslaw Zdziarski et al.   PLoS Pathogens

The consequences of genetic drift for bacterial genome complexity

(2009) C.-H. Kuo et al.   GENOME RESEARCH

Genome evolution and adaptation in a long-term experiment with Escherichia coli

(2009) Jeffrey E. Barrick et al.   NATURE

A replication clock for Mycobacterium tuberculosis

(2009) Wendy P Gill et al.   NATURE MEDICINE

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

Evolutionary analysis of the dynamics of viral infectious disease

(2009) Oliver G. Pybus et al.   NATURE REVIEWS GENETICS

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Virulence evolution and the trade-off hypothesis: history, current state of affairs and the future

(2008) S. ALIZON et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Rapid Evolution and the Importance of Recombination to the Gastroenteric Pathogen Campylobacter jejuni

(2008) D. J. Wilson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Horizontal versus Familial Transmission of Helicobacter pylori

(2008) Sandra Schwarz et al.   PLoS Pathogens