Background and purpose: Enterococci as a group of bacteria infecting raw foods and dairy products can contaminate different food products. The purpose of this study was to isolate strains of enterococci based on the Real time PCR method using melting curve analysis in food samples.

Materials and methods: In this experimental study, 510 samples were collected from which 138 different samples (chicken, meat, milk, and cheese) containing different strains of enterococci were investigated. Then, identification of Enterococcus species was performed by targeting specific sites and specific primers were designed according to Real time PCR-based melting curve analysis.

Results: Based on melting curve analysis by Real Time PCR, the Enterococcus species identified were as follows: E.faecalis in 84 isolates (60.86%), E.faecium in 48 ​​ (34.78%), E.gallinarum in 1 (0.7%), E.avium in 4 (2.8%), and E.Caselli flavus in 1 isolate (0.7%). The most frequent isolates were detected in 29 samples of chicken meat (51.44%) and red meat (n= 21, 24.63%). Considering the results of sequencing as a Gold a standard test, the sensitivity and specificity of phenotypic methods for E.faecalis, E.faecium, E.gallinarum, E.avium, and E.Caselli flavus were 94.78% and 90.74%, 89.13 % and 97.77 %, 50% and 98.52%, 66.66% and 98.52%, and 50% and 98.56%, respectively. A significant relationship was observed between the sample and distribution of Enterococcus species (P≤0.05).

Conclusion: Due to extensive viability error in identification of Enterococcus species isolated from food by phenotypic methods, using a rapid and sensitive method is necessary.