We found that the fibronectin-binding proteins efbA and efaAfs, endocarditis and biofilm-associated pili ebpABC, sortase A (srtA), adhesin to collagen of E. faecalis (ace), general stress proteins gls24 and glsB, membrane metalloprotease associated with endocarditis (eep), thiol peroxidase for oxidative stress resistance (tpx), and sex pheromones cCF10, cOB1, cad and camE were present in the genomes of all isolates, with variable nucleotide identities (97–100% versus the reference sequence). Here, YAP1 is linked to endocarditis.