Paratuberculosis, which is also known as Johne's disease, is a chronic, progressive enteric disease of ruminants and other species of animals including primates. Cattle become infected with Mycobacterium avium subsp. paratuberculosis(MAP) as calves but often do not develop clinical signs until 2 to 5 years of age. Therefore, it causes several economic losses in the cattle industry in all over world per year. Moreover, it has been evidenced by some researchers that MAP is also as the causal agent of Crohn's disease in the human population.

To evaluate the prevalence of paratuberculosis in dairy herds, and to determine the association between herd infection status and herd management practices, this research was conducted.

A nested-PCR method based on insertion sequence 900(IS900) was adapted for testing bulk-tank milk for the presence of the MAP in Shiraz, Marvdasht and Sepidan regions of Fars province dairy herds. Moreover, an extensive questionnaire based on the main risk factors of the disease was developed and used to collect data from the herds.

Twelve of the 110 examined bulk-tank milk samples (11%, 95%CI: 5-17%) tested IS900-PCR positive. The herd prevalence of the MAP in the Shiraz, Marvdasht and Sepidan regions were 8.6, 8.5 and 23.5 percent respectively. Statistical analysis using multivariable logistic regression showed that low sanitation of periparturient cows as measured by contamination of udders with manure (OR = 6.4, P = 0.02) and history of suspected Johne's disease in the herd (OR = 6.7, P = 0.04) were significantly associated with herd infection status. No relationship between breed, herd size and other management practices was found in this study.

As the bacterium is a slow-growing mycobacterium, the detection of MAP directly from bulk tank milk by IS900 nested PCR could become a valuable diagnostic or screening test for herds with Johne's disease.