Mycobacterium avium subspecies paratuberculosis (M. a. paratuberculosis) is the causative agent of paratuberculosis (Johne's disease), a chronic inflammatory disease of the gastrointestinal tract that affects mainly livestock and wild ruminants. M .a. paratuberculosis isolates have been classified into three major groups by using large restriction fragment analysis (RFLP, PFGE) and rapid molecular techniques based on Single Nucleotide Polymorphisms analysis (SNPs) or).

In this study the inh-A gene, an important gene in fatty acid biosynthesis, and previously classified as polymorphic, was analyzed for the detection of SNPs among the different M. a. paratuberculosis types. A panel of M. a .paratuberculosis strains from different types (I, II and III), different hosts (cattle, sheep and goat) and geographical origin (Spain, Scottland and Denmark) was selected. The complete inh-A gene from all strains was amplified by PCR, sequenced and then compared to detect the presence of SNPs.

The sequencing analysis of the inh-A gene was able to classify all M .a. paratuberculosis strains into Types I, II and III. These results are in agreement with previous studies in which these strains were classifed as well by gyrA and gyrB genes by using sequencing analysis. The SNPs were also used to design a restriction endonuclease analysis that allowed the classification of all M. a. paratuberculosis isolates into the three types with a simple PCR-REA analysis, this resulting in a fast and useful molecular technique. Therefore, the inh-A gene has been shown to be a valuable target to differentiate M. a. paratuberculosis isolates for epidemiological purposes.