Project definition


Multinational outbreaks of food-borne pathogens cause considerable threats to European public health. An increased level of cooperation between the local, national and European competent authorities by dedicated training, development of a common pathogen database and validation of new approaches in microbial characterization is warranted. Implementing whole genome sequencing (WGS) in routine surveillance and outbreak investigations is becoming a strategic goal for many public health authorities all over the world. However, small countries with limited resources might not be able to succeed in reaching this goal in the near future, putting several EU member states in a condition of inferior capabilities for outbreak detection and investigation. Therefore, to guarantee the reinforcement of European capacities to ensure protection of citizens against cross border health threats, EU must enable wider access to the new methodologies. The potential of widespread, routine use of WGS analysis for public health protection is essentially restricted by the absence of accessible IT framework, and the limited skills of public health microbiologists in handling these novel methodologies.


The overall objective of our proposal is to deliver a standardized, cross-sectorial framework for integration of bacterial whole genome sequencing in routine surveillance and epidemiological investigations to reduce the burden of disease caused by both epidemic and sporadic food-borne zoonotic infections.

SMART Objectives:

  1. to identify the functionalities and flaws in sharing data related to national and transnational outbreak investigations caused by foodborne pathogens 
  2. to calibrate the genetic diversity of foodborne pathogen populations using an evolutionary framework to assess the epidemiological relationship among bacterial isolates in the food chain
  3. to design an IT infrastructure and develop bioinformatics solutions for storage, mirroring, sharing and analysis of whole genome sequencing data for use in tracking foodborne pathogens 
  4. to develop a reactive standard framework for assessing the effectiveness of whole genome sequencing in outbreaks and surveillance, and evaluate the possibilities of efficient utilization of whole genome sequencing based information in solving the outbreaks

Who is involved?

To design an affordable and sustainable diagnostic infrastructure, our consortium includes governmental organizations, authorities and research institutes from the food, veterinary and human sectors of small countries such as Finland, Estonia, Latvia, Portugal, Basque Autonomous Community in Spain and Austria. Allowing project stakeholders to assess design choices early on in the development cycle ensures that the planned infrastructure will address the requirement for the integration of WGS in routine analysis in the food chain.

Project work packages


Please visit also the Project consortium overview page.

Innovative nature of the project

  • Thinking small: supporting small EU countries with limited resources
  • Network development and sharing data: communication protocols and cloud-based engine
  • The keyword is calibration: account to which degree the genetic diversity accumulated over time in a bacterial population influences the final interpretation
  • A pan-genome gene-by-gene approach: develop a flexible nomenclature server based on the pan-genome
  • A consistent, flexible and portable pipeline: QA/QC; establish different analytical strategies; hyperlink with available nomenclature servers

Technical and financial consistency of the proposal

The goal of INNUENDO is to allow a first step towards a full implementation of WGS in public health surveillance, which requires a time frame and an investment exceeding the limits of the project herein. The financial investment and the technical knowhow proposed by the consortium are consistent with a first phase calibration and validation process which is mainly concentrated to define procedures, finalize guidelines and developed the scaffold of the required infrastructure. The consortium has the intention to progress in the direction of a full implementation with future action depending on the results of the present project.