Workpackage 7

Underpinning research on food outbreaks using the COMPARE analytical framework

WP leader: Eva Møller Nielsen, SSI (3)
co-leaders: Tine Hald, DTU (1), & Michel-Yves Mistou, ANSES (5)

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.


Eva Møller Nielsen
Senior Scientist
Statens Serum Institut


Tine Hald
Senior Researcher
Technical University of Denmark


Michel-Yves Mistou
French Agency for Food, Environmental and Occupational Health and Safety
16 JULY 2024