The Opportunistic Pathogen Encephalitozoon Cuniculi in Wild Living Murinae and Arvicolinae in Central Europe.

•The occurrence of E. cuniculi in Apodemus spp. and Myodes glareolus was reported for the first time.•The highest infection rate was recorded for A. flavicollis.•E. cuniculi genotype II was the most frequently recorded.•Uncommon in rodents, E. cuniculi genotypes I and III, were also identified.