Clinostomiasis is a zoonotic disease of freshwater fish caused by digenetic trematodes in the genus Clinostomum. This parasite causes 'Laryngopharyngitis' disease in people and may result in human fatalities from asphyxiation when consumed improperly cooked Clinostomum complanatum-encysted metacercariae (EMC) infected fish. This study provides genetic confirmation, phylogenetic analysis and histopathological evaluation of Clinostomidae EMC recovered from infected wild-caught and farmed Nile tilapia (Oreochromis niloticus) in Egypt. Recovered parasites were identified as Clinostomum complanatum, C. phalacrocoracis and Euclinostomum heterostomum using macroscopic and microscopic examination. PCR amplification and sequencing of rDNA-ITS2 gene regions of C. complanatum; C. phalacrocoracis and mtDNA CO1 gene regions of E. heterostomum were carried out. Nucleotide sequences of C. complanatum, C. phalacrocoracis and E. heterostomum were registered in GenBank with accession numbers MT133890.1, MT158303.1 and MW193532.1, respectively. Histopathological findings in buccal cavities and kidney tissues of infected O. niloticus were described.
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