Encephalitozoon cuniculi strain III is a cause of encephalitozoonosis in both humans and dogs.

Microsporidia are obligate intracellular eukaryotic organisms found in a wide range of vertebrate and invertebrate hosts. Encephalitozoon cuniculi is commonly found in domestic rabbits and rodents and also occurs in dogs, other canids, and primates, including humans. DNA sequencing of the ribosomal RNA genes has been used to identify these parasites to a species level and to define E. cuniculi strains I, II, and III. Eight new dog isolates were characterized as E. cuniculi strain III by use of molecular methods. This strain has also been identified in isolates from immunocompromised humans, suggesting the zoonotic potential of this parasite species. Prolonged microsporidial spore shedding from asymptomatic dogs is also reported.