Paratuberculosis is one of the most hazardous infectious diseases, causing heavy economic losses due to poor health, low productivity and high fatality rate among domestic and wild ruminants. Mycobacterium avium subsp. paratuberculosis is the etiological agent of Bovine Johne's disease. In this study PCR were used to detect the presence of the Acid Fast Bacillus Mycobacterium paratuberculosis, in the intestinal tissues and Mesenteric Lymph Nodes of small ruminants causing Paratuberculosis. PCR was compared to HEY medium culture on the Herrold's Egg Yolk Media.

The samples were collected from Lahore Slaughter house and brought to the Molecular Pathology Laboratory at the Department of Pathology, University of Veterinary and Animal Sciences, Lahore. The study was conducted to compare PCR and the HEY medium culture for the diagnosis of paratuberculosis caused by M avium subsp. Paratuberculosis. A total of 500 tissue samples, 250 of the ileum and 250 of the mesenteric lymph nodes were collected randomly for the identification of Johne's disease. All samples were inoculated on the HEY medium prepared in the same laboratory aseptically. Followed by DNA extraction through the Kit method then run the PCR for insertion sequence IS 900, specific 626 bp fragment, were targetted in the genome of M paratuberculosis.

The results of the study showed more samples detected positive by PCR as compared to conventional culture methodology. Also they showed in the mass of 500 tissue samples that more bacilli are prone to the samples of small intestines than associated mesenteric lymph nodes. Regarding the sensitivity of the two techniques the PCR seemed more sensitive to detect the mycobacterium in the tissues than the conventional, laborious and time consuming HEY medium culture technique; though culture has been used as golden standard in this study also. When statistically analyzed results were insignificant due to small sample size.

The study will help in comparison of the two latest techniques for the diagnosis of M paratuberculosis, to check the validity of the better technique. In this study the sensitivity and specificity of PCR was checked and compared with culture on the HEY medium staining for the diagnosis of paratuberculosis in small ruminants.