الفهرس 
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Abstract
Out of 144 examined dairy cattle, 25 (17%) showed clinical signs of Johne’s disease. Mycobacterium avium subsp. paratuberculosis (MAP)-ELISA was applied to sera of 143 dairy cattle, 34 buffalo, 88 sheep, and 56 goats; with positive percentages of 56%, 47%, 47%, and 38%, respectively. Standard culture technique was able to detect 11 shedders (23%) out of 47 examined cattle. MAP DNA was detected in 14 (18%) out of 76 cattle fecal samples using IS900-PCR. MAP was not detected in feces of investigated buffaloes by culture or PCR. Duplex F57/IC real-time PCR was developed and was found to be more sensitive than IS900-PCR. The time to detection of MAP was reduced with increased sensitivity by combination of a pre-enrichment step on HEYM-MJ for 4 weeks followed by detection of MAP DNA with the developed real-time PCR. Genotyping using MIRU-VNTR typing method revealed slight genetic diversity among 10 Egyptian MAP DNAs and fair one among 17 German MAP isolates with detection of nine patterns using only 3 typing systems. Different diagnostics were evaluated compared to culture as gold standard, with variable estimates of sensitivity, specificity, and accuracy. There was a poor agreement (0.132) between serum ELISA and IS900-PCR, while agreement between milk and serum ELISAs was very good (0.8). There was a slight degree of agreement (0.128) between ASCA and MAP ELISAs as diagnostic tests for Crohn’s disease; which, somewhat, supports the relationship between MAP and Crohn’s disease.