Dissecting Vancomycin-Intermediate Resistance in Staphylococcus aureus Using Genome-Wide Association

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Predicting the virulence of MRSA from its genome sequence

(2014) M. Laabei et al.   GENOME RESEARCH

Comprehensive Identification of Mutations Responsible for Heterogeneous Vancomycin-Intermediate Staphylococcus aureus (hVISA)-to-VISA Conversion in Laboratory-Generated VISA Strains Derived from hVISA Clinical Strain Mu3

(2013) Miki Matsuo et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis

(2013) Bruno Contreras-Moreira et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The evolution of vancomycin intermediate Staphylococcus aureus (VISA) and heterogenous-VISA

(2013) Benjamin P. Howden et al.   INFECTION GENETICS AND EVOLUTION

Reduced susceptibility to vancomycin in isogenic Staphylococcus aureus strains of sequence type 59: tracking evolution and identifying mutations by whole-genome sequencing

(2013) C.-J. Chen et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Genome Sequence-Based Discriminator for Vancomycin-Intermediate Staphylococcus aureus

(2013) L. Rishishwar et al.   JOURNAL OF BACTERIOLOGY

IsdB-dependent Hemoglobin Binding Is Required for Acquisition of Heme by Staphylococcus aureus

(2013) Gleb Pishchany et al.   JOURNAL OF INFECTIOUS DISEASES

Alternative Mutational Pathways to Intermediate Resistance to Vancomycin in Methicillin-Resistant Staphylococcus aureus

(2013) Celine Vidaillac et al.   JOURNAL OF INFECTIOUS DISEASES

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

(2013) Maha R Farhat et al.   NATURE GENETICS

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

Contribution of Selected Gene Mutations to Resistance in Clinical Isolates of Vancomycin-Intermediate Staphylococcus aureus

(2012) Cory Hafer et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

A Mutation in the PP2C Phosphatase Gene in a Staphylococcus aureus USA300 Clinical Isolate with Reduced Susceptibility to Vancomycin and Daptomycin

(2012) Karla D. Passalacqua et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Short read sequence typing (SRST): multi-locus sequence types from short reads

(2012) Michael Inouye et al.   BMC GENOMICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

MRSA virulence and spread

(2012) Michael Otto   CELLULAR MICROBIOLOGY

The RpoB H481Y Rifampicin Resistance Mutation and an Active Stringent Response Reduce Virulence and Increase Resistance to Innate Immune Responses in Staphylococcus aureus

(2012) Wei Gao et al.   JOURNAL OF INFECTIOUS DISEASES

Serine/Threonine Phosphatase Stp1 Contributes to Reduced Susceptibility to Vancomycin and Virulence in Staphylococcus aureus

(2012) David R. Cameron et al.   JOURNAL OF INFECTIOUS DISEASES

Transforming clinical microbiology with bacterial genome sequencing

(2012) Xavier Didelot et al.   NATURE REVIEWS GENETICS

EvolView, an online tool for visualizing, annotating and managing phylogenetic trees

(2012) Huangkai Zhang et al.   NUCLEIC ACIDS RESEARCH

Genetic Pathway in Acquisition and Loss of Vancomycin Resistance in a Methicillin Resistant Staphylococcus aureus (MRSA) Strain of Clonal Type USA300

(2012) Susana Gardete et al.   PLoS Pathogens

A Comparison of Association Methods Correcting for Population Stratification in Case-Control Studies

(2011) Chengqing Wu et al.   ANNALS OF HUMAN GENETICS

walKandclpPMutations Confer Reduced Vancomycin Susceptibility inStaphylococcus aureus

(2011) Mitsutaka Shoji et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Mutation of RNA Polymerase β Subunit (rpoB) Promotes hVISA-to-VISA Phenotypic Conversion of Strain Mu3

(2011) Miki Matsuo et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Computational methods for Gene Orthology inference

(2011) D. M. Kristensen et al.   BRIEFINGS IN BIOINFORMATICS

Effectiveness of Measures to Eradicate Staphylococcus aureus Carriage in Patients with Community-Associated Skin and Soft-Tissue Infections: A Randomized Trial

