Abstract:
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.
Aims:
The project aims to develop a cross-sectorial platform for the integration of bacterial WGS in outbreak investigations and routine surveillance.
Keywords:
whole-genome sequencing, WGS, food safety, STEC, Campylobacter, Yersinia, Salmonella
Responsible project leader:
Mirko Rossi, Assistant professor DVM (PhD), University of Helsinki
Person at Finnish Food Authority responsible for the project:
Marjaana Hakkinen, Head of Section, Microbiology 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:
2016
Year of completion:
2019
Project finansed by:
European Food Safety Authority (GP/EFSA/AFSCO/2015/01/CT2)
Finnish Food Authority project code:
4080Y-000042
Webside: http://www.innuendoweb.org/