Phylogenetic analysis of closely related Enterococcus faecalis, Enterococcus faecium species based on partial housekeeping genes

Abstract:

[Objective] Using the 16S rRNA, clpX and recA gene sequences to identify the phylogenetic relationship among closely related Enterococcus faecalis and Enterococcus faecium species. [Methods] Nine E. faecium and one E. durans strains originally isolated from traditional dairy products were characterized by PCR methods. The gene sequences, clpX and recA, were amplified and assessed for their suitability as phylogenetic markers. Phylogenetic trees were constructed with 16S rRNA and the aforementioned housekeeping genes obtained from this study and public gene databases. [Results] In the phylogenetic tree of clpX and recA genes, 10 tested strains and E. faecalis belonged to the same branch. The sequence similarity was 99.6% and 98.6% with E. faecalis, and 61.5% and 33.5% with the Faecium-group (E. durans and E. faecium), respectively. The differences of these two genes between the closely related strains of E. durans and E. hirae were 20.3% and 39.0%. Based on the phylogenetic tree of 16S rRNA, the tested strains and Faecium-group (E. lactis, E. faecium, E. durans and E. hirae) belonged to the same branch. These members shared a similarity of higher than 99.6%, while an average homology of 98.4% with E. faecalis. No obvious difference was observed between closely related strains. [Conclusion] Based on the analysis results of the housekeeping genes, clpX and recA, we propose that nine E. faecium and one E. durans, could be transferred to E. faecalis. Meanwhile, the clpX and recA genes are suitable for classification and identification of some closely related E. faecalis and E. faecium species.