Molecular Detection and Genotypic Analysis of <i>Encephalitozoon cuniculi</i> in Pet Rabbits in Central Thailand

INTRODUCTION: Encephalitozoon cuniculi is an obligate intracellular microsporidian parasite that commonly infects rabbits and exhibits zoonotic potential by occasionally infecting humans. This study investigated the prevalence and genotypic distribution of E. cuniculi in pet rabbits in central Thailand. METHODS: In total, 101 voided urine samples from owned pet rabbits were screened for E. cuniculi using polymerase chain reaction-based technique targeting the internal transcribed spacer (ITS) region of ribosomal DNA. Fifteen positive samples were further analysed using multi-locus genotyping (ITS region, PTP and SWP1) and phylogenetic relationship analysis. RESULTS: In total, 21 (20.79%) pet rabbits tested positive for E. cuniculi. Although E. cuniculi prevalence was not associated with breed (p = 0.508), sex (p = 1.000) or age (p = 0.413), it was significantly higher in clinically affected rabbits (46.43%; 95% confidence interval [CI]: 27.5%-66.1%) than in clinically healthy rabbits (4.88%; 95% CI: 0.6%-16.2%). Multi-locus genotyping demonstrated the co-circulation of Genotypes I and III within the population. Phylogenetic analysis also revealed a close genetic relationship between rabbit-derived strains identified in the study and genotypes previously reported in humans. CONCLUSIONS: This study demonstrated the presence of E. cuniculi DNA in urine samples from both clinically affected and apparently healthy pet rabbits, with multi-locus genotyping revealing the presence of E. cuniculi Genotypes I and III. To the best of our knowledge, this is the first report describing molecular detection and genotypic characterization of E. cuniculi in pet rabbits in Thailand.