ORIGINAL PAPER Evaluation of an automated magnetic bead-based DNA extraction and real-time PCR in fecal samples as a pre-screening test for detection of Echinococcus multilocularis and Echinococcus canadensis in coyotes Maria A. Santa 1 & Sonya Pastran 1 & Claudia Klein 2 & Kathreen Ruckstuhl 1 & Alessandro Massolo 3,4,5 Received: 8 June 2018 /Accepted: 9 October 2018 # Springer-Verlag GmbH Germany, part of Springer Nature 2018 Abstract Efficient and sensitive diagnostic tools are essential for the study of the eco-epidemiology of Echinococcus species. We evaluated an automated magnetic bead-based DNA extraction commercial kit followed by qPCR (MB-qPCR), for the detection of Echinococcus multilocularis and Echinococcus canadensis in coyote (Canis latrans) fecal samples. The diagnostic sensitivity was determined by validating the method against the scraping, filtration, and counting technique (SFCT) for samples collected in Canada. From the 60 samples tested, 27 out of 31 SFCT positives samples for Echinococcus cestodes were positive in the MB- qPCR for E. multilocularis, with a sensitivity of 87.1% (95% CI 70.2 to 96.4%). Two samples were also positive for E. canadensis in the MB-qPCR and confirmed by morphological identification of adult worms. The agreement of the MB- qPCR and the SFCT was statistically significant with a kappa value of 0.67 (95% CI 0.48–0.85; p value < 0.001). The magnetic bead-based DNA extraction followed by qPCR proved to have a sensitivity comparable to the SFCT to detect E. multilocularis. Although the diagnostic sensitivity for E. canadensis was not estimated, MB-qPCR identified E. canadensis cases previously overlooked when using SFCT. We propose a combination of molecular and morphological identification using the MB-qPCR and the SFCT to detect both parasites, allowing for a more efficient large-scale surveillance, and detecting co-infections of Echinococcus species that can be difficult to identify when only based on morphology. Keywords Echinococcus multilocularis . Echinococcus canadensis . Coyote . Real-time PCR . Coprodiagnosis . Magnetic beads Introduction Echinococcus multilocularis and Echinococcus canadensis are two important, but often neglected, zoonotic parasites of public health concern (FAO/WHO 2014; Thompson 2015), being the etiological agents of alveolar (AE) and cystic echi- nococcosis (CE), respectively. Humans get infected by acci- dentally ingesting embryonated eggs excreted in feces of de- finitive hosts, mainly wild carnivores such as foxes (Vulpes vulpes), coyotes (Canis latrans), and wolves (Canis lupus), but also dogs. These parasites are present in the Northern hemisphere, including most provinces in Canada (Massolo et al. 2014; Davidson et al. 2016; Deplazes et al. 2017). Although human cases of AE are considered rare in North America, recent reports of an autochthonous case of human AE (Massolo et al. 2015), along with high prevalence in urban coyotes (Catalano et al. 2012; Massolo et al. 2014), multiple aberrant cases of liver infections (canine AE) in dogs (Peregrine et al. 2012; Skelding et al. 2014), and the presence of co-infections with both parasites in wolves in the subarctic region (Schurer et al. 2013), make the understanding of the transmission of these parasites a priority. To estimate the prev- alence of these parasites in their definitive hosts and to Handling Editor: Julia Walochnik * Alessandro Massolo alessandro.massolo@unipi.it 1 Department of Biology, University of Calgary, AB T2N 1N4, Canada 2 Department of Veterinary Clinical Diagnostic Sciences, Faculty of Veterinary Medicine, University of Calgary, AB T2N 4Z6, Canada 3 Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, AB T2N 4Z6, Canada 4 Ethology Unit, Department of Biology, University of Pisa, 56126 Pisa, Italy 5 UMR CNRS 6249 Chrono-environnement, Université Bourgogne Franche-Comté, 25030 Besançon, France Parasitology Research https://doi.org/10.1007/s00436-018-6125-y