Habitat of Enterococcus spp

Enterococci are widespread in nature, can grow and persist in harsh environments and have been detected in the fecal microbiota of most animals, from insects to mammals. They are also readily recovered from foods such as milk and meat products, from various environmental sources and in waste and surface water . Enterococci are considered important members of the intestinal microbiota of mammals, reptiles, birds, fish, and insects as well as in plant environments. Members of Enterococcus spp. can also be found in the soil, water, and food. More specifically, E. avium, E. durans, E. faecalis, E. faecium are frequently isolated from cheese products, whereas, E. avium, E. casseliflavus, E. durans, E. faecalis, E. faecium, E. gallinarum, and E. hirae have been described components of the microbiota of various raw meat products. It is important to note that members of these species are frequently employed as starter cultures in fermented food products. The high prevalence of these species in raw meat is closely related to the fecal microbiota from the food animal species. Despite the presence of enterococci in 82-100% of retail meat products, studies of cooked meat suggest that enterococci do not constitute the largest population on such products.

Enterococci are found in the feces of most healthy adults; in several recent studies from Japan, Federal Republic of Germany, and Scandinavia, enterococci were found in 97% of 71 individuals studied. The most frequently encountered species are E. faecalis and E. faecium. When enterococci from feces have been identified to species, many studies report that E. faecalis is more common and is found in higher numbers than E. faecium. Studies from other locations, however, have reported that E. faecium is found more often than E. faecalis.

In humans, typical concentrations of enterococci in stool are up to 108 colony forming unit (CFU) per gram. Although the oral cavity and vaginal tract can become colonized, enterococci are recovered from these sites in fewer than 20% of cases.

Enterococci are less commonly found at other sites such as in vaginal (17%) in one study, and oral specimens, and results are sometimes quite variable. In a study of the dental plaque of healthy students, academic staff, healthy toothache patients, and hemodialysis patients and staff, enterococci were found in approximately the same percentages in the various groups (10% overall). Although patients and staff in one particular hospital had carriage rates of 60%; almost all isolates were E. faecalis. In another study, higher rates of enterococcal carriage were found among long-term hemodialysis patients and cardiac patients than among their staff and acute dental patients; in the same study, E. faeciun outnumbered E. fecalis isolates. E. casseliflavus, E. durans, E. gallinarum, E. hirae also contribute significantly to the enterococcal fecal microbiota of humans, whereas E. avium and E. mundtii have only been occasionally isolated. Enterococci that have been isolated from domesticated pets include E. avium, E. durans, E. faecalis, E. faecium, and E. hirae. E. avium, E. casseliflavus, E. durans, E. faecalis, E. faecium, E. gallinarum, E. hirae, and E. mundtii have been isolated from surface waters, whereas only E. hirae has been identified from groundwater. E. casseliflavus, E. faecalis, E. faecium, and E. sulfureus have also been associated with plant materials. Among the more rarely isolated species, E. cecorum has been isolated from domesticated pets, and feces from bovine and poultry sources. E. dispar has been isolated from poultry feces.

Since its initial isolation from Gouda cheese, E. malodoratus has been isolated from poultry feces, and has been associated with spoilage of sausage. Although primarily associated with soil and plant material, E. mundtii has been isolated from fish and meat products. E. mundtii has also been identified as a component of the intestinal microbiota of chickens. E. pseudoavium has been isolated from pigs and poultry; E. raffinosus has rarely been isolated outside of the clinical environment, but has been identified from domestic pets. E. sulfureus has been isolated only from grass and fish sources. E. solitarius and E. seriolicida have been reclassified as members of the genera Tetragenococcus and Lactococcus, respectively. Recently, two new proposed species of pigmented enterococci, E. gilvus and E. pallens, were described from clinical isolates [34]. These species, in addition to E. asini, E. canis, E. haemoperoxidus, E. moraviensis, E. phoeniculicola, E. porcinus, E. ratti, and E. villorum, are recent additions to the genus and their distributions in different environments are unknown. It is worth noting that reports of the ecological distribution of Enterococcus spp. in different environments may be hard to compare due to differences in isolation methodology. Most surveys to date have been focused on the isolation of what are thought to be the most abundant species of enterococci, i.e., heavily influenced by those studies conducted in clinical settings.

Recent changes in the taxonomy of enterococci has revealed that an increasing number of species do not conform to long-held descriptions of the genus. For example, not until the description of the PYR-negative species of E. cecorum, E. columbae, and E. saccharolyticus has the PYR reaction been used other than as a definitive characteristic of Enterococcus spp. Other factors that might influence the recovery and/or prevalence of non-dominant species include the choice of media, the temperature of incubation, composition of the incubation atmosphere, and identification methodology. Given the close similarity of the newly described species to long-standing members of the genus, confident identification to the species level may not always be possible using traditional biochemical testing.