PARADISE: Parasite Detection, Isolation and Evaluation

Start: 1 January 2020
Duration: 2.5 Years
Domain: Emerging Threats
Key Words: Parasites, genomics, metagenomics, high resolution genotyping, enrichment strategies
Contact: Simone M. Cacciò (ISS)

The Project #PARADISE

Foodborne parasites (FBPs) are major contributors to the global burden of gastrointestinal disease. In Europe, according to recent estimates, protozoa of the genera Cryptosporidium and Giardia are of particular relevance. These parasites are transmitted through direct and indirect routes, and cause large outbreaks linked to contaminated water and food. Outbreak investigation and source attribution remain difficult, also due to the existence of genetically highly variable species and genotypes of zoonotic origin.

PARADISE aims to deliver informative typing schemes and innovative detection strategies applicable to food matrices for both parasites. Using NGS technologies (genomics and metagenomics), the project will generate much needed data that will enrich our understanding of the epidemiology and genomics of these organisms, and provide the basis on which improved strain-typing schemes will be developed and rigorously tested. In parallel, strategies (nanobodies, aptamers, use of hybridization probes) to enrich for the target pathogens in different matrices will also be developed and tested. Furthermore, PARADISE will engage in multicentre studies to validate the newly developed methods, testing their applicability across the spectrum of relevant matrices in an unprecedented effort at the EU level. These new methodologies will form the basis for integrated approaches aimed at controlling FBPs in the European food chain.


Franceschelli, A., Bonadonna, L., Cacciò, S. M., Sannella, A., R., Cintori C., Gargiulo R., Coccia A. M., Paradiso R., Iaconelli M., Briancesco R. and Tripodi A. (2022) An outbreak of cryptosporidiosis associated with drinking water in north-eastern Italy, August 2019: microbiological and environmental investigations. Eurosurveillance. 27(35), 2200038. DOI:

Franssen F., Janse I., Janssen D., Caccio SM., Vatta P., van der Giessen J., van Passel MWJ. (2021). Mining Public Metagenomes for Environmental Surveillance of Parasites: A Proof of Principle. Frontiers in Microbiology. 12:622356. DOI:

Stensvold, CR., Jirků-Pomajbíková, K., Tams, KW., Jokelainen, P., Berg, RPKD., Marving, E., Petersen, Randi F., Andersen, L O’Brien., Angen, Ø., Nielsen, HV. (2021). Parasitic Intestinal Protists of Zoonotic Relevance Detected in Pigs by Metabarcoding and Real-Time PCR. Microorganisms. 9, 1189. DOI:

Belkessa, S., Thomas-Lopez, D., Houali, K., Ghalmi, F., Stensvold, C R. (2021). Molecular Characterization of Giardia duodenalis in Children and Adults Sampled in Algeria. Microorganisms. 9 (1), 54. DOI: 

Lopez, T., Müller, L., Vestergaard, LS., Christoffersen, M., Andersen, A., Jokelainen, P., Agerholm, JS., Stensvold, CR. (2020) Veterinary Students Have A Higher Risk Of Contracting Cryptosporidiosis When Calves With High Fecal Cryptosporidium Loads Are Used For Fetotomy Exercises. Applied and Environmental Microbiology. DOI:

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