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Enterocytozoon bieneusi , an obligate intracellular microsporidian parasite, can infect humans and a wide variety of animals worldwide. However, information on the prevalence and molecular characterization of  E. bieneusi  in pet rats and guinea pigs is lacking. In this study, 325 fecal samples were collected from 152 pet fancy rats and 173 pet guinea pigs purchased from pet shops in Henan and Shandong provinces. The prevalence of  E. bieneusi  was 11.2% (17/152) in pet fancy rats and 20.2% (35/173) in pet guinea pigs. Genotypes D ( n  = 12), Peru11 ( n  = 3), S7 ( n  = 1) and SCC-2 ( n  = 1) were identified in pet fancy rats, and genotype S7 ( n  = 30) and a novel genotype PGP ( n  = 5) were identified in pet guinea pigs. The ITS sequence and its phylogenetic analysis showed that the novel genotype PGP was distinctly different; it exhibited less than 50% similarity to the reference sequences, and did not cluster with any of the known  E. bieneusi  genotype groups, forming a unique branch between groups 6 and 7. These data suggest that this is a new  E. bieneusi  genotype group. This is the first report of  E. bieneusi  infection in pet fancy rats and pet guinea pigs worldwide. The identification of zoonotic genotypes D, Peru11, and S7 suggests that pet fancy rats and guinea pigs can be potential sources of human microsporidiosis.

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First detection and genotyping of Enterocytozoon bieneusi in pet fancy rats (Rattus norvegicus) and guinea pigs (Cavia porcellus) in China