Abstract
A case of encephalitis of unknown origin in the horse was investigated. Postmortem examination findings revealed a nonsuppurative granulomatous meningoencephalitis in the right hemisphere of the cerebral cortex. Testing for West Nile virus, equine herpes virus, equine infectious anemia, Toxoplasma gondii, Neospora caninum, and Sarcocystis neurona were negative. The horse had a titer for Encephalitozoon cuniculi, and sections from the affected area of the brain tested positive for the organism using both polymerase chain reaction (PCR) and immunohistochemistry. Amplicons generated using PCR were sequenced, and E. cuniculi genotype II was identified. This is the first case of E. cuniculi genotype II associated with encephalitis in the horse.