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Faecal samples from 1237 pigs and 1150 cattle originating from 50 sow herds and 50 dairy herds, respectively, were analysed for the presence of the two parasites by immunofluorescence microscopy. A large proportion of the (oo)cyst containing samples were selected for molecular characterization. Sequencing and phylogenetic analysis of the 18S rDNA locus and\/or the <jats:italic>HSP70<\/jats:italic> gene of 183 pig and 154 cattle isolates of <jats:italic>Cryptosporidium<\/jats:italic> revealed the presence of <jats:italic>C. suis<\/jats:italic>, pig genotype II, <jats:italic>C. parvum<\/jats:italic> (cattle genotype), <jats:italic>C. bovis<\/jats:italic>, <jats:italic>Cryptosporidium<\/jats:italic> deer-like genotype and a novel <jats:italic>C. suis<\/jats:italic>-like genotype. For both cattle and pigs, a host age-related change in distribution of species\/genotypes was observed. The zoonotic <jats:italic>C. parvum<\/jats:italic> (cattle genotype) was most prevalent in young calves. For <jats:italic>Giardia<\/jats:italic>, 82 and 145 isolates from pigs and cattle, respectively, were analysed at the 18S rDNA locus and\/or the <jats:italic>gdh<\/jats:italic> gene. <jats:italic>Giardia<\/jats:italic> isolates belonging to the zoonotic Assemblage A was found in both young and older calves, as well as in weaners and piglets, whereas cows seemed to be infected purely by isolates of the livestock group, Assemblage E.<\/jats:p>","DOI":"10.1017\/s0031182006001533","type":"journal-article","created":{"date-parts":[[2006,11,1]],"date-time":"2006-11-01T08:52:51Z","timestamp":1162371171000},"page":"339-350","source":"Crossref","is-referenced-by-count":200,"title":["Molecular and phylogenetic characterization of <i>Cryptosporidium<\/i> and <i>Giardia<\/i> from pigs and cattle in Denmark"],"prefix":"10.1017","volume":"134","author":[{"given":"R. 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