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Genomes of a major nosocomial pathogen Enterococcus faecium are shaped by adaptive evolution of the chromosome and plasmidome

https://doi.org/10.1101/530725
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1001/jamainternmed.2013.7734openalex-snapshot
Rapid Bacterial Whole-Genome Sequencing to Enhance Diagnostic and Public Health Microbiology
inferredcites →https://doi.org/10.1007/s10096-011-1342-7openalex-snapshot
High-density fecal Enterococcus faecium colonization in hospitalized patients is associated with the presence of the polyclonal subcluster CC17
inferredcites →https://doi.org/10.1016/j.fm.2014.09.004openalex-snapshot
Role of csp genes in NaCl, pH, and ethanol stress response and motility in Clostridium botulinum ATCC 3502
inferredcites →https://doi.org/10.1016/j.ijantimicag.2016.09.001openalex-snapshot
Polyclonal spread of vanA Enterococcus faecium in Central Denmark Region, 2009–2013, investigated using PFGE, MLST and WGS
inferredcites →https://doi.org/10.1016/j.micpath.2008.05.001openalex-snapshot
Role of polyamine transport in Streptococcus pneumoniae response to physiological stress and murine septicemia
inferredcites →https://doi.org/10.1016/j.mimet.2009.10.012openalex-snapshot
A classification system for plasmids from enterococci and other Gram-positive bacteria
inferredcites →https://doi.org/10.1016/s0005-2728(00)00278-4openalex-snapshot
Catalytic properties of Na+-translocating V-ATPase in Enterococcus hirae
inferredcites →https://doi.org/10.1016/s1473-3099(01)00145-1openalex-snapshot
Vancomycin-resistant enterococci: why are they here, and where do they come from?
inferredcites →https://doi.org/10.1017/ice.2016.174openalex-snapshot
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
inferredcites →https://doi.org/10.1017/ice.2019.296openalex-snapshot
Antimicrobial-resistant pathogens associated with adult healthcare-associated infections: Summary of data reported to the National Healthcare Safety Network, 2015–2017
inferredcites →https://doi.org/10.1038/ng.2625openalex-snapshot
Population genomics of post-vaccine changes in pneumococcal epidemiology
inferredcites →https://doi.org/10.1038/ng.3145openalex-snapshot
Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution
inferredcites →https://doi.org/10.1038/nrmicro2761openalex-snapshot
The rise of the Enterococcus: beyond vancomycin resistance
inferredcites →https://doi.org/10.1038/s41559-018-0617-0openalex-snapshot
Gene exchange drives the ecological success of a multi-host bacterial pathogen
inferredcites →https://doi.org/10.1038/srep21847openalex-snapshot
Population structure and acquisition of the vanB resistance determinant in German clinical isolates of Enterococcus faecium ST192
inferredcites →https://doi.org/10.1086/315752openalex-snapshot
Host Specificity of Vancomycin‐ResistantEnterococcus faecium
inferredcites →https://doi.org/10.1086/591861openalex-snapshot
Antimicrobial-Resistant Pathogens Associated With Healthcare-Associated Infections: Annual Summary of Data Reported to the National Healthcare Safety Network at the Centers for Disease Control and Prevention, 2006–2007
inferredcites →https://doi.org/10.1093/bioinformatics/btg412openalex-snapshot
APE: Analyses of Phylogenetics and Evolution in R language
inferredcites →https://doi.org/10.1093/bioinformatics/btm039openalex-snapshot
Gepard: a rapid and sensitive tool for creating dotplots on genome scale
inferredcites →https://doi.org/10.1093/bioinformatics/btq706openalex-snapshot
phangorn: phylogenetic analysis in R
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btu153openalex-snapshot
Prokka: rapid prokaryotic genome annotation
inferredcites →https://doi.org/10.1093/bioinformatics/btv421openalex-snapshot
Roary: rapid large-scale prokaryote pan genome analysis
inferredcites →https://doi.org/10.1093/bioinformatics/btw493openalex-snapshot
plasmidSPAdes: assembling plasmids from whole genome sequencing data
inferredcites →https://doi.org/10.1093/gbe/evt111openalex-snapshot
Recent Recombination Events in the Core Genome Are Associated with Adaptive Evolution in Enterococcus faecium
inferredcites →https://doi.org/10.1093/infdis/jit076openalex-snapshot
Identification of a Genetic Determinant in Clinical Enterococcus faecium Strains That Contributes to Intestinal Colonization During Antibiotic Treatment
inferredcites →https://doi.org/10.1093/infdis/jiv597openalex-snapshot
Gastrointestinal Tract Colonization Dynamics by DifferentEnterococcus faeciumClades
inferredcites →https://doi.org/10.1093/jac/dkv142openalex-snapshot
Multiple hospital outbreaks ofvanA Enterococcus faeciumin Denmark, 2012–13, investigated by WGS, MLST and PFGE
inferredcites →https://doi.org/10.1093/jac/dkw312openalex-snapshot
