The interplay between community and hospital Enterococcus faecium clones within health-care settings: a genomic analysis

The global dissemination of hospital clones of Enterococcus faecium

(2021) Sebastiaan J. van Hal et al.   Genome Medicine

Plasmids Shaped the Recent Emergence of the Major Nosocomial Pathogen Enterococcus faecium

(2020) S. Arredondo-Alonso et al.   mBio

Genomic Epidemiology of Vancomycin-Resistant Enterococcus faecium (VREfm) in Latin America: Revisiting The Global VRE Population Structure

(2020) Rafael Rios et al.   Scientific Reports

Cell Wall Hydrolases in Bacteria: Insight on the Diversity of Cell Wall Amidases, Glycosidases and Peptidases Toward Peptidoglycan

(2019) Aurore Vermassen et al.   Frontiers in Microbiology

Validating the NCBI AMRFinder Tool and Resistance Gene Database Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of NARMS Isolates

(2019) Michael Feldgarden et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Genomic Surveillance of Enterococcus faecium Reveals Limited Sharing of Strains and Resistance Genes between Livestock and Humans in the United Kingdom

(2018) Theodore Gouliouris et al.   mBio

Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations

(2017) Rafal Mostowy et al.   MOLECULAR BIOLOGY AND EVOLUTION

A decade of genomic history for healthcare-associatedEnterococcus faeciumin the United Kingdom and Ireland

(2016) Kathy E. Raven et al.   GENOME RESEARCH

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

(2015) Xavier Didelot et al.   PLoS Computational Biology

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Mechanisms of antibiotic resistance in enterococci

(2014) William R Miller et al.   Expert Review of Anti-Infective Therapy

Recent Recombination Events in the Core Genome Are Associated with Adaptive Evolution in Enterococcus faecium

(2013) Mark de Been et al.   Genome Biology and Evolution

Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software

(2013) L. Cheng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Emergence of Epidemic Multidrug-Resistant Enterococcus faecium from Animal and Commensal Strains

(2013) F. Lebreton et al.   mBio

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

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

The rise of the Enterococcus: beyond vancomycin resistance

(2012) Cesar A. Arias et al.   NATURE REVIEWS MICROBIOLOGY

Restricted Gene Flow among Hospital Subpopulations of Enterococcus faecium

(2012) R. J. L. Willems et al.   mBio

Inference of Population Structure using Dense Haplotype Data

(2012) Daniel John Lawson et al.   PLoS Genetics

The prolipoprotein diacylglyceryl transferase (Lgt) of Enterococcus faecalis contributes to virulence

(2011) F. Reffuveille et al.   MICROBIOLOGY-SGM

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

A comparison of homologous recombination rates in bacteria and archaea

(2008) Michiel Vos et al.   ISME Journal