Highly polymorphic and modular extragenic (h.p.m.e.) markers within specific taxa of microorganisms and use thereof for their differentiation, identification and quantification

A Highly Polymorphic and Modular Extragenic (H.P.M.E.) marker, said H.P.M.E. being a microbial genome nucleotide sequence having a length of less than or equal to 2000 bp, and said HPME comprising at least one primary protein encoding gene and a secondary flanking extragenic region,

• wherein when said H.P.M.E. is aligned with two or more nucleotide sequences to obtain a
• sequence alignment, said sequence alignment has:
• a percentage of similarity lower or equal to than 78% in pairwise alignment, and three or more stretches from 9 to 30 bp having at least a 97% sequence identity in all the aligned sequences and one or more stretches are not in the protein coding region;
• the insertion or the deletion of 1 or more nucleotides in the extragenic region, even when the percentage similarity is higher than 78% in pairwise alignment;
• or
• a percentage of similarity lower or equal to 78% in pairwise alignment, and three stretches of from 9 to 30 bp having at least a 97% sequence identity in all the aligned sequences and at least one sequence variation due to insertion/deletion of one or more nucleotides in the extragenic region.