Single nucleotide polymorphism (SNP) analysis, a practical means of genomic interrogation for paratuberculosis studies in Iran

Genotyping of Mycobacterium avium subspecies paratuberculosis (MAP) remains a challenge in epidemiology of paratuberculosis even with availability of the traidional molecular techinques such as PFGE, RFLP, SSR and MIRU-VNTR assays as MAPs are genetically monomorphic bacteria. In the Iranian environment MAP seems to have extensively scatterd across the country as reports indicating frequent occurrence of the disease in bovine, caprine and ovine populations are now on rise. However, only little is known on population structure of MAP in this country. The few conducted observations are in support of existence of cattle (C) type of MAP with no trace of sheep (S) type isolates ever found. In this work, a recently-developed PCR-based Single Nucleotide Polymorphism (SNP) assay concentrating on 13 individual loci across the MAP genome was conducted on a single endogenous Iranian MAP isolate of caprine origin. PCRs were conducted using universal protocol with all amplicons Sanger sequenced in search for target SNPs. An identical pattern of SNPs with that of the MAP K10 laboratory strain was revealed to confirm the identity of this local strain as a cattle type. The Leao’s SNP analysis is a simple, straightforward assay that if used extensively, we might expect a better understanding of evolutionary scenario behind todays’ epidemiology of paratuberculosis in Iran.