Genetic characterization of Echinococcus multilocularis using deep amplicon sequencing

Echinococcus multilocularis is a tiny tapeworm whose adults live in the intestines of wild and domestic canids and shed their eggs with the host feces. If accidentally ingested by people, eggs can cause human alveolar echinococcosis (AE), a highly lethal parasitic disease. Despite Em being common in North America, only two locally acquired AE human cases were reported in North America until 2013. However, in the last 6 years, 14 new cases have been detected in Alberta, Canada, and recent findings showed that the European strain of this parasite is now common in wildlife in this province, which could potentially increase the risk of infection in humans and domestic animals. In this study, we genetically characterized Em in coyotes and red foxes to assess the extent of the European-type strain distribution in three Canadian provinces. We used deep amplicon sequencing, an innovative approach that allows us to detect co-infections and the presence of less prevalent genetic variants by sampling a larger proportion of the parasite subpopulation per host. Our study showed an overwhelming prevalence of the European strain over the native North American strain in both hosts, and a limited geographical distribution of some European genetic variants, likely due to multiple introduction events of this invasive strain.