COMPARE was a large EU European Union (European Union ) project that intended to speed up the detection of, and response to disease outbreaks among humans and animals worldwide, through the use of new genome technology. The aim was to reduce the impact and cost of disease outbreaks. To that end, 28 European partners, led by Technical University of Denmark and Erasmus Medical Center Rotterdam have received 20 million euro in funding from the Horizon 2020 program of the European Commission. RIVM participated in the project. 

The health of humans and animals around the world is increasingly under threat due to new and recurring epidemics and foodborne disease outbreaks, which place pressure on health services and the production of livestock. These epidemics also reduce consumer confidence in food and negatively impact trade and food security. The longer it takes from the start of an outbreak of, for example, Ebola, influenza or salmonella until it is detected and stopped, the greater the consequences. The most important factor in being able to limit the consequences and costs of such outbreaks is the ability to identify the disease-causing microorganisms that are causing the disease quickly.  Secondly, there is a need for knowledge about the mechanisms that cause the disease, and how the bacteria are transmitted to and between humans.

Use of genome sequencing

COMPARE aimed to develop a global platform that would make it possible to quickly identify disease-causing microorganisms which cause, or have the potential to cause, disease outbreaks around the world. The research project made use of whole genome sequencing, in which a disease-causing microorganism’s wholeDNA-profile is mapped out at one time. ”The platform we created in this project makes it possible in real time to exchange and interpret information about disease-causing microorganisms from around the world, and to compare this with other relevant information such as clinical and epidemiological data,”. The consortium leaders professor Frank Møller Aarestrup from the National Food Institute of Denmark, and professor Marion Koopmans from Erasmus MC the Netherlands explain. "The aim is that the platform can be used to harmonise the way scientists, authorities, doctors and organisations around the world collect samples, generate genome sequencing data and carry out risk assessments. This new approach to disease surveillance will be able to revolutionise the way we combat diseases globally," Aarestrup and Koopmans add.

One Health approach

Zoonoses – diseases that can spread from animals and food to humans – are the cause of many epidemics internationally. For this reason, COMPARE was based on collaboration across sectors and land borders. The project also developed tools that can be used to diagnose and treat patients, investigate outbreaks and communicate the risks associated with various disease-causing microorganisms.

COMPARE collaboration

COMPARE was a collaboration between the organisations behind the Global Microbial Identifier (GMI) project as well as some of Europe's leading institutions in the field of emerging epidemics and foodborne outbreaks. Amsterdam Medical Center, Erasmus iBMG and RIVM were also partners in the project. RIVM Strategic Programme provided co-funding. In the GMI project, a number of international institutions were working together to improve global disease surveillance and clinical diagnosis of diseases.

Main outcomes of the COMPARE project

COMPARE pioneered new techniques to detect and share information about infectious disease outbreaks. Some of the tools devised in the project were further developed to specifically tackle the spread of COVID-19, as well as the next potential infectious disease outbreaks.
The COMPARE project began by demonstrating how NGS Next Generation Sequencing (Next Generation Sequencing) technology could be used to sample, collect and sequence outbreak data. One interesting element was proving the usefulness of metagenomics. This is the study of genetic material recovered directly from environmental samples. For instance, COMPARE showed how antimicrobial resistance and viruses could be detected and analysed in sewage collected globally.
The results of the COMPARE project are also being sustained through a user-friendly data upload and analysis platform made up of datahubs. This is where all NGS data can be shared in the public domain. The platform addresses issues such as the long-term storage of high-density data, and the need to make such data easier to find and reuse.

The Horizon2020 VEO project engages core members of the COMPARE consortium, taking the COMPARE results even further, aiming to develop a versatile forecasting and tracking system. This will also serve as an interactive observatory to generate and distribute information for risk assessments and the monitoring of emerging infectious diseases.