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Currently, to the best of our knowledge, no information on<jats:italic>E. bieneusi<\/jats:italic>infection in Himalayan marmots (<jats:italic>Marmota himalayana<\/jats:italic>) and Alashan ground squirrels (<jats:italic>Spermophilus alashanicus<\/jats:italic>) is available worldwide. The aim of the present study was to understand the occurrence and genetic characterizations of<jats:italic>E. bieneusi<\/jats:italic>in Himalayan marmots and Alashan ground squirrels in the Qinghai-Tibetan Plateau area (QTPA), Gansu Province, China.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>A total of 498 intestinal contents were collected from 399 Himalayan marmots and 99 Alashan ground squirrels in QTPA. These samples were screened for the presence of<jats:italic>E. bieneusi<\/jats:italic>by using nested polymerase chain reaction and sequencing of the internal transcribed spacer (ITS) region of the ribosomal RNA (rRNA) gene. The ITS-positive sequences were aligned and phylogenetically analyzed to determine the genotypes of<jats:italic>E. bieneusi<\/jats:italic>.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The average infection rate of<jats:italic>E. bieneusi<\/jats:italic>was 10.0% (50\/498), with 11.8% (47\/399) in Himalayan marmots and 3.0% (3\/99) in Alashan ground squirrels. A total of 7 distinct<jats:italic>E. bieneusi<\/jats:italic>genotypes were confirmed: 1 known genotype, YAK1 (<jats:italic>n<\/jats:italic>\u2009=\u200918) and 6 novel genotypes, named as ZY37 (<jats:italic>n<\/jats:italic>\u2009=\u200927), HN39 (<jats:italic>n<\/jats:italic>\u2009=\u20091), HN96 (<jats:italic>n<\/jats:italic>\u2009=\u20091), SN45 (<jats:italic>n<\/jats:italic>\u2009=\u20091), XH47 (<jats:italic>n<\/jats:italic>\u2009=\u20091) and ZY83 (<jats:italic>n<\/jats:italic>\u2009=\u20091). All the genotypes obtained in the present study were classified into group 1.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>To our knowledge, this is the first report of<jats:italic>E. bieneusi<\/jats:italic>in Himalayan marmots and Alashan ground squirrels in China. The identification of genotype YAK1 in the two rodent species expanded the host range of this genotype. All the seven genotypes were clustered into zoonotic group 1, suggesting that these animal species can be potential epidemiological vectors of zoonotic microsporidiosis caused by<jats:italic>E. bieneusi<\/jats:italic>and pose a threat to ecological security. It is necessary to strengthen management practices and surveillance in the investigated areas to reduce the risk of<jats:italic>E. bieneusi<\/jats:italic>infection from the two rodent species to humans.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s13071-020-04233-9","type":"journal-article","created":{"date-parts":[[2020,7,22]],"date-time":"2020-07-22T12:03:38Z","timestamp":1595419418000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["Identification and genotyping of Enterocytozoon bieneusi in wild Himalayan marmots (Marmota himalayana) and Alashan ground squirrels (Spermophilus alashanicus) in the Qinghai-Tibetan Plateau area (QTPA) of Gansu Province, China"],"prefix":"10.1186","volume":"13","author":[{"given":"Jie","family":"Xu","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xin","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huaiqi","family":"Jing","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shengkui","family":"Cao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaofan","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanyan","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianhai","family":"Yin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianping","family":"Cao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yujuan","family":"Shen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2020,7,22]]},"reference":[{"key":"4233_CR1","doi-asserted-by":"publisher","first-page":"336","DOI":"10.1016\/j.pt.2015.12.004","volume":"32","author":"GD Stentiford","year":"2016","unstructured":"Stentiford GD, Becnel JJ, Weiss LM, Keeling PJ, Didier ES, Williams BP, et al. 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The protocol was approved by the Laboratory Animal Welfare & Ethics Committee (LAWEC), National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Permit Number: NIPD 2015-011).","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"367"}}