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The aims of this study were to assess differences in assemblages (i) between dogs living mainly in close proximity to humans (synanthropic dogs)<jats:italic>versus<\/jats:italic>dogs living mainly among other dogs, (ii) between samples of dogs with or without loose stool, and (iii) related to the amount of cysts shedding.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>One hundred eighty-nine qPCR<jats:italic>Giardia<\/jats:italic>positive fecal samples of dogs originating from four groups (household, sheltered, hunting, and dogs for which a veterinarian sent a fecal sample to a diagnostic laboratory) were used for genotyping. For this, multi-locus genotyping of beta-giardin, triose phosphate isomerase, and glutamate dehydrogenase and genotyping of<jats:italic>SSU rDNA<\/jats:italic>gene fragments were performed. Fecal consistency was scored (loose or non-loose stool), and cysts per gram of feces were determined with qPCR.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Assemblage D was the most prevalent in all groups, followed by the other canid assemblage C. Also, mixed C\/D was common. In two (synanthropic) household dogs, the potentially zoonotic assemblage AI was present. Although occurrence of assemblage AI in household dogs was not significantly different from dogs living among other dogs (sheltered and hunting dogs), it was significantly higher compared to dogs for which a sample was sent to a diagnostic laboratory. Dogs with assemblage D shed significantly more cysts than dogs with other assemblages (except for mixed C\/D results) or dogs in which no assemblage could be determined. None of the assemblages was significantly associated with loose stool.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Not only do dogs mainly shed the canid<jats:italic>Giardia duodenalis<\/jats:italic>assemblages D and\/or C, the numbers of cysts per gram for the canid assemblage D were also higher than for the potential zoonotic assemblage AI. Based on the assemblages shed by dogs, the risk to public health posed by dogs is estimated to be low, even though the dogs that shed AI were synanthropic household dogs. Loose stool in infected dogs was not associated with any particular<jats:italic>Giardia<\/jats:italic>assemblage.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s13071-020-04496-2","type":"journal-article","created":{"date-parts":[[2020,12,2]],"date-time":"2020-12-02T11:03:45Z","timestamp":1606907025000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Giardia duodenalis multi-locus genotypes in dogs with different levels of synanthropism and clinical signs"],"prefix":"10.1186","volume":"13","author":[{"given":"Mathilde","family":"Uiterwijk","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lapo","family":"Mughini-Gras","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rolf","family":"Nijsse","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jaap A.","family":"Wagenaar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harm W.","family":"Ploeger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3625-3432","authenticated-orcid":false,"given":"Frans N. 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