Enterococcus faecalis, a member of the natural microbiota of animal and human intestinal tracts, is also present as a natural contaminant in a variety of fermented foods. Over the last decade, E. faecalis has emerged as a major cause of nosocomial infections. We investigated the genetic diversity in 30 clinical and food isolates, including strains V583 and MMH594, in order to determine whether clinical and food isolates could be distinguished. Data were obtained using comparative genomic hybridization and specific PCR with a total of 202 probes of E. faecalis, selected using the available V583 genome sequence and part of the MMH594 pathogenicity island. The cognate genes encoded mainly exported proteins. Hybridization data were analyzed by a two-component mixture model that estimates the probability of any given gene to be either present or absent in the strains. A total of 78 genes were found to be variable, as they were absent in at least one isolate. Most of the variable genes were clustered in regions that, in the published V583 sequence, related to prophages or mobile genetic elements. The variable genes were distributed in three main groups: (i) genes equally distributed between clinical and dairy food isolates, (ii) genes absent from dairy food-related isolates, and (iii) genes present in MMH594 and V583 strains only. Further analysis of the distribution of the last gene group in 70 other isolates confirmed that six of the probed genes were always absent in dairy food-related isolates, whereas they were detected in clinical and/or commensal isolates. Two of them corresponded to prophages that were not detected in the cognate isolates, thus possibly extending the number of genes absent from dairy food isolates. Genes specifically detected in clinical isolates may prove valuable for the development of new risk assessment markers for food safety studies and for identification of new factors that may contribute to host colonization or infection.Enterococci are ubiquitous low-GC percentage gram-positive bacteria encountered in various environments, including animal and human intestinal tracts, soil, plants and water. They are found as members of the natural microbiota of a variety of fermented food products such as artisanal cheeses and fermented sausages and reportedly play an important role in food processing (23,28). Enterococci have been consumed for centuries, and both Enterococcus faecalis and Enterococcus faecium species are subdominant members of the digestive microbiota in human. However, isolates of both species are emerging as major causes of nosocomial infections, including urinary tract and abdominal infections, bacteremia, and endocarditis in patients with severe underlying diseases or an impaired immune system (40). E. faecalis causes 60 to 80% of enterococcal infections. Less than 2% of infections are due to strains resistant to clinically relevant antibiotics, ampicillin and vancomycin, implying that other genetic factors are necessary for E. faecalis infection and virulence potential (30).Phe...