Scientists advocate global genomic surveillance using cutting-edge technologies and a “One Health” approach to protect against new pathogens such as bird flu and antimicrobial resistance, catching epidemics before they start.

The COVID-19 pandemic has turned the world upside down. One of our most important weapons in the fight against this has been genomic surveillance based on whole genome sequencing, which collects all the genetic data of a particular microorganism. This powerful technology has tracked the spread and evolution of the virus, helping to guide public health interventions and the development of vaccines and treatments.

But genomic surveillance can do much more than just protect us from COVID-19 to reduce disease and death worldwide. In the magazine Frontiers in Science An international team of clinical and public health microbiologists from the European Society for Clinical Microbiology and Infectious Diseases (ESCMID) is calling for investment in technology, capacity, expertise and collaboration to bring genomic surveillance of pathogens to the forefront. a precursor to preparing for a future pandemic.

“Epidemic-prone infectious diseases are crossing borders at the same rate that people and commodities travel around the world,” said lead author Professor Marc Strulens of the Free University of Belgium and former chief microbiologist of the European Center for Disease Prevention and Control (ECDC). “Today’s local epidemic could be tomorrow’s next global epidemic.”

A significant advantage

Most diseases that have not been seen in humans before are zoonotic diseases that occur in animals and infect humans. Many diseases in animals are also treated with antibiotics and other antimicrobial drugs used in humans. However, the widespread use of antimicrobials in humans and animals has led to resistance as microbes evolve to survive. Therefore, we face two major overlapping public health threats: one from new infectious diseases that are zoonotic, and the other from the rise of antimicrobial resistance. Overcoming these threats requires a collaborative One Health approach, supported by the World Health Organization (WHO), which recognizes that human health depends on the health of our ecosystem.

The answer, scientists say, is to repurpose advanced genomic surveillance technology and the capabilities created by COVID-19 to act as sentinels. Genomic surveillance, which brings together health authorities, veterinarians and doctors, should be used to monitor human and animal diseases and antimicrobial resistance. By integrating epidemiological and clinical data from all these areas, we can obtain a complete picture of pathogens and the risks they pose.

“Surveillance of the pathogen genome is a tool to examine the interplay between antimicrobial selective pressures on microbial populations and the adaptive evolution of these microbes toward drug resistance,” Strulens said. “This allows us to detect the emergence of superfits resistant to various drugs, epidemic clones, i.e. ‘superbugs’, and unravel the dynamics of transmission. Genomic surveillance can help monitor both zoonotic and human-to-human transmission of virus variants, bacterial strains, and drug resistance signatures .”

Fast detection and response

Real-time genomic surveillance of pathogens can allow us to quickly identify new resistant bacterial strains and new diseases transmitted between humans and animals and monitor their spread and evolution. This information can inform vaccination campaigns, help develop targeted therapies, and guide public health interventions; all of which can help prevent outbreaks.

Monitoring the entire genome will also allow us to better study emerging diseases and the evolution of known diseases, assess their risks, and identify countermeasures. In a globalized world where pathogens move rapidly, genomic surveillance will enable equally rapid diagnosis and treatment of infections.

Strulens and colleagues highlight how new sequencing technologies, such as long-term genome sequencing, ultrafast and single-cell sequencing, and artificial intelligence, are helping to improve surveillance in some parts of the world.

“There are many places where genomic surveillance already provides significant protection against the spread of disease,” Struelens said. “This includes foodborne infections in Europe, North America and Australia, and epidemic viral diseases such as bird flu in many countries around the world.”

Building global surveillance networks

To make genomic surveillance effective, we need real-time data from around the world, scientists say. To achieve this, we need to make significant investment in capacity and expertise that takes into account the different levels of infrastructure and training available around the world. During the COVID-19 pandemic, countries that already had access to genomic surveillance expertise and equipment were at a major advantage in monitoring the outbreak and adapting their responses. The authors present a framework for the equitable implementation of globally interconnected surveillance systems, including low- and middle-income countries.

“The article by Struelens et al. A must-read for anyone interested in genomic surveillance as part of epidemic preparedness,” Professor Marion Koopmans of the Erasmus Medical Center in Rotterdam, the Netherlands, said in an accompanying editorial. “The means and the will are obvious; The next step is to create equitable, shared surveillance infrastructures for the future of global health. The “Pandemic Convention” proposed by WHO will play a key role by setting some rules for international participation for better preparation. Exciting times ahead!”

We also urgently need to invest in collaboration to build bridges between animal, human and public health disciplines and connect countries and health organizations. This will be critical not only for stakeholders to work together, but also for us to reach data governance and regulatory agreements to keep patient data anonymous and secure.

“To achieve universal participation in shared genomic surveillance systems around the world, our critical challenges are to have adequate laboratory and sequencing capacity, train an expert workforce, and access proven tools for genomic data analysis and sharing within a comprehensive secure digital health information framework. infrastructure,” Struelens said. “The integration of genomic information about an epidemic pathogen with epidemiological information must occur on a scale from the local to the global level.”