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However, there is a paucity of molecular data describing the genotypes and haplotypes of this important cestode in domestic ruminant hosts.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>Ninety-four cysts from the lungs and\/or livers of slaughtered beef cattle (76 samples), dairy cows (five samples) and sheep (13 samples) were collected from abattoirs in four states of the USA. Samples were genotyped at two mitochondrial loci, <jats:italic>cox1<\/jats:italic> and <jats:italic>nad5.<\/jats:italic> Sequences were used to determine species, genotypes and haplotypes using median joining networks and Bayesian phylogenetic analyses. Cyst fertility was assessed in hematoxylin and eosin-stained sections. Additionally, previously reported autochthonous <jats:italic>E. granulosus<\/jats:italic> infections in the USA in various hosts were mapped.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Based on <jats:italic>cox1<\/jats:italic> sequences obtained from 94 cysts, 89 (94.7%) were identified as <jats:italic>E. granulosus<\/jats:italic> G1\/G3, while five (5.3%) were <jats:italic>Taenia hydatigena. Taenia hydatigena<\/jats:italic> were only isolated from sheep. Based on <jats:italic>nad5<\/jats:italic> sequences obtained from 89 hydatid cysts, 96.6% and 3.4% belonged to <jats:italic>E. granulosus <\/jats:italic>sensu stricto genotypes G1 and G3 respectively. Two haplotypes were found among <jats:italic>E. granulosus cox1<\/jats:italic> sequences, neither of which was geographically unique. Six haplotypes were found among <jats:italic>nad5<\/jats:italic> sequences in genotype G1, of which five were novel, while one haplotype was found in genotype G3. In the concatenated <jats:italic>cox1-nad5<\/jats:italic> dataset, seven haplotypes were identified, of which six were geographically unique. All cysts from cattle were non-fertile. Four cysts from sheep were fertile.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>All genotyped samples belonged to <jats:italic>E. granulosus <\/jats:italic>s.s. This is the first study to our knowledge to confirm the presence of genotypes G1 and G3 in domestic cattle and sheep intermediate hosts in the USA and provide data for future diagnostic and epidemiological studies. Sequences have been deposited in GenBank (<jats:italic>cox1<\/jats:italic> sequences: OR398494-OR398496, <jats:italic>nad5<\/jats:italic> sequences: OR400695-OR400702).<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Graphical Abstract<\/jats:title>\n                \n              <\/jats:sec>","DOI":"10.1186\/s13071-024-06192-x","type":"journal-article","created":{"date-parts":[[2024,3,14]],"date-time":"2024-03-14T08:45:07Z","timestamp":1710405907000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Cystic echinococcosis in cattle and sheep caused by Echinococcus granulosus sensu stricto genotypes G1 and G3 in the USA"],"prefix":"10.1186","volume":"17","author":[{"given":"Jeba R. 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