Related references
Note: Only part of the references are listed.Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus
Henrique Machado et al.
COMMUNICATIONS BIOLOGY (2021)
Polyclonality, Shared Strains, and Convergent Evolution in Chronic Cystic Fibrosis Staphylococcus aureus Airway Infection
Dustin R. Long et al.
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE (2021)
YjbH regulates virulence genes expression and oxidative stress resistance in Staphylococcus aureus
Atmika Paudel et al.
VIRULENCE (2021)
Clinically relevant mutations in core metabolic genes confer antibiotic resistance
Allison J. Lopatkin et al.
SCIENCE (2021)
Distinct clonal lineages and within-host diversification shape invasive Staphylococcus epidermidis populations
Anna Both et al.
PLOS PATHOGENS (2021)
In-host population dynamics of Mycobacterium tuberculosis complex during active disease
Roger Vargas et al.
ELIFE (2021)
Stepwise pathogenic evolution of Mycobacterium abscessus
Josephine M. Bryant et al.
SCIENCE (2021)
Rapid evolution and host immunity drive the rise and fall of carbapenem resistance during an acute Pseudomonas aeruginosa infection
Rachel Wheatley et al.
NATURE COMMUNICATIONS (2021)
Common Adaptive Strategies Underlie Within-Host Evolution of Bacterial Pathogens
Yair E. Gatt et al.
MOLECULAR BIOLOGY AND EVOLUTION (2021)
Distinct Subpopulations of Intravalvular Methicillin-Resistant Staphylococcus aureus with Variable Susceptibility to Daptomycin in Tricuspid Valve Endocarditis
Christopher R. Miller et al.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2020)
De Novo Purine Biosynthesis Is Required for Intracellular Growth of Staphylococcus aureus and for the Hypervirulence Phenotype of a purR Mutant
Mariya Goncheva et al.
INFECTION AND IMMUNITY (2020)
Effect of Vancomycin or Daptomycin With vs Without an Antistaphylococcal β-Lactam on Mortality, Bacteremia, Relapse, or Treatment Failure in Patients With MRSA Bacteremia A Randomized Clinical Trial
Steven Y. C. Tong et al.
JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION (2020)
When antibiotics fail: a clinical and microbiological perspective on antibiotic tolerance and persistence of Staphylococcus aureus
Richard Kuehl et al.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY (2020)
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
Bui Quang Minh et al.
MOLECULAR BIOLOGY AND EVOLUTION (2020)
Safety of bacteriophage therapy in severe Staphylococcus aureus infection
Aleksandra Petrovic Fabijan et al.
NATURE MICROBIOLOGY (2020)
Evolution of vancomycin-resistant Enterococcus faecium during colonization and infection in immunocompromised pediatric patients
Gayatri Shankar Chilambi et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)
Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity
Patrick Phaneuf et al.
BMC GENOMICS (2020)
Within-host microevolution of Streptococcus pneumoniae is rapid and adaptive during natural colonisation
Chrispin Chaguza et al.
NATURE COMMUNICATIONS (2020)
Impact of insertion sequences on convergent evolution of Shigella species
Jane Hawkey et al.
PLOS GENETICS (2020)
Acapsular Staphylococcus aureus with a non-functional agr regains capsule expression after passage through the bloodstream in a bacteremia mouse model
Carlos M. Suligoy et al.
SCIENTIFIC REPORTS (2020)
Comprehensive Genomic Investigation of Adaptive Mutations Driving the Low-Level Oxacillin Resistance Phenotype in Staphylococcus aureus
Stefano G. Giulieri et al.
MBIO (2020)
Effect of tolerance on the evolution of antibiotic resistance under drug combinations
Jiafeng Liu et al.
SCIENCE (2020)
Chronic Staphylococcus aureus Lung Infection Correlates With Proteogenomic and Metabolic Adaptations Leading to an Increased Intracellular Persistence
Xin Tan et al.
CLINICAL INFECTIOUS DISEASES (2019)
Contribution of YjbIH to Virulence Factor Expression and Host Colonization in Staphylococcus aureus
Crystal M. Austin et al.
INFECTION AND IMMUNITY (2019)
Genomic characterization of inpatient evolution of MRSA resistant to daptomycin, vancomycin and ceftaroline
Daniel Wuthrich et al.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY (2019)
Stress-induced inactivation of the Staphylococcus aureus purine biosynthesis repressor leads to hypervirulence
Mariya Goncheva et al.
NATURE COMMUNICATIONS (2019)
Within-Host Adaptation Mediated by Intergenic Evolution in Pseudomonas aeruginosa
S. M. Hossein Khademi et al.
GENOME BIOLOGY AND EVOLUTION (2019)
Impact of antibiotic treatment and host innate immune pressure on enterococcal adaptation in the human bloodstream
Darla Van Tyne et al.
