COMPARE system

Project plan

The COMPARE analytical framework and its main components from sample and data collection to generating actionable information for stakeholders in the human, animal and food sectors.

A. Risk-assessment models and risk-based sampling and data collection strategies that enhance our capacity to detect potential disease outbreaks;

B. From samples and associated metadata to comparable data: harmonised standards for sample processing and sequencing to obtain high quality and comparable sequence data from and metadata associated with a specimen;

C. From comparable data to actionable information: designing analytical workflows for turning comparable data into actionable information for addressing questions in frontline diagnostics, food-borne infections and (re-) emerging infections. “Actionable Information” is defined as information that enables users generating/receiving this information to take well-informed decisions and actions in pursuit of:

  • Pathogen identification and characterization: Pathogen identification, genotyping and phenotyping, (e.g., detection of relevant antimicrobial resistance, virulence, epidemiological markers);
  • Outbreak detection: Detection of putative clusters by examining strain-specific clusters in time, place and host (person, animal and food);
  • Outbreak investigation: Rapid interrogation for given molecular strains to identify the potential origin of internationally distributed clones that may result in outbreaks; analysis tools to monitor extend of spread based on sequence diversity in relation to control measures;
  • Outbreak prediction: Automatic analyses for predicting risk of emergence of pathogens with outbreak potential.

D. Designing and building a common data and information platform supporting rapid sharing, integration and analysis of sequence-based pathogen data in combination with other contextual metadata; The system will be linked to existing and future complementary systems, networks and databases such as those used by ECDC, NCBI and EFSA.

E. Risk communication tools will be developed enabling authorities in the human and animal health and food safety sectors to effectively communicate the results obtained with the new analytical workflows;

F. The development of the analytical framework is underpinned by a set of supporting research, dissemination and communication activities promoting the acceptance of the system and its components. These activities encompass (i) consultations with our stakeholders serving on expert advisory panels throughout the project to maintain a prominent focus on user needs (ii) studies on the barriers (ethical, regulatory, administrative, logistical, political) to the implementation and widespread use of open-date sharing platforms, (iii) dissemination and training activities;

G. Finally COMPARE will include the development of a framework for estimating the cost-effectiveness of the COMPARE system, including the value of safety.
16 JULY 2024