Detection of Zoonotic Gastrointestinal Pathogens in Dairy Sheep and Goats by Using FilmArray Multiplex-PCR Technology.

The objectives of this study were (a) to detect gastrointestinal pathogens in faecal samples of sheep and goats using the FilmArray GI Panel and (b) to evaluate factors that were associated with their presence. Faecal samples from ewes or does in 70 sheep flocks and 24 goat herds in Greece were tested for the presence of 22 gastrointestinal pathogens by means of the BioFire FilmArray Gastrointestinal (GI) Panel. The most frequently detected pathogens were Shiga-like toxin-producing stx1/stx2 (94.7% of farms), (59.6%), and spp. (50.0% of farms). Other pathogens detected were spp., spp., enterotoxigenic lt/st, , O157, Rotavirus A, /enteroinvasive and . There was a difference in the prevalence of detection of pathogens between sheep and goat farms only for spp.: 18.3% versus 0.0%, respectively. Mixed infections were detected in 76 farms (80.9% of farms), specifically 57 sheep flocks and 19 goat herds, with on average, 2.5 ± 0.1 pathogens detected per farm. The body condition score of ewes in farms, in which only one pathogen was detected in faecal samples, was significantly higher than that of ewes in farms, in which at least two pathogens were detected: 2.55 ± 0.11 versus 2.31 ± 0.04. In sheep flocks, the number of pathogens in faecal samples was significantly higher in farms with semi-extensive management. In goat herds, the number of pathogens in faecal samples was positively correlated with average precipitation and inversely correlated with temperature range in the respective locations.