SCIENCE TRANSLATIONAL MEDICINE (2019)
MprF-mediated daptomycin resistance
Christoph M. Ernst et al.
INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY (2019)
Epistasis between antibiotic tolerance, persistence, and resistance mutations
Irit Levin-Reisman et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)
The purine biosynthesis regulator PurR moonlights as a virulence regulator in Staphylococcus aureus
William E. Sause et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)
Zinc-binding to the cytoplasmic PAS domain regulates the essential WalK histidine kinase of Staphylococcus aureus
Ian R. Monk et al.
NATURE COMMUNICATIONS (2019)
Long-Term Intrahost Evolution of Methicillin Resistant Staphylococcus aureus Among Cystic Fibrosis Patients With Respiratory Carriage
Taj Azarian et al.
FRONTIERS IN GENETICS (2019)
Immunity to Staphylococcus aureus: Implication for Vaccine Development
Richard A. Proctor
MICROBIOLOGY SPECTRUM (2019)
Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates
Michael Feldgarden et al.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2019)
Unstable chromosome rearrangements in Staphylococcus aureus cause phenotype switching associated with persistent infections
Romain Guerillot et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)
IS256-Mediated Overexpression of the WalKR Two-Component System Regulon Contributes to Reduced Vancomycin Susceptibility in a Staphylococcus aureus Clinical Isolate
Makoto Kuroda et al.
FRONTIERS IN MICROBIOLOGY (2019)
Improved characterisation of MRSA transmission using within-host bacterial sequence diversity
Matthew D. Hall et al.
ELIFE (2019)
Staphylococcus aureus Small Colony Variants (SCVs): News From a Chronic Prosthetic Joint Infection
Guilherme Loss et al.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY (2019)
Evolution of Daptomycin Resistance in Coagulase-Negative Staphylococci Involves Mutations of the Essential Two-Component Regulator WalKR
Jhih-Hang Jiang et al.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2019)
In-Host Evolution of Daptomycin Resistance and Heteroresistance in Methicillin-Resistant Staphylococcus aureus Strains From Three Endocarditis Patients
Shujuan Ji et al.
JOURNAL OF INFECTIOUS DISEASES (2019)
Improved metagenomic analysis with Kraken 2
Derrick E. Wood et al.
GENOME BIOLOGY (2019)
AureoWiki-The repository of the Staphylococcus aureus research and annotation community
Stephan Fuchs et al.
INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY (2018)
PBP4 activity and its overexpression are necessary for PBP4-mediated high-level beta-lactam resistance
Li Basuino et al.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY (2018)
The Microevolution and Epidemiology of Staphylococcus aureus Colonization during Atopic Eczema Disease Flare
Catriona P. Harkins et al.
JOURNAL OF INVESTIGATIVE DERMATOLOGY (2018)
PANNZER2: a rapid functional annotation web server
Petri Toronen et al.
NUCLEIC ACIDS RESEARCH (2018)
Genomic evolution of Staphylococcus aureus isolates colonizing the nares and progressing to bacteremia
Jeanne B. Benoit et al.
PLOS ONE (2018)
Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica
Nicole E. Wheeler et al.
PLOS GENETICS (2018)
Mutation of Agr Is Associated with the Adaptation of Staphylococcus aureus to the Host during Chronic Osteomyelitis
Carlos M. Suligoy et al.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY (2018)
Convergent Evolution Driven by Rifampin Exacerbates the Global Burden of Drug-Resistant &ITStaphylococcus aureus&IT
Romain Guerillot et al.
MSPHERE (2018)
Genome Plasticity of agr-Defective Staphylococcus aureus during Clinical Infection
Deena R. Altman et al.
INFECTION AND IMMUNITY (2018)
Azithromycin Resistance through Interspecific Acquisition of an Epistasis-Dependent Efflux Pump Component and Transcriptional Regulator in Neisseria gonorrhoeae
Crista B. Wadsworth et al.
MBIO (2018)
Inactivation of TCA cycle enhances Staphylococcus aureus persister cell formation in stationary phase
Ying Wang et al.
SCIENTIFIC REPORTS (2018)
Genomic exploration of sequential clinical isolates reveals a distinctive molecular signature of persistent Staphylococcus aureus bacteraemia
Stefano G. Giulieri et al.
GENOME MEDICINE (2018)
Comprehensive antibiotic-linked mutation assessment by resistance mutation sequencing (RM-seq)
Romain Guerillot et al.
GENOME MEDICINE (2018)
Emergence and Within-Host Genetic Evolution of Methicillin-Resistant Staphylococcus aureus Resistant to Linezolid in a Cystic Fibrosis Patient
Caroline Rouard et al.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2018)
In vivo competition and horizontal gene transfer among distinct Staphylococcus aureus lineages as major drivers for adaptational changes during long-term persistence in humans
Lars Langhanki et al.
