The online infrastructure, Global Pathogen Analysis Platform (GPAP), is supported by the Novo Nordisk Foundation with up to DKK 200 million over the next six years. GPAP is led by DTU National Food Institute, which has decades of experience in disease prevention and pathogen surveillance.
“GPAP will be open to all countries and institutions worldwide, but its primary aim is to enable low- and middle-income countries to independently conduct research and surveillance of infectious diseases. DTU National Food Institute has several decades of experience in monitoring pathogenic microorganisms and infection tracking, and we are truly excited to serve as the incubator for this new global online infrastructure,” says Professor Tine Rask Licht, Director of DTU National Food Institute.
The institute publishes annual surveillance reports on zoonoses, as well as on antimicrobial consumption and resistance (DANMAP), and has played a key role in positioning Denmark as a role model for other countries in the One Health field—not only in Europe, but also globally, including in Africa and Asia.
Success measured by the absence of pandemics
GPAP will offer support to the many experts around the world working on tracking infectious diseases, facilitated through a free online infrastructure for researchers and healthcare professionals from low- and middle-income countries.
“The task is to help extinguish numerous small outbreaks before they develop into epidemics or pandemics. We cannot provide active assistance for the thousands of daily outbreaks and incidents occurring around the world. But by creating the online infrastructure and offering free access, we can strengthen those responsible in low- and middle-income countries,” says Professor Henrik C. Wegener, former Rector of the University of Copenhagen and Head of GPAP at DTU National Food Institute.
Success will therefore to some extent be measured by what does not happen, namely, the absence of pandemics.
Henrik C. Wegener, who also served as Director of DTU National Food Institute (2006–2011) and Provost at DTU (2011–2017), was a driving force in the 1990s behind today’s understanding of the link between animal and human health. In 1994, he became the first head of the Danish Zoonosis Centre, which was integrated into DTU with the National Food Institute in 2007.
Today, the One Health concept, which emphasizes the close connection between human health, the environment, and animal health, is well established globally. Disease prevention and control are thus inextricably linked to food, which is a key focus area for DTU National Food Institute, including food safety, disease control, and antimicrobial resistance in a range of international forums.
GPAP to detect pandemics through co-creation with users
GPAP’s ability to detect pandemics will be based on many small, local actions across the globe, where, for example, healthcare professionals or researchers can upload and have DNA sequences from potential pathogens (bacteria, viruses or fungi) analysed. When a genetic sequence is uploaded, the software will identify the organism it originates from and compare it with known genetic patterns. In this way, relationships and potential health risks can be mapped.
The system will be used for both research and disease surveillance, where data on time, location and symptoms can be linked with genetic findings to detect patterns and emerging outbreaks, including microorganisms and diseases in animals, humans and plants.
“GPAP will allow users of the online infrastructure to retain full control over their own data. The shared information is often politically and commercially sensitive, and therefore the possibility of anonymity is a prerequisite for trust and participation. Experience from COVID-19 has shown how difficult it is to share health data when such information may threaten national interests,” says Professor Henrik C. Wegener.
Built on online resources for characterising pathogenic microorganisms
In addition to Henrik C. Wegener, Professor Frank Møller Aarestrup and Professor René S. Hendriksen from DTU National Food Institute are part of the GPAP leadership team. The two professors lead the Research Group for Genomic Epidemiology and the Research Group for Global Capacity Building, respectively.
The Research Group for Genomic Epidemiology, headed by Frank Møller Aarestrup, has developed the online infrastructures that will serve as core resources for the new GPAP. These are free tools that help understand and monitor bacteria using their DNA.
The first online tools were established in 2011, and today the group offers 37 different solutions that collectively analyse around 1,000 bacterial genomes per day. The focus on online bioinformatics stems from it being one of the key bottlenecks in expanding the use of genome sequencing for global surveillance and data sharing.
The available online tools include, for example, PathogenFinder and ResFinder.
PathogenFinder, established in 2014, predicts whether a bacterium may be pathogenic to humans. The programme analyses the bacterium’s DNA and compares it with known pathogenic bacteria. Based on the analysis, PathogenFinder calculates the likelihood that the bacterium may cause disease.
ResFinder, launched in 2012, identifies whether a bacterium contains genes that makes it resistant to antibiotics. The programme compares bacterial DNA with a large database of known resistance genes and shows which types of antibiotics the bacterium is likely not to respond to. ResFinder is used by researchers and laboratories worldwide to monitor the spread of antimicrobial resistant bacteria in humans, animals and the environment.
“GPAP will serve as an extension of the open-source systems previously developed by DTU National Food Institute. This has now become possible because new genomic technologies make it feasible to monitor pathogens in animals, humans, and the environment with a very high level of detail and at the population level, for example by monitoring wastewater. In addition, artificial intelligence has entered the field and can add a new dimension, enabling users not only to obtain an analysis result but also to receive suggestions for actions based on that result,” says Professor Frank Møller Aarestrup.
The platform will provide an overview of what the results mean, how they can be used, and where action can be taken. It will be designed to make something highly complex easily accessible to users who are not necessarily specialists.
Extensive network for disease surveillance professionals
DTU National Food Institute plays a central role in the international landscape of disease prevention. The Research Group for Global Capacity Building works to strengthen global surveillance of infectious microorganisms and antimicrobial resistance by developing and implementing methods and guidelines, as well as ensuring the quality of laboratory results used in surveillance—particularly in low- and middle-income countries. DTU National Food Institute has been designated as a reference laboratory for antimicrobial resistance by the WHO, FAO and the EU.
Based on this, the group is a key player in the global effort to combat disease outbreaks and antimicrobial resistance and has an extensive network in low- and middle-income countries, which often lack advanced technical expertise and laboratory capacity in whole genome sequencing and resistance monitoring.
“Funding to build and support laboratory capacity in low- and middle-income countries is often project-based and limited. Therefore, in the long term, countries themselves must contribute by getting on board and integrating surveillance capacity permanently into their healthcare systems. With GPAP, we hope to create a stable and free resource that will provide countries with accessible capacity to draw upon,” says Professor René S. Hendriksen.
