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In this context, this study aimed to perform an epidemiological survey of gastrointestinal parasites using non-invasive faecal samples from carnivores and artiodactyls identified by stool macroscopy, guard hair morphology and DNA sequencing in Itatiaia National Park. Between 2017 and 2018, faeces from carnivores and artiodactyls were collected along trails in the park. The host species were identified through macroscopic and trichological examinations and molecular biology. To investigate the parasites, the Faust, Lutz and modified Ritchie and Sheather techniques and enzyme immunoassays to detect<jats:italic>Cryptosporidium<\/jats:italic>sp. antigens were used.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>A total of 244 stool samples were collected. The species identified were<jats:italic>Chrysocyon brachyurus<\/jats:italic>,<jats:italic>Leopardus guttulus<\/jats:italic>,<jats:italic>Canis familiaris<\/jats:italic>,<jats:italic>Cerdocyon thous<\/jats:italic>,<jats:italic>Puma yagouaroundi<\/jats:italic>,<jats:italic>Leopardus pardalis<\/jats:italic>,<jats:italic>Puma concolor<\/jats:italic>and<jats:italic>Sus scrofa<\/jats:italic>. There were 81.1% samples that were positive for parasites distributed mainly in the high part of the park. Helminths, especially eggs of the family Ascarididae, were more frequently detected in carnivore faeces (70.9%). Protozoa, especially<jats:italic>Cryptosporidium<\/jats:italic>sp., represented the highest frequency of infection in artiodactyl faeces (87.1%). This zoonotic protozoon was detected in eight mammalian species, including in a wild boar. High values of structural richness and Shannon and Simpson diversity indices were observed for the parasites, especially in the faeces of<jats:italic>C. brachyurus<\/jats:italic>. Significant differences in parasite diversity were observed between wild and domestic animals, such as<jats:italic>C. brachyurus<\/jats:italic>and<jats:italic>C. familiaris<\/jats:italic>, respectively, and between taxonomically distant species, such as<jats:italic>C. brachyurus<\/jats:italic>and<jats:italic>S. scrofa<\/jats:italic>. The highest values for parasite similarity were found among the species that frequented similar areas of the park, such as<jats:italic>C. brachyurus<\/jats:italic>and<jats:italic>L. guttulus<\/jats:italic>.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>The animals and parasite infections were identified through the combination of three techniques. High frequency parasite structures were diagnosed. Zoonotic protozoa were found and mainly occurred in samples from introduced species.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12917-020-02490-5","type":"journal-article","created":{"date-parts":[[2020,8,17]],"date-time":"2020-08-17T10:03:15Z","timestamp":1597658595000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Non-invasive sampling in Itatiaia National Park, Brazil: wild mammal parasite detection"],"prefix":"10.1186","volume":"16","author":[{"given":"La\u00eds Verdan","family":"Dib","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jo\u00e3o Pedro Siqueira","family":"Palmer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Camila","family":"de Souza Carvalho Class","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jessica Lima","family":"Pinheiro","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Raissa Cristina Ferreira","family":"Ramos","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Claudijane Ramos","family":"dos Santos","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ana Beatriz Monteiro","family":"Fonseca","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karen Gisele","family":"Rodr\u00edguez-Castro","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Camila Francisco","family":"Gon\u00e7alves","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"suffix":"Jr.","given":"Pedro Manoel","family":"Galetti","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Otilio Machado Pereira","family":"Bastos","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Claudia Maria Antunes","family":"Uch\u00f4a","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"La\u00eds Lisboa","family":"Corr\u00eaa","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Augusto Cezar Machado Pereira","family":"Bastos","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria Regina Reis","family":"Amendoeira","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5007-1339","authenticated-orcid":false,"given":"Alynne","family":"da Silva Barbosa","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2020,8,17]]},"reference":[{"key":"2490_CR1","volume-title":"The mammals of the world","author":"DE Wilson","year":"2009","unstructured":"Wilson DE, Mittermeier RA. 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