Prevalence and genotyping of Enterocytozoon bieneusi in cattle from Shanxi and Inner Mongolia, China

Enterocytozoon bieneusi is a zoonotic pathogen, with cattle serving as major reservoirs and important mediums for its transmission. However, data on the prevalence and subtypes of E. bieneusi in cattle from Northern Shanxi and Central Inner Mongolia, China, are limited. This study aimed to evaluate the zoonotic risk associated with E. bieneusi in cattle from the Shanxi North and Inner Mongolia Central Connection Area. In this study, the internal transcribed spacer (ITS) gene of E. bieniusi was assessed. Fecal samples (n = 1338) were randomly collected from 15 intensive and free-range cattle farms in Northern Shanxi and Central Inner Mongolia between 2021 and 2022. Samples were subjected to processing, nucleic acid extraction, polymerase chain reaction, sequencing, and sequence analysis to determine the prevalence and genetic characteristics of E. bieneusi. The prevalence of E. bieneusi in cattle was 34.23% (458/1338), varying from 4.29% (3/70) to 66.34% (67/101) among 15 sampling points. The prevalence rates of E. bieneusi in cattle from Shanxi and Inner Mongolia were 30.42% (261/858) and 41.04% (197/480), respectively. The prevalence in dairy and beef cattle was 35.72% (304/851) and 31.62% (154/487), respectively. Moreover, the prevalence across preweaned calves, postweaned calves, young cattle, and adult cattle was 27.81% (42/151), 53.95% (123/228), 45.60% (140/307), and 23.47% (153/652), respectively. Diarrheal and nondiarrheal cattle showed prevalence rates of 50.34% (148/294) and 29.69% (310/1044), respectively. Sequencing identified 458 ITS gene sequences, comprising 4 known genotypes (J [65.94%, 302/458], I [6.99%, 32/458], BEB4 [16.38%, 75/458], and BEB6 [1.75%, 8/458]) and 41 novel genotypes (SX1-SX18 and NMG1-NMG23: 8.95%, 41/458). All identified genotypes belonged to zoonotic Group 2, with genotype J being predominant. This study highlights variations in E. bieneusi prevalence among cattle from different taxonomic units in Northern Shanxi and Central Inner Mongolia. It confirms E. bieneusi infection in cattle from Shanxi and Inner Mongolia, marking the first report of E. bieneusi in dairy cattle from these regions. Specifically, 4 known and 41 novel E. bieneusi genotypes belonging to zoonotic Group 2 were identified, with J being the dominant genotype.