Paratuberculosis (Johne’s disease) is a chronic enteric progressive disease, characterized clinically by chronic or intermittent diarrhea, emaciation, and death. The disease has worldwide distribution and economic impact on ruminant livestock production (Stabel, 1998). The disease is considered one of the most important diseases of ruminant population (Tripathi et al 2002 and Sivakumar et al 2005). Johne’s disease cause huge economic losses and has high impact on dairy and beef cattle industry due to premature culling of animals, reduced weight gain, reduced feed efficiency, reduced carcass value, reduced milk production, increased susceptibility to mastitis and reproductive disorders leading to increased calving intervals, reduced fertility and additional veterinary costs (Hasonova and Pavlik 2006). Mycobacterium avium subsp. paratuberculosis is biochemically relatively inactive and identification is currently based on mycobactin dependency and detection of the insertion sequence IS900 by the means of the polymerase chain reaction (Collins et al 1989).

Faecal culture may remain the most definitive test to date for identification of both sub-clinically and clinically infected cattle but the prolonged incubation period (12- 16 weeks) required for accurate diagnosis was a distinct disadvantage (Stabel and Whitlock 2001). In addition, the need of a specialized medium for propagation of the organism and frequent contamination is often a problem when culturing MAP from faecal specimens. Despite some of these disadvantages, faecal culture is still considered as the “gold standard” diagnostic test for the detection of Map (Sweeney et al 1992). It is the only test that does not produce false positive results (100% specificity) (OIE 2004). Although the ‘gold standard’ for detection and confirmation of viable or more specifically culturable. MAP remains isolation of the organism in culture, PCR has made rapid detection of this fastidious, slow-growing organism possible in milk, faeces and clinical samples (Grant et al 2000, Pillai and Jayarao 2002 and Fang et al 2002).

The most widely used target gene for detection of MAP IS900 was first described in 1989 (Green et al 1989) and presently considered specific for MAP. The MAP genome has 15 to 20 copies of the insertion element, and the sequenced strain K-10 has 17 copies (Li et al 2005). This high copy number target gives an increased sensitivity compared to systems targeting single copy genes, which makes it popular in molecular diagnostic methods for paratuberculosis. IS900 has a unique nucleotide sequence which can be specifically detected by hybridization or PCR techniques (Collins et al 1993 and Moss et al 1992). Sequences of IS900 proved to be highly sensitive and specific markers of MAP among other slowly growing, acid-fast bacteria, because IS900 has been detected in all reference and vaccine strains as well as in field isolates of MAP from several hosts but never in other bacterial species (Ahrens et al 1995 and Whipple et al 1990).

Since Johne’s disease is so insidious within an animal population, early diagnosis and proper management are considered to be the most useful tools for controlling the disease within domestic livestock herds. Keeping the above points in mind the present study was planned with the objective to detect Mycobacterium avium subsp. paratuberculosis in bovine fecal samples using faecal culture and IS900 PCR assay.