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

Bile salt hydrolases: Gatekeepers of bile acid metabolism and host-microbiome crosstalk in the gastrointestinal tract

(2019) Matthew H. Foley et al.   PLoS Pathogens

New insights into bacterial bile resistance mechanisms: the role of bile salt hydrolase and its impact on human health

(2018) Ana Y. Bustos et al.   FOOD RESEARCH INTERNATIONAL

Systematic discovery of antiphage defense systems in the microbial pangenome

(2018) Shany Doron et al.   SCIENCE

Linezolid resistance genes and genetic elements enhancing their dissemination in enterococci and streptococci

(2018) Ewa Sadowy   PLASMID

A Type I Restriction-Modification System Associated with Enterococcus faecium Subspecies Separation

(2018) Wenwen Huo et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Intestinal carriage of ampicillin- and vancomycin-resistant Enterococcus faecium in humans, dogs and cats in the Netherlands

(2017) G van den Bunt et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

Evolutionary origins of the emergent ST796 clone of vancomycin resistantEnterococcus faecium

(2017) Andrew H. Buultjens et al.   PeerJ

plasmidSPAdes: assembling plasmids from whole genome sequencing data

(2016) Dmitry Antipov et al.   BIOINFORMATICS

CRISPRDetect: A flexible algorithm to define CRISPR arrays

(2016) Ambarish Biswas et al.   BMC GENOMICS

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

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

Antimicrobial-Resistant Pathogens Associated With Healthcare-Associated Infections: Summary of Data Reported to the National Healthcare Safety Network at the Centers for Disease Control and Prevention, 2011–2014

(2016) Lindsey M. Weiner et al.   INFECTION CONTROL AND HOSPITAL EPIDEMIOLOGY

Multilevel population genetic analysis ofvanAandvanB Enterococcus faeciumcausing nosocomial outbreaks in 27 countries (1986–2012)

(2016) Ana R. Freitas et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Partial Diversity Generates Effector Immunity Specificity of the Bac41-Like Bacteriocins of Enterococcus faecalis Clinical Strains

(2016) Jun Kurushima et al.   JOURNAL OF BACTERIOLOGY

Transferable genes putatively conferring elevated minimum inhibitory concentrations of narasin in Enterococcus faecium from Swedish broilers

(2016) Oskar Nilsson et al.   VETERINARY MICROBIOLOGY

iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers)

(2016) T. C. Hsieh et al.   Methods in Ecology and Evolution

Global Emergence and Dissemination of Enterococci as Nosocomial Pathogens: Attack of the Clones?

(2016) Ana M. Guzman Prieto et al.   Frontiers in Microbiology

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Investigating the mobilome in clinically important lineages of Enterococcus faecium and Enterococcus faecalis

(2015) Theresa Mikalsen et al.   BMC GENOMICS

fitdistrplus: AnRPackage for Fitting Distributions

(2015) Marie Laure Delignette-Muller et al.   Journal of Statistical Software

The mazEF toxin–antitoxin system as an attractive target in clinical isolates of Enterococcus faecium and Enterococcus faecalis

(2015) Sobhan Ghafourian et al.   Drug Design Development and Therapy

NbClust: AnRPackage for Determining the Relevant Number of Clusters in a Data Set

(2015) Malika Charrad et al.   Journal of Statistical Software

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

A widespread bacteriophage abortive infection system functions through a Type IV toxin–antitoxin mechanism

(2014) Ron L. Dy et al.   NUCLEIC ACIDS RESEARCH

Functional genomic analysis of bile salt resistance in Enterococcus faecium

(2013) Xinglin Zhang et al.   BMC GENOMICS

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

Identification of a Genetic Determinant in Clinical Enterococcus faecium Strains That Contributes to Intestinal Colonization During Antibiotic Treatment

(2013) X. Zhang et al.   JOURNAL OF INFECTIOUS DISEASES

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

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

Comparative Genomics of Enterococci: Variation in Enterococcus faecalis, Clade Structure in E. faecium, and Defining Characteristics of E. gallinarum and E. casseliflavus

(2012) K. L. Palmer et al.   mBio

Human and Swine Hosts Share Vancomycin-Resistant Enterococcus faecium CC17 and CC5 and Enterococcus faecalis CC2 Clonal Clusters Harboring Tn1546 on Indistinguishable Plasmids

(2011) A. R. Freitas et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Detection of recombination events in bacterial genomes from large population samples

(2011) Pekka Marttinen et al.   NUCLEIC ACIDS RESEARCH

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Mobile genetic elements and their contribution to the emergence of antimicrobial resistant Enterococcus faecalis and Enterococcus faecium

(2010) K. Hegstad et al.   CLINICAL MICROBIOLOGY AND INFECTION

Horizontal gene transfer and the genomics of enterococcal antibiotic resistance

(2010) Kelli L Palmer et al.   CURRENT OPINION IN MICROBIOLOGY

Vancomycin tolerance in clinical and laboratory Streptococcus pneumoniae isolates depends on reduced enzyme activity of the major LytA autolysin or cooperation between CiaH histidine kinase and capsular polysaccharide

(2010) Miriam Moscoso et al.   MOLECULAR MICROBIOLOGY

Multidrug-Resistant Enterococci Lack CRISPR-cas

(2010) K. L. Palmer et al.   mBio