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Simple Summary: Enterocytozoon bieneusi is one of the most common parasites in human and animals, and a threat to public health. So far, no data are available for E. bieneusi prevalence and genotypes in black goats in Yunnan Province, Southwestern China. Therefore, the objective of this study was to detect the prevalence and genotypes of E. bieneusi by examining 907 fecal samples collected from 5 counties in Yunnan Province. Ninety-three fecal samples (10.3%) were E. bieneusi-positive by PCR amplification. Four new genotypes and 11 known genotypes were identified, and all genotypes considered to be the zoonotic potential. Phylogenetic analysis showed that all of these genotypes were allocated into the zoonotic groups of E. bieneusi indicating its zoonotic potential. These results indicated that effective strategies and measures must be taken to prevent and control E. bieneusi transmission to other animals and humans. Enterocytozoon bieneusi is a fungus-like protist that can parasitize in the intestines of humans and various animals causing a threat to public health. However, there has been no data for E. bieneusi prevalence and genotypes in black goats in Yunnan Province, Southwestern China. In this study, 907 fecal samples were collected from black goats in 5 counties from Yunnan Province. The prevalence and genotypes of E. bieneusi were examined by nested PCR amplification targeting the nuclear internal transcribed spacer (ITS). Multi-locus sequence typing (MLST) was used to further examine the potential occurrence of genetic segregation. The overall prevalence of E. bieneusi in black goats in Yunnan Province was 10.3% (93/907). Statistical analysis revealed that E. bieneusi prevalence was significantly associated with the region, age and gender of black goats (p < 0.001). Four new genotypes (CYG-1, CYG-2, CYG-3, CYG-4) and 11 known genotypes (CHG1, CHG2, CHG3, CHG5, CHG28, J, D, BEB6, Wildboar3, CD6, SDD1) of E. bieneusi were identified. At the microsatellite and minisatellite loci, 15, 2, 17, and 33 sequences were obtained, respectively, forming one new multi-locus genotype (MLG27). Phylogenetic analysis revealed that all 15 genotypes were clustered into group 1 and group 2, with zoonotic potential. This is the first report of E. bieneusi prevalence and genotypes in black goats in Yunnan Province, China. Effective control strategies and measures should be taken to reduce the risk of E. bieneusi transmission between black goats, other animals, and humans. [ABSTRACT FROM AUTHOR]

Abstract Enterocytozoon bieneusi is a common pathogen in sheep and goats worldwide, threatening husbandry development and public health. However, there were few reports on native breeds of sheep and goats in China. In the present study, we investigated the prevalence and multi-locus genotypes (MLGs) of E. bieneusi in two important local breeds, black-boned sheep and goats, in Yunnan province, southwestern China. Of 661 faecal specimens collected from five counties of Yunnan province, 70 (10.59%) were positive for E. bieneusi infection. Infections were found in both black-boned sheep and goats, but no significant difference in prevalence was detected between two species. E. bieneusi was found in all age groups of black-boned sheep, while no infections were observed in 0–2-month black-boned goats. 12 genotypes were identified based on sequence variations of the internal transcribed spacer, including 10 known genotypes (BEB6, COS I, SX1, CM21, CHG3, CHG1, CHS5, EbpC, COS II, PigEb4) and two novel genotypes (named as YNS1 and YSM1), with BEB6 as the prevalent genotype both in black-boned sheep and goats. Phylogenetic analysis indicated that three genotypes of them, namely EbpC, CHS5 and PigEb4, were clustered into the zoonotic group 1, while the remaining nine genotypes were belonged to the host-adapted group 2. Multi-locus sequence typing (MLST) revealed 12 distinct multilocus genotypes (MLGs), with 11 MLGs detected in black-boned sheep and only one found in one black-boned goat. These findings expanded the reservoirs of E. bieneusi and provided fundamental data for controlling E. bieneusi infection in native small ruminants as well as other hosts in this province. Graphical abstract Unlabelled Image Highlights • E. bieneusi infection were found in both black-boned sheep and goats. • 12 genotypes were identified, including 10 known genotypes and two novel genotypes. • 12 distinct novel MLGs were identified. [ABSTRACT FROM AUTHOR]