In our experiment, 3 species-specific primer pairs cultivated in cell lines were used: Encephalitozoon cuniculi-specific primer pairs (ECUNF and ECUNR), Encephalitozoon hellem-specific primer pairs (EHELF and EHELR), and Encephalitozoon intestinalis-specific primer pairs (SINTF and SINTR). The PCR products were estimated to be 550 bp in E. cuniculi, 547 bp in E. hellem and 545 bp in E. intestinalis respectively, which can prove the precision and reliability of this method in the species identification of the genus Encephalitozoon. All 3 primer pairs were species-specific and none of them amplified gene sequences from other Encephalitozoon spp.
A total of 47 avian faecal samples of wild waterfowl (great cormorant — Phalacrocorax carbo, great crested grebe — Podiceps cristatus, white stork — Ciconia ciconia) trapped in the eastern Slovakia were screened for the presence of human pathogenic microsporidia by microscopy and real-time SYBR Green PCR method using species primers and sequenced. Microscopic analysis showed presence in 32 samples (29 cormorants, 3 dippers). Microsporidial DNA (Encephalitozoon cuniculi genotype I) was identified in 19 faeces samples (40.4%) namely cormorants in 17 out of 40, one dipper of 5 and a stork out of 2. The present work describes three new host species of the bird population in microsporidium Encephalitozoon cuniculi genotype I which confirms the theory of low specificity of this species.