Cryptosporidium spp. and Enterocytozoon bieneusi are significant enteric pathogens that affect a wide range of animal hosts, posing potential zoonotic risks. Wildlife–livestock interfaces are increasingly recognized as key settings for pathogen spillover, yet molecular epidemiological data from Xinjiang, China, remain limited. In this study, 191 fecal samples were collected from wild rodents and sympatric artiodactyls on the northern slope of the Tianshan Mountains in Bortala Prefecture, Xinjiang. Nested PCR targeting the small subunit (SSU) rRNA gene of Cryptosporidium spp. and the internal transcribed spacer (ITS) region of E. bieneusi was performed, followed by sequencing and phylogenetic analyses. Selected Cryptosporidium ‐positive samples were further characterized at the actin and hsp70 genes. Overall, Cryptosporidium spp. and E. bieneusi were detected in 5.8% (11/191) and 4.2% (8/191) of samples, respectively. Four Cryptosporidium genotypes were identified, including chipmunk genotype V, ground squirrel genotype II, C. rubeyi , and C. xiaoi . Rodent‐adapted genotypes predominated in long‐tailed ground squirrels and gray marmots, whereas C. xiaoi was detected in yak. While SSU rRNA and actin genes showed consistent clustering for several isolates, discordant phylogenetic signals at the hsp70 gene suggested the possibility of coinfections. Four E. bieneusi genotypes were identified, including the zoonotic genotypes A, BEB6, XJHT4, as well as a novel genotype, XJWR1. The detection of genotype A in both rodents and sheep suggests potential interspecies transmission occurring at shared grazing sites. These findings expand the molecular evidence on Cryptosporidium spp. and E. bieneusi in Xinjiang and highlight wildlife–livestock interfaces as potential hotspots for pathogen exchange in transboundary pastoral ecosystems.
Li et al. (2026) studied this question.