Comparative genomics of Enterococcus faecalis from healthy Norwegian infants - PubMed (original) (raw)

Comparative genomics of Enterococcus faecalis from healthy Norwegian infants

Margrete Solheim et al. BMC Genomics. 2009.

Abstract

Background: Enterococcus faecalis, traditionally considered a harmless commensal of the intestinal tract, is now ranked among the leading causes of nosocomial infections. In an attempt to gain insight into the genetic make-up of commensal E. faecalis, we have studied genomic variation in a collection of community-derived E. faecalis isolated from the feces of Norwegian infants.

Results: The E. faecalis isolates were first sequence typed by multilocus sequence typing (MLST) and characterized with respect to antibiotic resistance and properties associated with virulence. A subset of the isolates was compared to the vancomycin resistant strain E. faecalis V583 (V583) by whole genome microarray comparison (comparative genomic hybridization (CGH)). Several of the putative enterococcal virulence factors were found to be highly prevalent among the commensal baby isolates. The genomic variation as observed by CGH was less between isolates displaying the same MLST sequence type than between isolates belonging to different evolutionary lineages.

Conclusion: The variations in gene content observed among the investigated commensal E. faecalis is comparable to the genetic variation previously reported among strains of various origins thought to be representative of the major E. faecalis lineages. Previous MLST analysis of E. faecalis have identified so-called high-risk enterococcal clonal complexes (HiRECC), defined as genetically distinct subpopulations, epidemiologically associated with enterococcal infections. The observed correlation between CGH and MLST presented here, may offer a method for the identification of lineage-specific genes, and may therefore add clues on how to distinguish pathogenic from commensal E. faecalis. In this work, information on the core genome of E. faecalis is also substantially extended.

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Figures

Figure 1

Figure 1

The different sequence types that were detected in infants A-C during their first year of life. ST; sequence type.

Figure 2

Figure 2

Presence and divergence of PAI genes (123 of 129 open reading frames represented on the microarray) in nine E. faecalis baby isolates, as detected by CGH. Genes PAIef**** correspond to EF**** genes in the PAI of strain MMH594 [25]. Putative enterococcal virulence genes located on the PAI include aggregation substance (agg; EF0485), cytolysin (cyl; EF0523–27 + PAIef0047–49) and enterococcal surface protein (esp; PAIef0056). Dark gray = present, light gray = divergent.

Figure 3

Figure 3

Phylogenomic relationship of community-derived fecal baby isolates based on (A) total microarray probe set and (B) core variable (CV) genes, as detected by CGH. Isolate names and sequence type (ST) are indicated at the end of the branches. Numerical values represent the posterior probability (PP) of support for internal branches.

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