Molecular diagnostics of Cryptosporidium species in pigs on private farms in the Vologda Region of the North-Western Federal District of the Russian Federation

The purpose of the research is to determine infection rate and oocyst isolation degree followed by identification of taxa of Cryptosporidium species in piglets of different age groups using the latest molecular genetic methods, on private farms in the Vologda Region of the North-Western Federal District of the Russian Federation.Materials and methods. These studies were performed in the Russian Federation for the first time. The research was performed on private pig farms located in the Vologda Region of the North-Western Federal District of the Russian Federation from January to September 2022. Feces were taken from piglets of different age groups, namely, sucklings under the age of 1 month, weaners (1–3 months), feeder pigs (4 months and older), as well as from milking sows. Age groups were formed taking into consideration technological parameters of keeping animals on farms. Using microscopic research methods, “positive” samples were detected in which Cryptosporidium oocysts were found, and the number of oocysts was determined. Subsequently, the samples were studied using the equipment of the resource center «Genomic Technologies, Proteomics and Cell Biology» of ARRIAM. Cryptosporidium species were identified in samples of animal feces using high-throughput sequencing of 18S rRNA gene fragment amplicon libraries as obtained by nested PCR.Results and discussion. Cryptosporidium species were identified in each studied age group both in the animal’s presenting indigestion and the animals without any clinical sign of the disease. The average cryptosporidium infection rate was 32.4% in the animals on private farms. The most infected with cryptosporidium oocysts were feeder pigs aged 4–6 months (72%). As a result of sequencing of 18S rRNA gene fragment amplicon libraries obtained using selected primers and subsequent taxonomic analysis of the resulting nucleotide sequences, it was shown that only representatives of the Cryptosporidium scrofarum species were present in all the studied samples.