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The present study examined the prevalence and zoonotic potential of <jats:italic>Cryptosporidium<\/jats:italic> spp. and <jats:italic>G. duodenalis<\/jats:italic> in Himalayan marmots and Alashan ground squirrels in China's Qinghai-Tibetan Plateau area (QTPA) for the first time. Four hundred ninety-eight intestinal content samples were collected from five counties of QTPA of Gansu province, China.\nAll samples were examined for <jats:italic>Cryptosporidium<\/jats:italic> spp. and <jats:italic>G. duodenalis<\/jats:italic> by PCR amplification. The resultant data were statistically analyzed by chi-square, Fisher's test and Bonferroni correction using SPSS software 25. 0. <jats:italic>Cryptosporidium<\/jats:italic> positive samples were further subtyped through analysis of the 60-kDa glycoprotein (<jats:italic>gp60<\/jats:italic>) gene sequence. A total of 11 and 8 samples were positive for <jats:italic>Cryptosporidium<\/jats:italic> spp. and <jats:italic>G. duodenalis<\/jats:italic>, respectively. Prevalence of <jats:italic>Cryptosporidium<\/jats:italic> spp. and <jats:italic>G. duodenalis<\/jats:italic> were 2.5% (10\/399) and 1.5% (6\/399) in Himalayan marmots, 1.0% (1\/99) and 2.0% (2\/99) in Alashan ground squirrels, respectively. Sequence analysis confirmed the presence of <jats:italic>C. rubeyi<\/jats:italic> (n\u2009=\u20092), ground squirrel genotype II (n\u2009=\u20097), chipmunk genotype V (n\u2009=\u20091) and horse genotype (n\u2009=\u20091). The horse genotype was further subtyped as novel subtype VIbA10. <jats:italic>G. duodenalis<\/jats:italic> zoonotic assemblages A (n\u2009=\u20091), B (n\u2009=\u20096), E (n\u2009=\u20091) were identified in the present study. This is the first study to identify <jats:italic>Cryptosporidium<\/jats:italic> spp. and <jats:italic>G. duodenalis<\/jats:italic> in Himalayan marmots and Alashan ground squirrels, suggesting the potential zoonotic transmission of the two pathogens in QTPA.<\/jats:p>","DOI":"10.1038\/s41598-022-16196-1","type":"journal-article","created":{"date-parts":[[2022,7,16]],"date-time":"2022-07-16T09:03:45Z","timestamp":1657962225000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["Genotyping and subtyping of Cryptosporidium spp. and Giardia duodenalis isolates from two wild rodent species in Gansu Province, China"],"prefix":"10.1038","volume":"12","author":[{"given":"Jie","family":"Xu","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hua","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanyan","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huaiqi","family":"Jing","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianping","family":"Cao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianhai","family":"Yin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Teng","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yeting","family":"Sun","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yujuan","family":"Shen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xin","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2022,7,16]]},"reference":[{"key":"16196_CR1","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1016\/j.vetpar.2004.09.004","volume":"126","author":"R Fayer","year":"2004","unstructured":"Fayer, R. 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