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Wildlife is known to be a source of high-impact pathogens affecting people. However, the distribution, genetic diversity, and zoonotic potential of  Cryptosporidium ,  Enterocytozoon bieneusi , and  Giardia duodenalis  in wildlife are poorly understood. Here, we conducted the first molecular epidemiological investigation of these three pathogens in wildlife in Zhejiang and Shanghai, China. Genomic DNAs were derived from 182 individual fecal samples from wildlife and then subjected to a nested polymerase chain reaction–based sequencing approach for detection and characterization. Altogether, 3 (1.6%), 21 (11.5%), and 48 (26.4%) specimens tested positive for  Cryptosporidium  species,  E. bieneusi , and  G. duodenalis , respectively. Sequence analyses revealed five known (BEB6, D, MJ13, SC02, and type IV) and two novel (designated SH_ch1 and SH_deer1) genotypes of  E. bieneusi . Phylogenetically, novel  E. bieneusi  genotype SH_deer1 fell into group 6, and the other genotypes were assigned to group 1 with zoonotic potential. Three novel  Cryptosporidium  genotypes ( Cryptosporidium  avian genotype V-like and  C. galli -like 1 and 2) were identified,  C. galli -like 1 and 2 formed a clade that was distinct from  Cryptosporidium  species. The genetic distinctiveness of these two novel genotypes suggests that they represent a new species of  Cryptosporidium.  Zoonotic assemblage A ( n  = 36) and host-adapted assemblages C ( n  = 1) and E ( n  = 7) of  G. duodenalis  were characterized. The overall results suggest that wildlife act as host reservoirs carrying zoonotic  E. bieneusi  and  G. duodenalis , potentially enabling transmission from wildlife to humans and other animals.

Wildlife Is a Potential Source of Human Infections of Enterocytozoon bieneusi and Giardia duodenalis in Southeastern China