This work is part of a Project, started in September 2004 and with the duration of three years, aiming the study of the incidence of Paratuberculosis in sheep herds in one of the best Portuguese cheese production region, Serra da Estrela.

Thirteen sheep herds were selected and submitted to an epidemiological inquiry focused on the herd size, animal movement, clinical history and sanitation measures, type of bedding and manure management and human involvement.

Several diagnostic methods were used and correlated with each other: clinical signs, serology, pathological lesions at necropsies, histopathological and immunohistochemical tests, Ziehl-Neelsen staining, direct PCR and bacteriological culture.

The epidemiological inquiry revealed that factors such as: the great size of the herds, poor herd management and sanitary conditions, type of bedding, the absence of suspected animals sequester, as well as common transhumance routes, favoured the spreading of the disease. A serological survey by ELISA and AGID tests performed in 2 562 animals, revealed that 234 samples (9.1%) were positive in ELISA and 30 (1.2%) in AGID.

Twenty seven from 34 animals submitted to necropsies presented clinical signs compatible with the disease. Histophatological lesions were present in 21 animals, and in 18 of them acid-alcohol resistant bacilli were observed. Only two animals were tested by immunohistochemical and showed positive results. From 28 PCR positive samples collected at necropsies, Mycobacterium avium subsp. paratuberculosis was isolated in 20 of them. The correlation between all the diagnostic tests used was performed.

Mycobacterium avium subsp. paratuberculosis isolates are being molecular typed by single nucleotide polymorphisms of gyrA and gyrB genes.

Paratuberculosis is endemic in sheep herds in Serra da Estrela region and special measures are being taken in order to control further spreading of the disease between herds.