Molecular survey of Enterocytozoon bieneusi in sheep and goats in China

BACKGROUND: Over recent years, several studies have conducted genotyping of Enterocytozoon bieneusi in various hosts worldwide using sequence analysis of the ribosomal internal transcribed spacer (ITS), however, relatively little is known about E. bieneusi in sheep and goats in China. Therefore this research was conducted to understand the prevalence and genotype distribution of E. bieneusi in farmed sheep and goats in China. RESULTS: A total of 1025 fecal specimens from farmed animals in various geographic areas were collected. Overall, PCR and sequence analysis of the ITS detected E. bieneusi in 34.4 % (353/1025) of isolates; of which the prevalence in goats was 28.8 % (176/611) and in sheep was 42.8 % (177/414). Phylogenetic analysis of ITS sequences identified 42 genotypes (nine known and 33 novel ones). These consisted of four known genotypes (D, KIN-1, EbpC, and F) and 10 novel genotypes (CHG6, CHG7, CHG9, CHG19, CHG23, CHG25, CHS5 and CHS10–CHS12) which all belonged to the so-called zoonotic group 1. A further four known genotypes (CD6, COS-I, BEB6, and J) and 22 novel genotypes (CHG1–CHG3, CHG5, CHG8, CHG10–CHG14, CHG16–CHG18, CHG20, CHG22, CHG24, CHS3, CHS4 and CHS6–CHS9) formed a clade within the group 2. One novel genotype (CHG21) was clustered in the group 9 with the genotype CM4. CONCLUSIONS: E. bieneusi is highly prevalent, widely distributed, and genetically diverse in Chinese farmed goats and sheep. Some of the genotypes identified are potentially zoonotic. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13071-016-1304-0) contains supplementary material, which is available to authorized users.