VIDEO Health experts call for a global genetic alert system to combat the next pandemic and antimicrobial resistance

Genomic surveillance can help control infectious diseases and antimicrobial resistance, scientists say. In a paper published Thursday, they outline how new genomic sequencing technologies as well as artificial intelligence (AI) could help advance the surveillance of infectious and pandemic-potential diseases.

In the fight against the Covid-19 pandemic, one of the most important weapons 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 responses and the development of vaccines and treatments.

But genomic surveillance could do much more to reduce global disease and death than protect us from Covid-19.

In an article published Thursday in the magazine Frontiers in Sciencean international collective of clinical microbiology and public health specialists within the European Society for Clinical Microbiology and Infectious Diseases (ESCMID) calls for investment in technology, capacity, expertise and collaboration to place genomic surveillance of pathogens at the forefront of preparation for future pandemics.

“Epidemic-prone infectious diseases cross borders as quickly as people and commercial goods travel around the world,” said lead author Professor Marc Struelens of the Free University of Brussels, Belgium, and former chief microbiologist at the European Center for Prevention and Disease Control (ECDC). “A local outbreak today can become the next global pandemic crisis tomorrow.”

A vital advance

Most diseases not previously seen in humans are zoonotic – diseases found in animals that infect humans.

Many diseases in animals are also treated with antibiotics and other antimicrobials that are used for humans.

However, the widespread use of antimicrobials in humans and animals has led to resistance as microbes (bacteria, fungi and viruses) evolve to survive.

We therefore face two major overlapping public health threats, experts say: one from new infectious diseases that are zoonotic, and one from the rise of antimicrobial resistance.

Addressing these threats requires a collaborative One Health approach – promoted by the World Health Organization (WHO) – that recognizes that human health depends on the health of our ecosystem.

The answer, scientists say, is to repurpose the technology and increased genomic surveillance capacity brought about by Covid-19 to act as sentinels.

Genomic surveillance that brings together public health agencies, veterinarians and human doctors must be used to monitor human and animal disease and antimicrobial resistance, experts argue.

By integrating epidemiological and clinical data from all these fields, a comprehensive picture of pathogens and the risks they pose can be obtained, they say.

“Genomic surveillance of pathogens is a tool that analyzes the interplay between antimicrobial selective pressure on microbial populations and the adaptive evolution of these microbes towards drug resistance,” explains Prof. Struelens.

Pandemic preparedness requires globally interconnected One Health surveillance systems.

“It allows us to detect the emergence and discern the transmission dynamics of epidemic super-resistant and multidrug-resistant clones – the “superbugs”. Genomic surveillance can help track both zoonotic and human-to-human transmission of viral variants, bacterial strains, and signs of drug resistance,” he notes.

Quick response

Real-time genomic surveillance of pathogens can allow us to rapidly detect new strains of resistant bacteria and new diseases that jump between humans and animals, as well as monitor their spread and evolution.

This information can inform vaccination campaigns, help design specific treatments, and guide public health responses—all of which could help prevent outbreaks.

Monitoring whole genomes would also allow new diseases and the evolution of known diseases to be studied more deeply, to assess how dangerous they are and to identify countermeasures.

In a globalized world where pathogens travel quickly, genomic surveillance would make it possible to diagnose and treat infections just as quickly, experts say.

Prof. Struelens and colleagues highlight how new sequencing technologies, including long-read genomic sequencing, ultra-rapid sequencing and single-cell sequencing, as well as artificial intelligence (AI) are helping to advance surveillance in some parts of the world.

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

A connected world

For genomic surveillance to be effective, scientists say, it requires worldwide, accessible, real-time data.

Achieving this requires massive investment in capacity and expertise that takes into account the different levels of infrastructure and training available around the world, they stress.

During the Covid-19 pandemic, countries that already had access to genomic surveillance expertise and equipment had a major advantage in monitoring the pandemic and adapting their response.

The authors provide a framework for equitable implementation of globally interconnected surveillance systems that include low- and middle-income countries.

The ‘Pandemics Treaty’ proposed by the WHO will be essential, defining some of the rules of international engagement for better preparedness. Exciting times lie ahead,” said Professor Marion Koopmans of the Erasmus Medical Center in Rotterdam, the Netherlands, in an accompanying editorial.

Experts also say there is an urgent need to invest in collaboration, to build bridges between animal, human and public health disciplines and to link countries and health agencies.

This will be essential to ensure not only that stakeholders can work together, but also that we reach agreements on data management and regulation so that patient data is anonymised and protected, experts stressed.

“To ensure universal participation in collaborative genomic surveillance systems worldwide, our key challenges are sufficient laboratory and sequencing capacity, training an expert workforce, and access to validated tools for analyzing and sharing genomic data in within a digital infrastructure of comprehensive and secure medical information”, stated Prof. Struelens.

“The integration of genomic information of epidemic pathogens with epidemiological information needs to take place on a large scale, from the local to the global level,” he added.

Whole-genome sequencing has been instrumental in combating the Covid-19 pandemic – from monitoring the spread and evolution of SARS-CoV-2 (the coronavirus that causes the disease) in real time, to guiding public health responses, treatments and vaccine development.

Starting from this idea, Prof. Struelens et al. advocate in this article for the integration of pathogen genomic data and epidemiological data into globally interconnected One Health surveillance systems.

The main article outlines the enabling factors needed to implement real-time genomic surveillance of pathogens and antimicrobial resistance worldwide – including data-sharing platforms, new sequencing technologies and cross-sector collaborations.

What is needed for genomic surveillance to protect against future pandemics?

Genomic surveillance is already being used successfully in some countries.

Wastewater monitoring systems used by some public health bodies allow them to detect signs of vaccine-preventable diseases circulating in the population and plan vaccination campaigns.

Genomic surveillance is also used in some countries and internationally to monitor foodborne diseases, to identify their source and to avoid mass outbreaks.

The authors present the key steps for the global implementation of genomic surveillance systems:

• modernization of the whole-genome sequencing infrastructure worldwide, including new sequencing technologies and analytical tools;
• increasing technical expertise through laboratory technician and health professional training;
• improving collaboration between countries, public health agencies, relevant scientific disciplines, doctors and veterinarians, adopting a “One Health” approach;
• ensuring interoperability and interconnectivity between genomic, clinical and epidemiological surveillance systems to enable real-time monitoring of pathogens;
• facilitating data sharing and access to data in a fair manner, in accordance with different regulatory regimes and protecting patient privacy;

“This must happen before another new disease emerges, as we know from Covid-19 that surveillance will be more effective if it can detect new infectious diseases early,” the experts conclude.