The aim of this study was to draw attention to the risk of transmission of Encephalitozoon, Cryptosporidium and Blastocystis infection due to high animal migration and to point out that even wild animals can be a source of many zoonotic diseases. Encephalitozoon cuniculi, Cryptosporidium spp. and Blastocystis spp. are frequent microscopic organisms that parasitise humans, domestic and wild animals. Two hundred and fifty-five faecal specimens were collected from wild boars, badgers, wolves, bears, foxes and deer from 15 locations in Slovakia. Sequencing of positive PCR products and subsequent sequence comparison with GenBank sequences identified Blastocystis spp. in five wild boars. The ST 5 (n = 4) and ST 10 (n = 1) subtypes were determined by genotyping. We identified Encephalitozoon cuniculi in five wild boars, and genotype II (n = 5) was determined on the basis of ITS repeat sequences. Cryptosporidium scrofarum was sequenced in wolves (n = 4) and wild boars (n = 1), while Cryptosporidium suis only in wild boars (n = 2). None of the wild boars had a mixed infection.
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