Underpinning research on food outbreaks using the COMPARE analytical framework
WP leader: Eva Møller Nielsen, SSI (3) emn@ssi.dk
co-leaders: Tine Hald, DTU (1) tiha@food.dtu.dk, & Michel-Yves Mistou, ANSES (5) michel-yves.mistou@anses.fr
Objectives:
To establish robust analytic procedures of NGS/WGS data for Salmonella, STEC/EHEC, Listeria, norovirus, hepatitis A, and Cryptosporidium to be able to identify epidemiologically linked isolates and differentiate these from similar unrelated isolates.
- To develop guidelines for interpretation criteria for defining clusters of disease and linking of isolates from various sources and reservoirs.
- To enable backward compatibility to important previous nomenclature (e.g. serotypes, species, MLST).
- To perform pilot studies in collaboration with global partners and networks including ECDC and EFSA.
In collaboration with WPs 3, 4 and 5:
- To evaluate analysis tools developed in WP3 and WP5 to predict phenotypic traits such as antimicrobial resistance, invasiveness and virulence.
- To improve the evolutionary reconstruction of the organisms and thus provide a rational framework for investigations into the population structure, genetic diversity, epidemiology and transmission and identification of spatial-temporal clusters.
- To provide the input for the epidemiological, source attribution and risk assessment models developed in WP4.