BMC MICROBIOLOGY (2018)
Epistasis analysis uncovers hidden antibiotic resistance-associated fitness costs hampering the evolution of MRSA
Maho Yokoyama et al.
GENOME BIOLOGY (2018)
What drives parallel evolution? How population size and mutational variation contribute to repeated evolution
Susan F. Bailey et al.
BIOESSAYS (2017)
Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution
Christopher Abbosh et al.
NATURE (2017)
The commensal lifestyle of Staphylococcus aureus and its interactions with the nasal microbiota
Bernhard Krismer et al.
NATURE REVIEWS MICROBIOLOGY (2017)
Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis
Marcin J. Skwark et al.
PLOS GENETICS (2017)
Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration
John A. Lees et al.
ELIFE (2017)
Severe infections emerge from commensal bacteria by adaptive evolution
Bernadette C. Young et al.
ELIFE (2017)
PaperBLAST: Text Mining Papers for Information about Homologs
Morgan N. Price et al.
MSYSTEMS (2017)
Universal Patterns of Selection in Cancer and Somatic Tissues
Inigo Martincorena et al.
CELL (2017)
Large scale genomic analysis shows no evidence for pathogen adaptation between the blood and cerebrospinal fluid niches during bacterial meningitis
John A. Lees et al.
MICROBIAL GENOMICS (2017)
TSS-EMOTE, a refined protocol for a more complete and less biased global mapping of transcription start sites in bacterial pathogens
Julien Prados et al.
BMC GENOMICS (2016)
Adaptive processes of Staphylococcus aureus isolates during the progression from acute to chronic bone and joint infections in patients
Sophie Trouillet-Assant et al.
CELLULAR MICROBIOLOGY (2016)
Identification and treatment of the Staphylococcus aureus reservoir in vivo
Bas G. J. Surewaard et al.
JOURNAL OF EXPERIMENTAL MEDICINE (2016)
cooccur: Probabilistic Species Co-Occurrence Analysis inR
Daniel M. Griffith et al.
Journal of Statistical Software (2016)
Genomic diversity in autopsy samples reveals within-host dissemination of HIV-associated Mycobacterium tuberculosis
Tami D. Lieberman et al.
NATURE MEDICINE (2016)
Within-host evolution of bacterial pathogens
Xavier Didelot et al.
NATURE REVIEWS MICROBIOLOGY (2016)
Environmental fatty acids enable emergence of infectious Staphylococcus aureus resistant to FASII-targeted antimicrobials
Claire Morvan et al.
NATURE COMMUNICATIONS (2016)
Staphylococcus aureus Transcriptome Architecture: From Laboratory to Infection-Mimicking Conditions
Ulrike Maeder et al.
PLOS GENETICS (2016)
Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host
Elizabeth J. Klemm et al.
NATURE MICROBIOLOGY (2016)
Population Genomics of Reduced Vancomycin Susceptibility in Staphylococcus aureus
Lavanya Rishishwar et al.
MSPHERE (2016)
SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments
Andrew J. Page et al.
MICROBIAL GENOMICS (2016)
CNOGpro: detection and quantification of CNVs in prokaryotic whole-genome sequencing data
Ola Brynildsrud et al.
BIOINFORMATICS (2015)
Staphylococcus aureus Infections: Epidemiology, Pathophysiology, Clinical Manifestations, and Management
Steven Y. C. Tong et al.
CLINICAL MICROBIOLOGY REVIEWS (2015)
Complete Bypass of Restriction Systems for Major Staphylococcus aureus Lineages
Ian R. Monk et al.
MBIO (2015)
Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission
Gavin K. Paterson et al.
NATURE COMMUNICATIONS (2015)
Evolutionary Trade-Offs Underlie the Multifaceted Virulence of Staphylococcus aureus
Maisem Laabei et al.
PLOS BIOLOGY (2015)
Analysis of Bottlenecks in Experimental Models of Infection
Soeren Abel et al.
PLOS PATHOGENS (2015)
Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis
Rasmus Lykke Marvig et al.
NATURE GENETICS (2015)
Large tandem chromosome expansions facilitate niche adaptation during persistent infection with drug-resistant Staphylococcus aureus
Wei Gao et al.
MICROBIAL GENOMICS (2015)
Prokka: rapid prokaryotic genome annotation
Torsten Seemann
BIOINFORMATICS (2014)
Development of Oxacillin Resistance in a Patient with Recurrent Staphylococcus aureus Bacteremia
Eileen M. Burd et al.
JOURNAL OF CLINICAL MICROBIOLOGY (2014)
Reductive genome evolution at both ends of the bacterial population size spectrum
Berenice Batut et al.
NATURE REVIEWS MICROBIOLOGY (2014)
Clonal Expansion during Staphylococcus aureus Infection Dynamics Reveals the Effect of Antibiotic Intervention
Gareth McVicker et al.
