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Equine protozoal myeloencephalitis (EPM) was initially identified by J.R. Rooney in 1964. The first cases were recognized among Standardbreds returning to Kentucky from racetracks in the Northeastern United States. Subsequent cases have been reported among native horses in most of the US as well as in Canada, Mexico, Argentina, Panama, and Brazil. As more cases were examined, it became apparent that the brain was frequently involved, thus changing the name to focal myelitis-encephalitis. Ten years later, a "Toxoplasma-like" protozoan was recognized in histopathologic sections and the disease gradually became known as EPM.

Dubey was the first to suggest that EPM was caused by a Sarcocystis organism. In 1991 he was able to culture the organism from the spinal cord of an affected horse and subsequently the organism was named Sarcocystis neurona because it often develops within neurons. Further work done by Dr. Granstrom and his group resulted in an antemortem diagnostic test for this disease using Western blot analysis to determine the presence of antibody to S. neurona in CSF.

Research completed in 1995 shed considerably more light on the life cycle through work done at the University of Kentucky and at the University of Florida. It was discovered through the use of PCR that the organism was very closely related to Sarcocystis falcatula which has the Opossum as it's definitive host. The natural intermediate hosts are the grackle and cowbird, although numerous other intermediate hosts may be affected. Further evidence for this organism being the causative agent of EPM was confirmed by experimental induction of the disease which was recently completed by the researchers at the University of Kentucky.