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Cercariae emerging from infected snails cannot be precisely identified morphologically to the species level. We used molecular tools to clarify the distribution of the <jats:italic>Schistosoma haematobium<\/jats:italic> group species infecting bulinid snails in a large part of C\u00f4te d\u2019Ivoire and confirmed the presence of interspecific hybrid schistosomes.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>Between June 2016 and March 2017, <jats:italic>Bulinus<\/jats:italic> snails were sampled in 164 human-water contact sites from 22 villages of the northern and central parts of C\u00f4te d\u2019Ivoire. Multi-locus genetic analysis (mitochondrial <jats:italic>cox<\/jats:italic>1 and nuclear ITS) was performed on individual schistosome cercariae shed from snails, in the morning and in the afternoon, for species and hybrid identification.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Overall, 1923 <jats:italic>Bulinus truncatus<\/jats:italic>, 255 <jats:italic>Bulinus globosus<\/jats:italic> and 1424 <jats:italic>Bulinus forskalii<\/jats:italic> were obtained. Among 2417 <jats:italic>Bulinus<\/jats:italic> screened, 25 specimens (18 <jats:italic>B. truncatus<\/jats:italic> and seven <jats:italic>B. globosus<\/jats:italic>) shed schistosomes, with up to 14% infection prevalence per site and time point. Globally, infection rates per time point ranged between 0.6 and 4%. <jats:italic>Schistosoma bovis<\/jats:italic>, <jats:italic>S. haematobium<\/jats:italic> and <jats:italic>S. bovis<\/jats:italic>\u2009\u00d7\u2009<jats:italic>S. haematobium<\/jats:italic> hybrids infected 0.5%, 0.2% and 0.4% of the snails screened, respectively. <jats:italic>Schistosoma bovis<\/jats:italic> and hybrids were more prevalent in <jats:italic>B. truncatus<\/jats:italic>, whereas <jats:italic>S. haematobium<\/jats:italic> and hybrid infections were more prevalent in <jats:italic>B. globosus<\/jats:italic>. <jats:italic>Schistosoma bovis<\/jats:italic>-infected <jats:italic>Bulinus<\/jats:italic> were predominantly found in northern sites, while <jats:italic>S. haematobium<\/jats:italic> and hybrid infected snails were mainly found in central parts of C\u00f4te d\u2019Ivoire.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>The data highlight the necessity of using molecular tools to identify and understand which schistosome species are transmitted by specific intermediate host snails. The study deepens our understanding of the epidemiology and transmission dynamics of <jats:italic>S. haematobium<\/jats:italic> and <jats:italic>S. bovis<\/jats:italic> in C\u00f4te d\u2019Ivoire and provides the first conclusive evidence for the transmission of <jats:italic>S. haematobium\u2009<\/jats:italic>\u00d7\u2009<jats:italic>S. bovis<\/jats:italic> hybrids in this West African country.<\/jats:p>\n                <jats:p><jats:italic>Trial registration<\/jats:italic> ISRCTN, ISRCTN10926858. Registered 21 December 2016; retrospectively registered (see: <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.isrctn.com\/ISRCTN10926858\">http:\/\/www.isrctn.com\/ISRCTN10926858<\/jats:ext-link>)<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s13071-019-3381-3","type":"journal-article","created":{"date-parts":[[2019,4,17]],"date-time":"2019-04-17T10:36:20Z","timestamp":1555497380000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":41,"title":["Molecular characterization and distribution of Schistosoma cercariae collected from naturally infected bulinid snails in northern and central C\u00f4te d\u2019Ivoire"],"prefix":"10.1186","volume":"12","clinical-trial-number":[{"clinical-trial-number":"isrctn10926858","registry":"10.18810\/isrctn"}],"author":[{"given":"Yves-Nathan T.","family":"Tian-Bi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bonnie","family":"Webster","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cyrille K.","family":"Konan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fiona","family":"Allan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nana R.","family":"Diakit\u00e9","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mamadou","family":"Ouattara","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Diabat\u00e9","family":"Salia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amani","family":"Kon\u00e9","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adolphe K.","family":"Kakou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muriel","family":"Rabone","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean T.","family":"Coulibaly","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefanie","family":"Knopp","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aboulaye","family":"Me\u00eft\u00e9","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J\u00fcrg","family":"Utzinger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eli\u00e9zer K.","family":"N\u2019Goran","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Rollinson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,3,19]]},"reference":[{"key":"3381_CR1","unstructured":"WHO. 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