Paratuberculosis (Johne's disease) caused by Mycobacterium avium subspecies paratuberculosis (MAP), is the most costly production disease of animals, has zoonotic concerns and invites trade restrictions. Johne's disease is endemic in Indian domestic livestock population (cattle, buffalo, goat and sheep) and wild animals. MAP has been recovered from cases of Crohn's disease, normal and in-contact animal attendance. India possesses huge population of animals however, per animal productivity is very low as compared to other countries. Despite test and cull policy, incidence of disease continues to increase, resulting in heavy economic losses that have never been estimated or realized.

Lack of effective vaccine has increased the demand of devising preventive measures based on epidemiological information. In India work on the characterization of strain was started from 1999 with the help of Australian and Spanish laboratories (Sevilla et al., 2005, Whittington, 2001, personal communication) giving first indication that Indian MAP strains may be different from other known strains of MAP in the world. In the present study, based on genome sequence of International Reference isolate (MAP K10), assays were designed to have insights of various molecular markers including IS elements, LSPs and SSRs of MAP 'Bison type' 9S5) of goat origin. In some of IS1311 loci a novel polymorphism was observed in MAP 'Bison type' S5, not seen in MAP K10 genome and MAP isolates from outside India. This is the first report of this polymorphism and so far these polymorphisms have not been observed in Indian and non-India strains. In the next stage presence of this polymorphism was tested in a panel of Indian MAP isolates (from different host species and diverse geographical regions) and non-Indian MAP isolates. Novel polymorphism was consistently present in all Indian MAP isolates tested despite differences in host species and diverse geographical regions and this polymorphism was not seen for non-Indian MAP isolates. Non-Indian MAP isolates were identical to International Reference isolate (MAP K10). Study provided unique characteristic molecular signature that can distinguish Indian MAP from other isolates. Study indicated the need for analyzing large number of Indian MAP isolates in order to confirm this polymorphism as a characteristic of Indian MAP isolates. This effort will provide new dimensions to paratuberculosis research in the coutnry.