Multilevel population genetic analysis ofvanAandvanB Enterococcus faeciumcausing nosocomial outbreaks in 27 countries (1986–2012)
inferredcites →https://doi.org/10.1093/jac/dkw360openalex-snapshot
Genomic analysis of 495 vancomycin-resistantEnterococcus faeciumreveals broad dissemination of avanAplasmid in more than 19 clones from Copenhagen, Denmark
inferredcites →https://doi.org/10.1093/jac/dkw539openalex-snapshot
Polyclonal emergence ofvanAvancomycin-resistantEnterococcus faeciumin Australia
inferredcites →https://doi.org/10.1093/jac/dkx455openalex-snapshot
Intestinal carriage of ampicillin- and vancomycin-resistant Enterococcus faecium in humans, dogs and cats in the Netherlands
inferredcites →https://doi.org/10.1093/molbev/mst028openalex-snapshot
Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software
inferredcites →https://doi.org/10.1093/nar/gkr928openalex-snapshot
Detection of recombination events in bacterial genomes from large population samples
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025808openalex-snapshot
BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data
inferredcites →https://doi.org/10.1098/rspb.2014.1679openalex-snapshot
Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses
inferredcites →https://doi.org/10.1099/mgen.0.000048openalex-snapshot
Evolutionary dynamics of Enterococcus faecium reveals complex genomic relationships between isolates with independent emergence of vancomycin resistance
inferredcites →https://doi.org/10.1099/mgen.0.000184openalex-snapshot
SuperDCA for genome-wide epistasis analysis
inferredcites →https://doi.org/10.1099/mgen.0.000220openalex-snapshot
PANINI: Pangenome Neighbour Identification for Bacterial Populations
inferredcites →https://doi.org/10.1099/mgen.0.000224openalex-snapshot
mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species
inferredcites →https://doi.org/10.1101/gr.204024.116openalex-snapshot
A decade of genomic history for healthcare-associated Enterococcus faecium in the United Kingdom and Ireland
inferredcites →https://doi.org/10.1111/1755-0998.12676openalex-snapshot
treespace : Statistical exploration of landscapes of phylogenetic trees
inferredcites →https://doi.org/10.1111/2041-210x.12628openalex-snapshot
ggtree : an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data
inferredcites →https://doi.org/10.1111/j.1365-2958.2008.06295.xopenalex-snapshot
Structure and functional properties of the Bacillus subtilis transcriptional repressor Rex
inferredcites →https://doi.org/10.1126/science.aaf3552openalex-snapshot
A secreted bacterial peptidoglycan hydrolase enhances tolerance to enteric pathogens
inferredcites →https://doi.org/10.1126/sciimmunol.aai7732openalex-snapshot
Exploiting a host-commensal interaction to promote intestinal barrier function and enteric pathogen tolerance
inferredcites →https://doi.org/10.1128/9781555817923.ch3openalex-snapshot
Enterococci as Members of the Intestinal Microflora of Humans
inferredcites →https://doi.org/10.1128/aac.43.3.483openalex-snapshot
Molecular Diversity and Evolutionary Relationships of Tn 1546 -Like Elements in Enterococci from Humans and Animals
inferredcites →https://doi.org/10.1128/aem.01378-08openalex-snapshot
Identification of a Novel Genomic Island Specific to Hospital-Acquired Clonal Complex 17 Enterococcus faecium Isolates
inferredcites →https://doi.org/10.1128/aem.02979-05openalex-snapshot
Copper Resistance in Enterococcus faecium , Mediated by the tcrB Gene, Is Selected by Supplementation of Pig Feed with Copper Sulfate
inferredcites →https://doi.org/10.1128/aem.68.12.6425-6428.2002openalex-snapshot
Quantitative Determination of Bile Salt Hydrolase Activity in Bacteria Isolated from the Small Intestine of Chickens
inferredcites →https://doi.org/10.1128/genomea.01275-15openalex-snapshot
Complete Genome Sequence of the Gut Commensal and Laboratory Strain Enterococcus faecium 64/3
inferredcites →https://doi.org/10.1128/jb.00259-12openalex-snapshot
Comparative Analysis of the First Complete Enterococcus faecium Genome
inferredcites →https://doi.org/10.1128/jb.00348-16openalex-snapshot
Partial Diversity Generates Effector Immunity Specificity of the Bac41-Like Bacteriocins of Enterococcus faecalis Clinical Strains
inferredcites →https://doi.org/10.1128/jcm.01750-10openalex-snapshot
Human and Swine Hosts Share Vancomycin-Resistant Enterococcus faecium CC17 and CC5 and Enterococcus faecalis CC2 Clonal Clusters Harboring Tn 1546 on Indistinguishable Plasmids
inferredcites →https://doi.org/10.1128/mbio.00151-12openalex-snapshot
Restricted Gene Flow among Hospital Subpopulations of Enterococcus faecium
inferredcites →https://doi.org/10.1128/mbio.00412-13openalex-snapshot
Genomic Insights to Control the Emergence of Vancomycin-Resistant Enterococci
inferredcites →https://doi.org/10.1128/mbio.00534-13openalex-snapshot
