Genomic and SNP analyses demonstrate a distant separation of the hospital and community-associated clades of Enterococcus faecium.

TitleGenomic and SNP analyses demonstrate a distant separation of the hospital and community-associated clades of Enterococcus faecium.
Publication TypeJournal Article
Year of Publication2012
AuthorsGalloway-Peña, J, Roh, JHyeob, Latorre, M, Qin, X, Murray, BE
JournalPLoS One
Volume7
Issue1
Paginatione30187
Date Published2012
ISSN1932-6203
KeywordsCommunity-Acquired Infections, Cross Infection, DNA, Bacterial, Enterococcus faecium, Evolution, Molecular, Genetic Speciation, Genome, Bacterial, Gram-Positive Bacterial Infections, Hospitals, Humans, Models, Genetic, Phylogeny, Polymorphism, Single Nucleotide, Sequence Analysis, DNA
Abstract

Recent studies have pointed to the existence of two subpopulations of Enterococcus faecium, one containing primarily commensal/community-associated (CA) strains and one that contains most clinical or hospital-associated (HA) strains, including those classified by multi-locus sequence typing (MLST) as belonging to the CC17 group. The HA subpopulation more frequently has IS16, pathogenicity island(s), and plasmids or genes associated with antibiotic resistance, colonization, and/or virulence. Supporting the two clades concept, we previously found a 3-10% difference between four genes from HA-clade strains vs. CA-clade strains, including 5% difference between pbp5-R of ampicillin-resistant, HA strains and pbp5-S of ampicillin-sensitive, CA strains. To further investigate the core genome of these subpopulations, we studied 100 genes from 21 E. faecium genome sequences; our analyses of concatenated sequences, SNPs, and individual genes all identified two distinct groups. With the concatenated sequence, HA-clade strains differed by 0-1% from one another while CA clade strains differed from each other by 0-1.1%, with 3.5-4.2% difference between the two clades. While many strains had a few genes that grouped in one clade with most of their genes in the other clade, one strain had 28% of its genes in the CA clade and 72% in the HA clade, consistent with the predicted role of recombination in the evolution of E. faecium. Using estimates for Escherichia coli, molecular clock calculations using sSNP analysis indicate that these two clades may have diverged ≥1 million years ago or, using the higher mutation rate for Bacillus anthracis, ∼300,000 years ago. These data confirm the existence of two clades of E. faecium and show that the differences between the HA and CA clades occur at the core genomic level and long preceded the modern antibiotic era.

DOI10.1371/journal.pone.0030187
Alternate JournalPLoS ONE
PubMed ID22291916
PubMed Central IDPMC3266884
Grant ListF31 AI092891 / AI / NIAID NIH HHS / United States
F31AI092891 / AI / NIAID NIH HHS / United States
R01AI067861 / AI / NIAID NIH HHS / United States
T32 A155449 / / PHS HHS / United States
T32 AI055449 / AI / NIAID NIH HHS / United States