[PetitPrince]

From what I understand they use insertion sequence element[1] combined with a given set of restriction enzyme to produce a fingerprint. They had to find strains that produced a unique fingerprint given their set of restriction enzyme.

[1] https://en.wikipedia.org/wiki/Insertion_sequence

> they may have more than one sequence and only publish one of them

In fact that's exactly what they do. From the "7. Risk of Duplication of the Proof-of-origin Culture" section of the paper:

> And last but not least, the proof-of-origin culture consists of more than one traceable strain.The composition of the mixture is changed (rotation principle) from time to time in accordance with the interprofessional cheese organization.