(2011) Stephanie A. Fritz et al.   INFECTION CONTROL AND HOSPITAL EPIDEMIOLOGY

Relevance of vancomycin-intermediate susceptibility and heteroresistance in methicillin-resistant Staphylococcus aureus bacteraemia

(2011) R. Khatib et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Clinical and Laboratory Characteristics of Invasive Infections Due to Methicillin-Resistant Staphylococcus aureus Isolates Demonstrating a Vancomycin MIC of 2 Micrograms per Milliliter: Lack of Effect of Heteroresistant Vancomycin-Intermediate S. aureus Phenotype

(2011) S. W. Satola et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Impact of rpoB Mutations on Reduced Vancomycin Susceptibility in Staphylococcus aureus

(2011) Yukiko Watanabe et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Detection of Staphylococcus aureus Isolates with Heterogeneous Intermediate-Level Resistance to Vancomycin in the United States

(2011) S. S. Richter et al.   JOURNAL OF CLINICAL MICROBIOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Whole Genome Sequencing and Complete Genetic Analysis Reveals Novel Pathways to Glycopeptide Resistance in Staphylococcus aureus

(2011) Adriana Renzoni et al.   PLoS One

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

ROADTRIPS: Case-Control Association Testing with Partially or Completely Unknown Population and Pedigree Structure

(2010) Timothy Thornton et al.   AMERICAN JOURNAL OF HUMAN GENETICS

An RpoB Mutation Confers Dual Heteroresistance to Daptomycin and Vancomycin in Staphylococcus aureus

(2010) L. Cui et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Molecular characterization of resistance to Rifampicin in an emerging hospital-associated Methicillin-resistant Staphylococcus aureus clone ST228, Spain

(2010) Virginie Mick et al.   BMC MICROBIOLOGY

Reduced Vancomycin Susceptibility in Staphylococcus aureus, Including Vancomycin-Intermediate and Heterogeneous Vancomycin-Intermediate Strains: Resistance Mechanisms, Laboratory Detection, and Clinical Implications

(2010) B. P. Howden et al.   CLINICAL MICROBIOLOGY REVIEWS

Community-Associated Methicillin-Resistant Staphylococcus aureus: Epidemiology and Clinical Consequences of an Emerging Epidemic

(2010) M. Z. David et al.   CLINICAL MICROBIOLOGY REVIEWS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Comparison of Detection Methods for Heteroresistant Vancomycin-Intermediate Staphylococcus aureus, with the Population Analysis Profile Method as the Reference Method

(2010) S. W. Satola et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Contribution of vraSR and graSR Point Mutations to Vancomycin Resistance in Vancomycin-Intermediate Staphylococcus aureus

(2009) L. Cui et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

VanA-Type Vancomycin-Resistant Staphylococcus aureus

(2009) B. Perichon et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Selection of Heterogeneous Vancomycin-Intermediate Staphylococcus aureus by Imipenem

(2009) Y. Katayama et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

ABACAS: algorithm-based automatic contiguation of assembled sequences

(2009) S. Assefa et al.   BIOINFORMATICS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Lack of Heteroresistance among Staphylococcus aureus Isolates with Vancomycin MICs of 2 Micrograms per Milliliter by Automated Testing

(2009) S. W. Satola et al.   JOURNAL OF CLINICAL MICROBIOLOGY

The First Vancomycin-Intermediate Staphylococcus aureus Strains Isolated from Patients in Thailand

(2009) A. Lulitanond et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Characterization of Methicillin-Resistant Staphylococcus aureus Isolates Collected in 2005 and 2006 from Patients with Invasive Disease: a Population-Based Analysis

(2009) B. Limbago et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Waves of resistance: Staphylococcus aureus in the antibiotic era

(2009) Henry F. Chambers et al.   NATURE REVIEWS MICROBIOLOGY

Genomic Analysis Reveals a Point Mutation in the Two-Component Sensor Gene graS That Leads to Intermediate Vancomycin Resistance in Clinical Staphylococcus aureus

(2008) B. P. Howden et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Identification of the First Vancomycin Intermediate-Resistant Staphylococcus aureus (VISA) Isolate from a Hospital in Portugal

(2008) S. Gardete et al.   Microbial Drug Resistance