Genomic analysis of 495 vancomycin-resistantEnterococcus faeciumreveals broad dissemination of avanAplasmid in more than 19 clones from Copenhagen, Denmark

A SilencedvanAGene Cluster on a Transferable Plasmid Caused an Outbreak of Vancomycin-Variable Enterococci

(2016) Audun Sivertsen et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Whole-genome sequencing reveals transmission of vancomycin-resistant Enterococcus faecium in a healthcare network

(2016) Hayley J. Brodrick et al.   Genome Medicine

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Environmental survival of vancomycin-sensitive ampicillin-resistant Enterococcus faecium (AREfm)

(2015) J. H. T. Wagenvoort et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Multiple hospital outbreaks ofvanA Enterococcus faeciumin Denmark, 2012–13, investigated by WGS, MLST and PFGE

(2015) Mette Pinholt et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Epidemiology and molecular typing of VRE bloodstream isolates in an Irish tertiary care hospital

(2015) L. Ryan et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

In SilicoDetection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

(2014) Alessandra Carattoli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

A Multicentre Hospital Outbreak in Sweden Caused by Introduction of a vanB2 Transposon into a Stably Maintained pRUM-Plasmid in an Enterococcus faecium ST192 Clone

(2014) Audun Sivertsen et al.   PLoS One

National Surveillance on Vancomycin-Resistant Enterococcus faecium in Taiwan: Emergence and Widespread of ST414 and a Tn1546-Like Element with Simultaneous Insertion of IS1251-like and IS1678

(2014) An-Jing Kuo et al.   PLoS One

Molecular Analysis of VanA Outbreak ofEnterococcus faeciumin Two Warsaw Hospitals: The Importance of Mobile Genetic Elements

(2014) Ewa Wardal et al.   Biomed Research International

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

Genomic Insights to Control the Emergence of Vancomycin-Resistant Enterococci

(2013) B. P. Howden et al.   mBio

Genetic features and molecular epidemiology of Enterococcus faecium isolated in two university hospitals in Brazil

(2012) Leila Priscilla Pinheiro da Silva et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Comparative Analysis of the First Complete Enterococcus faecium Genome

(2012) M. M. C. Lam et al.   JOURNAL OF BACTERIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Novel Vancomycin-Resistance Transposon, Plasmid Replicon Types, and Virulence Factors of Vancomycin-Resistant Enterococci in Zhejiang, China

(2012) Ting-Ting Qu et al.   Microbial Drug Resistance

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Genomic and SNP Analyses Demonstrate a Distant Separation of the Hospital and Community-Associated Clades of Enterococcus faecium

(2012) Jessica Galloway-Peña et al.   PLoS One

Restricted Gene Flow among Hospital Subpopulations of Enterococcus faecium

(2012) R. J. L. Willems et al.   mBio

Microevolutionary analysis of Clostridium difficile genomes to investigate transmission

(2012) Xavier Didelot et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

Txe, an endoribonuclease of the enterococcal Axe-Txe toxin-antitoxin system, cleaves mRNA and inhibits protein synthesis

(2010) E. M. Halvorsen et al.   MICROBIOLOGY-SGM

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

High prevalence of ST-78 infection-associated vancomycin-resistant Enterococcus faecium from hospitals in Asunción, Paraguay

(2009) M.A. Khan et al.   CLINICAL MICROBIOLOGY AND INFECTION

PCR-based plasmid typing inEnterococcus faeciumstrains reveals widely distributed pRE25-, pRUM-, pIP501- and pHTβ-related replicons associated with glycopeptide resistance and stabilizing toxin–antitoxin systems

(2009) Torill C.S. Rosvoll et al.   FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY

Diversity of Tn1546 and Its Role in the Dissemination of Vancomycin-Resistant Enterococci in Portugal

(2008) C. Novais et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

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

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