Molecular Identification and Genotyping of Enterocytozoon bieneusi in Sheep in Shanxi Province, North China

SIMPLE SUMMARY: Enterocytozoon bieneusi is a fungus-like protist that is distributed worldwide and can cause malabsorption and diarrhea in sheep, other animals, and humans, threatening the development of animal husbandry and public health. However, little is known of the prevalence and genotypes of E. bieneusi in sheep in Shanxi Province, North China. Thus, 492 fecal samples were collected from sheep in three representative counties in northern, central, and southern Shanxi Province, and nested PCR amplification targeting the internal transcribed spacer (ITS) region of the rRNA gene was carried out to detect the prevalence and identify the genotypes of E. bieneusi. The overall E. bieneusi prevalence in the examined sheep in Shanxi Province was 34.2% (168/492). Four known genotypes (BEB6, COS-I, CHS7, and CHC8) and one novel genotype (SY-1) were detected, and the prevalent genotype was BEB6. The five genotypes observed in this study belong to the host-adapted Group 2. This is the first report on the occurrence and genotypes of E. bieneusi in sheep in Shanxi Province, which enhances an understanding of the global distribution and genetic diversity of E. bieneusi and has implications for the better control of E. bieneusi in animals and humans. ABSTRACT: Enterocytozoon bieneusi is a fungus-like protist that can cause malabsorption and diarrhea in sheep, other animals, and humans, threatening the development of animal husbandry and public health. To date, there are no data about the prevalence and genotypes of E. bieneusi in sheep in Shanxi Province, North China. In this study, 492 fecal samples were collected from sheep in three representative counties in northern, central, and southern Shanxi Province. Nested PCR amplification was performed to detect the prevalence and identify the genotypes of E. bieneusi based on the internal transcribed spacer (ITS) region of the rRNA gene. Overall, 168 of 492 examined samples were E. bieneusi-positive, with a prevalence of 34.2% (168/492). Significant differences in the prevalence of E. bieneusi were observed among the three sampled regions (χ2 = 95.859, df = 2, p < 0.001), but the differences in E. bieneusi prevalence were not statistically significant between different genders and age groups (p > 0.05). Sequence analysis showed that four known genotypes (BEB6, COS-I, CHS7, and CHC8) and one novel genotype (named SY-1) were identified. BEB6 was the prevalent genotype found within the three counties. Phylogenetic analysis revealed that the five genotypes observed in this study belong to Group 2. The present study reported the presence and genotypes of E. bieneusi infection in sheep in Shanxi Province for the first time, which enriches the knowledge of the genetic diversity of E. bieneusi and provides baseline data for the prevention and control of E. bieneusi infection in animals and humans.