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.
Highlights
Over the past 30 years, the epidemiology of enterococcal infections has changed with Enterococcus faecium progressively increasing from causing,5% of enterococcal infections to causing,35% of these infections [1,2]
Several studies have shown that E. faecium strains that cause hospital-associated infections are often different from strains that colonize the gastro-intestinal tracts of community-based healthy individuals and food animals, with the former having higher frequencies of ampicillin resistance, espefm, hylefm, microbial surface components recognizing adhesive matrix molecules (MSCRAMMs), and the presence of IS16 [1,3,4,5,6,7,8,9,10,11]
Other studies based on comparative genome array, amplified fragment length polymorphism (AFLP), and pyrosequencing have indicated the existence of two different subpopulations or ‘‘clades’’ in which the clinical, hospitalassociated (HA) strains belong to a group that is distinct from the group that consists primarily of non-clinical, community-associated (CA) strains, such as those found in the stools of healthy individuals in the community [6,18]
Summary
Over the past 30 years, the epidemiology of enterococcal infections has changed with Enterococcus faecium progressively increasing from causing ,5% of enterococcal infections to causing ,35% of these infections [1,2]. Population-based studies by Willems and colleagues using multi-locus sequence typing (MLST) and the algorithm eBURST suggested that strains from nosocomial infections belonged to a distinct genetic lineage named Clonal Complex 17 [5,12,13]. It has since been reported using Bayesian modeling and other methods that eBURST-based clustering is inaccurate for determining evolutionary decent for species, like E. faecium, with high levels of recombination [14,15,16,17]. Fundamental differences have been suggested by analysis of pyrosequenced genomes [18] and by our previous study’s findings that strains separated clearly into two distinct groups based on four genes, with a 3% nucleotide difference for gls20, 5% for pbp5, 7% for pbp, and 10% for wlcA between these genes from strains in the two groups [19]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
