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COMPARE (COllaborative Management Platform for detection and Analyses of (Re-) emerging and foodborne outbreaks in Europe) - OZ0157

Description
1.1
OBJECTIVES
COMPARE (COllaborative Management Platform for detection and Analyses of (Re-) emerging and foodborne
outbreaks in Europe) is a collaboration of founding members of the Global Microbial Identifier (GMI) initiative
(http://www.globalmicrobialidentifier.org) and institutions with hands-on experience in outbreak detection and
response. GMI was established in 2011 with the vision to develop the potential of breakthrough sequencing
technologies for the field of infectious diseases through a joint research and development agenda, with applications
in clinical and public health laboratories across the world. In order to achieve that long-term goal, the GMI group
aims to promote development and deployment of novel applications, data sharing and analysis systems across the
diversity of pathogens, domains and sectors. The COMPARE project is set up to put this vision into action in
Europe, addressing the following main objective:
• TO IMPROVE RAPID IDENTIFICATION, CONTAINMENT AND MITIGATION OF EMERGING INFECTIOUS DISEASES
AND FOODBORNE OUTBREAKS,
• BY DEVELOPING A CROSS-SECTOR AND CROSS-PATHOGEN ANALYTICAL FRAMEWORK AND GLOBALLY LINKED
DATA AND INFORMATION SHARING PLATFORM,
• THAT INTEGRATES STATE-OF-THE-ART STRATEGIES, TOOLS, TECHNOLOGIES AND METHODS FOR COLLECTING,
PROCESSING AND ANALYZING SEQUENCE-BASED PATHOGEN DATA IN COMBINATION WITH ASSOCIATED
(CLINICAL, EPIDEMIOLOGICAL AND OTHER) DATA,
• FOR THE GENERATION OF ACTIONABLE INFORMATION TO RELEVANT AUTHORITIES AND OTHER USERS IN THE
HUMAN HEALTH, ANIMAL HEALTH AND FOOD SAFETY DOMAINS;
Next Generation Sequencing (NGS) used for
Whole Genome Sequencing (WGS) or Whole
Community Sequencing (WCS or metagenomics)
are opening and dominating a new field of data
generation and connection, revolutionizing
pathogen detection and typing in human and
animal health just as much as in food science.
These technologies are rapidly dropping in cost
and starting to become in reach of routine clinical
and public health laboratories (Köser et al. 2012,
Didelot et al. 2012). NGS/WGS/WCS enables
generating the complete genomic information
from the isolate or sample independent of both the
sector (public health, veterinary health, food
safety), and the type of pathogen (viruses,
bacteria, parasites). The outputs (sequence data)
provide one common language that can be
exchanged and compared between laboratories
and over time, in combination with other
associated data defined here as “metadata”
including contextual data (e.g. data on sample type and process, clinical, microbiological, epidemiological and
other data) primary data (raw sequence reads) and derived data (e.g., genomic alignments of reads, assemblies
and functional annotation data sets).
COMPARE aims to harness the rapid advances in these technologies to improve identification, and mitigation of
emerging infectious diseases and foodborne outbreaks. To this purpose COMPARE will establish a “One serves
all” analytical framework and data exchange platform that will allow real time analysis and interpretation of
sequence-based pathogen data in combination with associated data.
Figure 1: Genomic Information as the pathogen independent
language across locations, sectors and time
COMPARE 3
In order to achieve this, COMPARE will pursue specific objectives A through G, to be realized within the fiveyear
duration of COMPARE. Together these 7 project objectives shape the overall structure of COMPARE – as
depicted in figure 2 – showing the different components of the COMPARE Analytical Framework.
The project follows a common trajectory necessary to obtain high quality information for stakeholders to improve
rapid identification, containment and mitigation of emerging infectious diseases and foodborne outbreaks.
A. Starting from the design of 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: The process to obtain high quality and
comparable sequence data from and metadata associated with a specimen;
C. From comparable data to actionable information: The downstream analyses involved in 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. Researchers focusing on these steps team up with system developers that will build a data and information
platform supporting rapid sharing, integration and analysis of sequence-based pathogen data in
combination with other contextual metadata;
FIGURE 2: the COMPARE analytical framework and its main components from sample and data collection to
generating actionable information to stakeholders in the human, animal and food sectors.
COMPARE 4
E. Risk communication tools will be developed enabling authorities in the human and animal health and food
safety sectors to effectively communicate to their stakeholders 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.
Project Documents
• OTH - Other : COMPARE part B 1-3   (2287k)
Time-Scale and Cost
From: 2013

To: 2016

Cost: £75,000
Contractor / Funded Organisations
APHA (Animal and Plant Health Agency)
Keywords