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It has been a reportable disease in Canada since 2000; however, routine molecular surveillance is not conducted. Therefore, sources of contamination are unknown. The aim of this project was to identify species and subtypes of <jats:italic>Cryptosporidium<\/jats:italic> in clinical cases from Ontario, the largest province in Canada, representing one third of the Canadian population, in order to understand transmission patterns.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>A total of 169 frozen, banked, unpreserved stool specimens that were microscopy positive for <jats:italic>Cryptosporidium<\/jats:italic> over the period 2008\u20132017 were characterized using molecular tools. A subset of the 169 specimens were replicate samples from individual cases. DNA was extracted directly from the stool and nested PCR followed by Sanger sequencing was conducted targeting the small subunit ribosomal RNA (SSU) and glycoprotein 60 (<jats:italic>gp60<\/jats:italic>) genes.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Molecular typing data and limited demographic data were obtained for 129 cases of cryptosporidiosis. Of these cases, 91 (70.5 %) were due to <jats:italic>Cryptosporidium parvum<\/jats:italic> and 24 (18.6%) were due to <jats:italic>Cryptosporidium hominis<\/jats:italic>. Mixed infections of <jats:italic>C. parvum<\/jats:italic> and <jats:italic>C. hominis<\/jats:italic> occurred in four (3.1%) cases. Five other species observed were <jats:italic>Cryptosporidium ubiquitum<\/jats:italic> (<jats:italic>n<\/jats:italic> = 5), <jats:italic>Cryptosporidium felis<\/jats:italic> (<jats:italic>n<\/jats:italic> = 2), <jats:italic>Cryptosporidium meleagridis<\/jats:italic> (<jats:italic>n<\/jats:italic> = 1), <jats:italic>Cryptosporidium cuniculus<\/jats:italic> (<jats:italic>n<\/jats:italic> = 1) and <jats:italic>Cryptosporidium muris<\/jats:italic> (<jats:italic>n<\/jats:italic> = 1). Subtyping the <jats:italic>gp60<\/jats:italic> gene revealed 5 allelic families and 17 subtypes of <jats:italic>C. hominis<\/jats:italic> and 3 allelic families and 17 subtypes of <jats:italic>C. parvum<\/jats:italic>. The most frequent subtype of <jats:italic>C. hominis<\/jats:italic> was IbA10G2 (22.3%) and of <jats:italic>C. parvum<\/jats:italic> was IIaA15G2R1 (62.4%).<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>The majority of isolates in this study were <jats:italic>C. parvum<\/jats:italic>, supporting the notion that zoonotic transmission is the main route of cryptosporidiosis transmission in Ontario. Nonetheless, the observation of <jats:italic>C. hominis<\/jats:italic> in about a quarter of cases suggests that anthroponotic transmission is also an important contributor to cryptosporidiosis pathogenesis in Ontario.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Graphical Abstract<\/jats:title>\n                \n              <\/jats:sec>","DOI":"10.1186\/s13071-020-04546-9","type":"journal-article","created":{"date-parts":[[2021,1,22]],"date-time":"2021-01-22T06:02:58Z","timestamp":1611295378000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":38,"title":["Molecular characterization of Cryptosporidium isolates from humans in Ontario, Canada"],"prefix":"10.1186","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9833-4994","authenticated-orcid":false,"given":"Rebecca A.","family":"Guy","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christine A.","family":"Yanta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pia K.","family":"Muchaal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marisa A.","family":"Rankin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karine","family":"Thivierge","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachel","family":"Lau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea K.","family":"Boggild","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,1,22]]},"reference":[{"key":"4546_CR1","doi-asserted-by":"publisher","first-page":"e568","DOI":"10.1016\/S2214-109X(19)30076-2","volume":"7","author":"KL Kotloff","year":"2019","unstructured":"Kotloff KL, Nasrin D, Blackwelder WC, Wu Y, Farag T, Panchalingham S, et al. 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