PLOS PATHOGENS (2014)
Antibiotic-Induced Autoactivation of IS256 in Staphylococcus aureus
Franziska Schreiber et al.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2013)
Decreased Vancomycin Susceptibility in Staphylococcus aureus Caused by IS256 Tempering of WalKR Expression
Christopher R. E. McEvoy et al.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2013)
The RpoB H148Y Rifampicin Resistance Mutation and an Active Stringent Response Reduce Virulence and Increase Resistance to Innate Immune Responses in Staphylococcus aureus
Wei Gao et al.
JOURNAL OF INFECTIOUS DISEASES (2013)
Within-Host Evolution of Staphylococcus aureus during Asymptomatic Carriage
Tanya Golubchik et al.
PLOS ONE (2013)
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3
Pablo Cingolani et al.
FLY (2012)
The YjbH Adaptor Protein Enhances Proteolysis of the Transcriptional Regulator Spx in Staphylococcus aureus
Jakob Engman et al.
JOURNAL OF BACTERIOLOGY (2012)
Serine/Threonine Phosphatase Stp1 Contributes to Reduced Susceptibility to Vancomycin and Virulence in Staphylococcus aureus
David R. Cameron et al.
JOURNAL OF INFECTIOUS DISEASES (2012)
Nasal Carriage as a Source of agr-Defective Staphylococcus aureus Bacteremia
Davida S. Smyth et al.
JOURNAL OF INFECTIOUS DISEASES (2012)
Nutritional immunity: transition metals at the pathogen-host interface
M. Indriati Hood et al.
NATURE REVIEWS MICROBIOLOGY (2012)
clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters
Guangchuang Yu et al.
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY (2012)
Whole Genome Characterization of the Mechanisms of Daptomycin Resistance in Clinical and Laboratory Derived Isolates of Staphylococcus aureus
Anton Y. Peleg et al.
PLOS ONE (2012)
Predicting the Functional Effect of Amino Acid Substitutions and Indels
Yongwook Choi et al.
PLOS ONE (2012)
Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease
Bernadette C. Young et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
New Role of the Disulfide Stress Effector YjbH in β-Lactam Susceptibility of Staphylococcus aureus
Nadine Goehring et al.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2011)
Extraribosomal functions of bacterial ribosomal proteins
L. V. Aseev et al.
MOLECULAR BIOLOGY (2011)
Estimation of the Neutrality Index
Nina Stoletzki et al.
MOLECULAR BIOLOGY AND EVOLUTION (2011)
Are bloodstream leukocytes Trojan Horses for the metastasis of Staphylococcus aureus?
Guy E. Thwaites et al.
NATURE REVIEWS MICROBIOLOGY (2011)
Whole Genome Sequencing and Complete Genetic Analysis Reveals Novel Pathways to Glycopeptide Resistance in Staphylococcus aureus
Adriana Renzoni et al.
PLOS ONE (2011)
Helicobacter pylori genome evolution during human infection
Lynn Kennemann et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
Evolution of Multidrug Resistance during Staphylococcus aureus Infection Involves Mutation of the Essential Two Component Regulator WalKR
Benjamin P. Howden et al.
PLOS PATHOGENS (2011)
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan et al.
BIOINFORMATICS (2010)
Evolutionary microbial genomics: insights into bacterial host adaptation
Christina Toft et al.
NATURE REVIEWS GENETICS (2010)
MicrobesOnline: an integrated portal for comparative and functional genomics
Paramvir S. Dehal et al.
NUCLEIC ACIDS RESEARCH (2010)
EXPERIMENTAL EVOLUTION, LOSS-OF-FUNCTION MUTATIONS, AND THE FIRST RULE OF ADAPTIVE EVOLUTION
Michael J. Behe
QUARTERLY REVIEW OF BIOLOGY (2010)
Quorum Sensing in Staphylococci
Richard P. Novick et al.
ANNUAL REVIEW OF GENETICS (2008)
Prevalence of agr dysfunction among colonizing Staphylococcus aureus strains
Bo Shopsin et al.
JOURNAL OF INFECTIOUS DISEASES (2008)
Epistasis - the essential role of gene interactions in the structure and evolution of genetic systems
Patrick C. Phillips
NATURE REVIEWS GENETICS (2008)
Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer
Timothy P. Stinear et al.
GENOME RESEARCH (2007)
Isolates with low-level vancomycin resistance associated with persistent methicillin-resistant Staphylococcus aureus bacterernia
Benjamin P. Howden et al.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2006)
The role of nasal carriage in Staphylococcus aureus infections
HFL Wertheim et al.
LANCET INFECTIOUS DISEASES (2005)
Hypermutable and fluoroquinolone-resistant clinical isolates of Staphylococcus aureus
HNG Trong et al.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2005)
Share Paper
