Cross-Species Transmission Risk of <i>Enterocytozoon bieneusi</i> in Captive Tarim Red Deer from Southern Xinjiang, China

Enterocytozoon bieneusi is a widespread intracellular fungal pathogen that infects a variety of hosts. To investigate its prevalence and genetic diversity in captive Tarim red deer in southern Xinjiang, we collected 630 fresh fecal samples from 10 farms between 2020 and 2021. PCR targeting the ITS gene revealed an overall infection rate of 23.5% (148/630), with 8 out of 10 farms testing positive. Infection rates varied significantly by farm (12.2%-83.9%, P < 0.01) and age group (P < 0.01), peaking at 53.9% in 12-24-month-old deer and dropping to 0.6% in 6-12-month-old individuals. Sequencing identified 22 genotypes: 7 known and 15 novel (XJRD1-XJRD15), with BEB6 (54.7%) and D (21.6%) being the most prevalent. Phylogenetic analysis categorized 16 genotypes into zoonotic Group 1 and 6 into host-adapted Group 2, with novel genotypes forming distinct subclades. Tarim red deer serve as a crucial reservoir for E. bieneusi diversity and pose zoonotic risks, highlighting the need for targeted One Health interventions.