Emergence of Epidemic Multidrug-Resistant Enterococcus faecium from Animal and Commensal Strains
inferredcites →https://doi.org/10.1128/mbio.01780-18openalex-snapshot
Genomic Surveillance of Enterococcus faecium Reveals Limited Sharing of Strains and Resistance Genes between Livestock and Humans in the United Kingdom
inferredcites →https://doi.org/10.1146/annurev-micro-091213-113003openalex-snapshot
Friend Turned Foe: Evolution of Enterococcal Virulence and Antibiotic Resistance
inferredcites →https://doi.org/10.1172/jci43918openalex-snapshot
Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans
inferredcites →https://doi.org/10.1186/1471-2164-14-299openalex-snapshot
Functional genomic analysis of bile salt resistance in Enterococcus faecium
inferredcites →https://doi.org/10.1186/1471-2164-14-595openalex-snapshot
Comparative analysis of the complete genome of an epidemic hospital sequence type 203 clone of vancomycin-resistant Enterococcus faecium
inferredcites →https://doi.org/10.1186/1471-2180-12-135openalex-snapshot
Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes
inferredcites →https://doi.org/10.1186/s13059-016-0997-xopenalex-snapshot
Mash: fast genome and metagenome distance estimation using MinHash
inferredcites →https://doi.org/10.1186/s13059-016-1108-8openalex-snapshot
Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary
inferredcites →https://doi.org/10.1186/s13073-015-0259-7openalex-snapshot
Whole-genome sequencing reveals transmission of vancomycin-resistant Enterococcus faecium in a healthcare network
inferredcites →https://doi.org/10.1371/journal.pcbi.1005595openalex-snapshot
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads
inferredcites →https://doi.org/10.1371/journal.pgen.1004547openalex-snapshot
Comprehensive Identification of Single Nucleotide Polymorphisms Associated with Beta-lactam Resistance within Pneumococcal Mosaic Genes
inferredcites →https://doi.org/10.1371/journal.pone.0030319openalex-snapshot
Hospital and Community Ampicillin-Resistant Enterococcus faecium Are Evolutionarily Closely Linked but Have Diversified through Niche Adaptation
inferredcites →https://doi.org/10.18637/jss.v061.i06openalex-snapshot
NbClust : An R Package for Determining the Relevant Number of Clusters in a Data Set
inferredcites →https://doi.org/10.18637/jss.v064.i04openalex-snapshot
fitdistrplus : An R Package for Fitting Distributions
inferredcites →https://doi.org/10.2217/fmb.09.82openalex-snapshot
Transition of Enterococcus Faecium from Commensal Organism to Nosocomial Pathogen
inferredcites →https://doi.org/10.32614/cran.package.ggpubropenalex-snapshot
ggpubr: 'ggplot2' Based Publication Ready Plots
inferredcites →https://doi.org/10.3389/fmicb.2016.00788openalex-snapshot
Global Emergence and Dissemination of Enterococci as Nosocomial Pathogens: Attack of the Clones?
inferredcites →https://doi.org/10.7717/peerj.2916openalex-snapshot
Evolutionary origins of the emergent ST796 clone of vancomycin resistant Enterococcus faecium

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.cmi.2019.10.027openalex-snapshot
Antimicrobial resistance classification using MALDI-TOF-MS is not that easy: lessons from vancomycin-resistant Enterococcus faecium
inferred← citeshttps://doi.org/10.1073/pnas.1917130117openalex-snapshot
Evolution of vancomycin-resistant Enterococcus faecium during colonization and infection in immunocompromised pediatric patients
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa233openalex-snapshot
gplas: a comprehensive tool for plasmid analysis using short-read graphs
inferred← citeshttps://doi.org/10.1101/2019.12.20.884395openalex-snapshot
Applying Nanopore sequencing to a One-Health scenario for colistin resistance transmission among pigs, cows and the farmer
inferred← citeshttps://doi.org/10.1101/2025.05.16.654303openalex-snapshot
Amira: detection of AMR genes directly from long reads using gene-space de Bruijn graphs
inferred← citeshttps://doi.org/10.1128/aem.01559-19openalex-snapshot
Chicken Meat-Associated Enterococci: Influence of Agricultural Antibiotic Use and Connection to the Clinic
inferred← citeshttps://doi.org/10.17605/osf.io/2f8w7openalex-snapshot
Preprint - Applying Nanopore sequencing to a One-Health scenario for colistin resistance transmission among pigs, cows and the farmer
inferred← citeshttps://doi.org/10.3389/fmicb.2026.1774907openalex-snapshot
From cognition to response: clinical challenges, antibiotic resistance mechanisms, and prevention and control strategies of Elizabethkingia meningoseptica infections
inferred← citeshttps://doi.org/10.3390/pathogens13050409openalex-snapshot
The Impact of Enterococcus spp. in the Immunocompromised Host: A Comprehensive Review
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