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Background   Giardia duodenalis  and  Enterocytozoon bieneusi  are widespread pathogens that can infect humans and various animal species. Thus far, there are only a few reports of  G. duodenalis  and  E. bieneusi  infections in ruminant wildlife. Thus, the objective of this study was to examine the prevalence of  G. duodenalis  and  E. bieneusi  in forest musk deer in Sichuan, China, as well as identifying their genotypes.    Results  In total, we collected 223 faecal samples from musk deer at the Sichuan Institute of Musk Deer Breeding in Dujiangyan ( n  = 80) and the Maerkang Breeding Institute ( n  = 143). Five (2.24%) faecal samples were positive for  G. duodenalis ; three belonged to assemblage E, and two belonged to assemblage A based on the sequence analysis of the β-giardin ( bg ) gene. One sample each was found to be positive based on the glutamate dehydrogenase ( gdh ) and triosephosphate isomerase ( tpi ) gene, respectively. Thirty-eight (17.04%) faecal samples were found to be  E. bieneusi- positive based on the internal transcribed spacer (ITS) sequence, and only SC03 genotype was identified, which belonged to the zoonotic group 1 according to the phylogenic analysis. The infection rates were significantly different among the different geographical areas and age groups but had no apparent association with gender or clinical symptoms.    Conclusions  To our knowledge, this was the first molecular characterisation of  G. duodenalis  and  E. bieneusi  in musk deer. Identification of the zoonotic genotypes indicated a potential public health threat, and our study suggested that the forest musk deer is an important carrier of these parasites.

First report of Giardia duodenalis and Enterocytozoon bieneusi in forest musk deer (Moschus berezovskii) in China