Emergence of zoonotic Cryptosporidium, Giardia duodenalis and Enterocytozoon bieneusi in wild rodent from Yunnan: first detection of C. parvum IIdA24G1 in wild rodents in China

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Introduction Cryptosporidium spp., Giardia duodenalis , and Enterocytozoon bieneusi are critical zoonotic diarrheal pathogens threatening human and animal health. Wild rodents act as key reservoirs for cross-species pathogen transmission, while systematic epidemiological data of these pathogens in Yunnan rodents remain scarce. Methods To elucidate the prevalence and genetic characteristics of Cryptosporidium , G. duodenalis , and E. bieneusi in wild rodents in Yunnan Province, a total of 304 wild rodent samples were collected from seven cities in Yunnan Province, China: Baoshan, Chuxiong, Dali, Diqing, Kunming, Lincang, and Yuxi. Intestinal contents were collected for DNA extraction, and the infection status and species/assemblages/genotypes of Cryptosporidium (targeting SSU rRNA gene), G. duodenalis (targeting TPI gene), and E. bieneusi (targeting ITS gene) in these animals were determined by nested PCR and DNA sequencing. Results The results showed that the overall prevalence of Cryptosporidium spp., G. duodenalis , and E. bieneusi were 13.8% (42/304), 18.1% (55/304), and 11.2% (34/304), respectively. The prevalence varied significantly across regions and rodent species. Notably, Apodemus chevrieri had a significantly higher risk of Cryptosporidium prevalence (OR = 8.70, 95% CI: 2.81–26.94) compared to Rattus norvegicus . Eight Cryptosporidium species/genotypes: C. muris, C. meleagridis , C. baileyi , C. parvum , rat genotype I-IV, two G. duodenalis assemblages (B and G) and five E. bieneusi genotypes: three zoonotic genotypes (D, EpbC, Type IV), as well as two known genotype (SDD5, CHY1) were identified. Notably, the zoonotic C. parvum IIdA24G1 subtype was first documented in wild rodents in China. Discussion Multiple zoonotic genotypes were detected with potential public health risks. This study fills the epidemiological gap of intestinal zoonotic pathogens in Yunnan wild rodents. The newly identified endemic IIdA24G1 subtype and prevalent zoonotic genotypes reveal high spillover risks, providing baseline data for regional pathogen surveillance and public health prevention.

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