genetic structure of ssr1 & ssr2 loci from iranian mycobacterium avium subspecies paratuberculosis isolates by a short sequence repeat analysis approach

abstract         background and objective: paratuberculosis has been repeatedly reported from iranian ruminant herds. the extrem fastidious nature of mycobacterium avium subspecies paratuberculsos hinders genomic diversity studies of the pathogen. short sequence repeat analysis is one of the genome-based approches recently developed to overcome this difficulty. in this study we describe the application of ssr genotyping on three iranian map type strains plus the iii & v vaccinal strain.         methods: all the bacteria were examined by pcr-f57 and pcr-is900 experiments in order to authenticate their identity as map. ssr genotyping using ssr1 & ssr2 loci was conducted according to the amonsin method. pcr amplicons were sequenced to guarantee the accuracy of findings.         results: at ssr1 locus two allels were identified, a larger allel of 770 bp and a smaller allel of 763 bp long. at ssr2 only a single allele, 800 bp long, was detected. two iranian bovine and ovine map isolates along with the vaccinal iii & v strain shared a single ssr1/ssr2 pattern while a different ssr1/ssr2 was represented by the third (caprine) iranian map isolate.         conclusion: while finding a shared ssr type between the two iranian map isolates and the iii & v strain might represent a mutual ancestral background but this has to be assessed through further studies. detection of two ssr genotypes between three iranian type strains is likely a reflection of more map clones in iran.        keywords: mycobacterium avium subspecies paratuberculosis (map), ssr genotyping, genetic marker, genetic locus