DiSCoVer: Discovering the sources of Salmonella, Campylobacter, VTEC and antimicrobial resistance

Start: 1 January 2020
Duration: 2.5 Years
Domain: Foodborne Zoonoses
Key Words: Source attribution, risk assessment, epidemiology, foodborne
Contact: Tine Hald (DTU)

The Project #DISCOVER

This project brings together experts from different disciplines (microbiology, bioinformatics and epidemiology) and sectors (veterinary science, food safety, public health and environmental health) from 19 institutions in 13 European countries into a unique consortium to address the challenges of source attribution in an interdisciplinary manner. As there is no gold standard for source attribution, we will take a comprehensive approach applying several different methodologies and models in a comparative fashion.

The project will map the existing knowledge gaps and recommend new studies and/or methods that are needed to fill them. The work will start by mapping existing data and establishing a joint data-sharing platform for the project partners. We will include data from a broad range of reservoirs and sources, including those that are not traditionally part of existing monitoring and surveillance activities, e.g. pets (incl. reptiles), wildlife, and environmental sources.

The work will also focus on cataloguing, evaluating and advancing existing methods for source attribution and develop methods for the critical assessment of source attribution models. Novel approaches for source attribution will also be explored, developed and assessed. Existing approaches that will be investigated include the microbial subtyping, meta-analysis of case-control studies and outbreak data, and risk-assessment based methods. The source attribution estimates  will focus on three pathogens (Salmonella, Campylobacter, and STEC) and AMR.

We expect by the end of the project to have identified and filled important knowledge, methodological and data gaps for source attribution of zoonotic pathogens and AMR determinants through systematic collection and analysis of existing and new data and by applying existing, modified and novel approaches. We will make recommendations on how source attribution estimates can be translated to policy action to support the surveillance, control and prevention of foodborne infections in EU. These recommendations will be presented for and discussed with stakeholders such as ECDC and EFSA, and farmer and consumer organisations.


Lopez-Chavarrias, V., Dieguez Roda, B., Torre Fuentes, L., Ugarte-Ruiz, M., Saez, J. L., Moreno, M. A., Dominguez, L. & Alvarez, J. (2022). Mapping antimicrobial resistance markers for aminoglycosides and macrolides in Campylobacter in Spanish livestock. Abstract for oral presentation to be delivered at 16th International Symposium of Veterinary Epidemiology and Economics. Halifax, Nova Scotia, Canada. 7th August 2022. DOI:

Ribeiro, S., Fontes, M., Lopes, I., Silveira, L. & Pista, A. (2022). Colistin Resistance Genes in Escherichia coli and Salmonella spp. Isolates from Pets, Wild and Food-producing Animals in Portugal, 2019-2021. Poster presentation for 32nd European Congress of Clinical Microbiology & Infectious Diseases. Lisbon, Portugal. 23-26th April 2022. DOI:

Lopez-Chavarrias, V., Wieczorek, K., Osek, J., Dieguez Roda, B., Torre Fuentes, L., Ugarte-Ruiz, M., Moreno, M. A., Dominguez, L., & Alvarez, J. (2022). Epidemiological comparison of Campylobacter jejuni isolates from Poland and Spain combining MLST and antimicrobial resistance whole genome analyses. Poster presentation for OHEJP ASM 2022. Orvieto, Italy. 11-13th April 2022. DOI:

Mughini-Gras, L.Benincà, E.McDonald, S. Jong, A.Chardon, J.Evers, E., & Bonačić Marinović, A. A. (2022). A statistical modelling approach for source attribution meta-analysis of sporadic infection with foodborne pathogensZoonoses and Public Health001– 12. DOI:

Lopez-Chavarrias, V., Ugarte-Ruiz, M., Barcena, C., Olarra, A., Garcia, M., Saez, JL., de Frutos, C., Serrano, T., Perez, I., Moreno, MA., Dominguez, L., Alvarez, J. (2021). Monitoring of Antimicrobial Resistance to Aminoglycosides and Macrolides in Campylobacter coli and Campylobacter jejuni From Healthy Livestock in Spain (2002–2018). Frontiers in Microbiology. 12:689262. DOI:

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