Mycobacterium avium subspecies paratuberculosis (MAP) the cause of Johne's disease in animals is distributed world over and has also been associated with inflammatory bowel disease (IBD or Crohn's disease) of human beings. Despite low productivity (1/6 in Asian countries), huge animal (>450 millions) and human population (>1.3 billion), has not been extensively screened for the presence of MAP. Limited studies have shown that MAP was endemic in animal herds and flocks in the country. Preliminary characterization of MAP showed that native strain of MAP prevalent in domestic ruminants was ' Bison type' (Sevilla et al., 2005)..

Presently India lacks a referral laboratory to look into different aspects of research on Mycobacterium avium subspecies paratuberculosis in the huge population of domestic ruminants and human beings. Johnin has been used for last 40-50 years and was the only diagnostic reagent available to screen animals against Johne's disease. Johnin production was based on a strain of MAP imported from UK. Johnin production was discontinued due loss of strain in serial passages and has been restarted by importing a new strain of MAP, as there is no standard Indian MAP strain. Limited studies on diagnostics and vaccines developed utilizing antigens from strains prevalent outside the country were not as efficacious as to that indigenously developed utilizing antigens from native MAP 'Bison type' strain of goat origin. Therefore genetic contents including different markers (IS elements, short sequence repeats and large sequence polymorphisms) of native MAP strains were analyzed and compared with MAP K10 genome to have inference of differences in native MAP 'Bison type' isolate and to study the phylogeny of native isolates. Results of present study confirmed that MAP 'Bison type' (S5) genome has genetic differences in terms of SNPs, locus polymorphisms and genomic duplications and there is need to extensively analyze Indian MAP isolates to have insights in to their evolution and pathogenicity. In the present study different methods of the strain typing were also optimized for the first time in the country to guide geno-typing and futuristic molecular epidemiological studies.