INNUENDO: A novel cross-sectorial platform for the integration of genomics in surveillance of foodborne pathogens


Whole-genome sequencing (WGS) of foodborne bacteria has become an important strategic goal among public health authorities worldwide. However, implementing WGS routinely is hindered by the lack of accessible IT framework and by the limited skills of microbiologists in handling the novel methodology. INNUENDO project aims to develop an affordable software platform and communication protocol for WGS-based outbreak investigations, supporting especially small countries with limited resources. In the platform, genomic comparisons are performed based on allele differences (wgMLST), for which genetic diversity is calibrated for each bacterium (STEC, Campylobacter, Yersinia and Salmonella) in the project. Besides genomic comparisons, the platform enables analysis of, for example, virulence and resistance genes. In addition, an automatic pipeline is developed for the QA/QC of sequence assemblies before analyses, and function of the platform is validated by simulating national and multinational outbreak investigations.


The project aims to develop a cross-sectorial platform for the integration of bacterial WGS in outbreak investigations and routine surveillance.


whole-genome sequencing, WGS, food safety, STEC, Campylobacter, Yersinia, Salmonella

Responsible project leader:

Mirko Rossi, Assistant professor DVM (PhD), University of Helsinki

Person at Evira responsible for the project:

 Marjaana Hakkinen, Senior researcher PhD, Food and Feed Microbiology Research Unit

In cooperation with:

University of Helsinki;
University of Lisbon;
University of Basque Country;
University of Veterinary Medicine Vienna;
Finnish National Institute for Health and Welfare;
Portuguese National Health Institute;
Estonian Veterinary and Food Laboratory;
Latvian Institute of Food Safety, Animal Health and Environment

Project status:

In progress

Year of commencement:


Year of completion:


Project finansed by:

European Food Safety Authority (GP/EFSA/AFSCO/2015/01/CT2)

Evira project code: