Enterocytozoon bieneusi is an important microsporidian protozoa that causes intestinal disorders in humans. We collected 191 fecal samples from roadkill deer carcasses, among which 13 (6.8%) showed positive reaction for E. bieneusi by polymerase chain reaction assay. Phylogenetic analysis revealed 6 distinct genotypes, 1 of which was novel. All genotypes belonged to Group 1, which has low host specificity, indicating possible transmission through sylvatic cycle. E. bieneusi infection was predominant in female deer (p<0.05).
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