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Background  Exotic reptiles such as tortoises, have become increasingly common domestic pets worldwide and are known to host different gastrointestinal parasites. Some of these parasites bear zoonotic potential. In the present survey, we parasitologically examined tortoise faecal samples ( n  = 1005) from 19 different species held as pets in private German households and German zoological gardens.    Methods  Saline faecal smears were used to generate prevalence data for potentially health-compromising gastrointestinal parasites. In addition, we performed complete parasitological dissections of dead tortoises ( n  = 49) to estimate endoparasite burdens precisely.    Results  Analysed tortoise faecal samples contained a broad spectrum of endoparasites. We detected ten taxa of endoparasites; oxyurid nematodes (e.g.  Tachygonetria  spp.) were the most prevalent parasites in faecal samples (43.18%), followed by ascarids ( Angusticaecum  spp.) (0.01%),  Hexamita  spp. (0.007%),  Balantidium  spp. (0.007%), trichomonads (0.004%),  Strongyloides  spp. (0.003%),  Entamoeba  spp. (0.005%),  Hartmanella  spp. (0.001%),  Blastocystis  spp. (0.002%) ,  heterakids (0.001%) and  Trimitus  spp. (0.001%) .  Additionally, we investigated dead tortoise individuals ( n  = 49; of 10 different species) for aetiological diagnosis and estimation of endoparasite burden. Of these individuals, 38 (77.6%) were infected with parasites and 14 (28.6%) of them died most probably due to severe parasitic infection. Oxyurid infections correlated positively with calcium deficiency and metabolic bone disease (MBD) as well as nephrosis/nephritis, mainly occurring in juvenile tortoises (< 5 years of age).    Conclusions  The saline faecal smear technique proved to be efficient in detecting different metazoan and protozoan parasite stages in tortoise faeces. The prevalence of oxyurid infections was particularly high. In combination with pathological findings in clinical oxyuridosis obtained from necropsied animals, our findings call for further, detailed investigations on pathogenesis and immunology of oxyurids in pet reptiles. Coprological analyses for parasite detection should be mandatory before tortoises are transferred to a new owner, animal group, or public and private enclosures such as zoos. We advocate for regular health screenings in pet tortoises and, if parasitic infections are diagnosed, adequate medication or alternative hygiene management should be considered to improve and maintain individual and population health.    Electronic supplementary material  The online version of this article (10.1186/s13071-018-2936-z) contains supplementary material, which is available to authorized users.

Occurrence of health-compromising protozoan and helminth infections in tortoises kept as pet animals in Germany