Naturally occurring genetic markers in lactobacilli and their use to verify the authenticity of Swiss Emmental PDO cheese

A general method for the detection and identification of specific strains of bacteria is described. The assay is based on the observation that insertion sequences (IS) in different strains of bacteria occur at diverse loci on the bacterial genome. Exclusive PCR primers can be selected for a particular strain where one of the primers is specific for a particular IS element and the other is specific for the adjacent DNA sequence in the genome. Only bacterial strains containing the IS element at the particular point on the genome will yield an amplicon of the expected size after PCR. We have illustrated this method by selecting primers to detect some lactobacilli strains that are used exclusively in the manufacture of Swiss Emmental cheese. Using this method we were able to differentiate cheeses manufactured in Switzerland from those made in other European countries.