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Genomic Vigilance: The Key To Pandemic-Proofing Our Future

Representation of next-generation sequencing.
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The following article is an opinion piece written by Neil Ward. The views and opinions expressed in this article are those of the author and do not necessarily reflect the official position of Technology Networks.

The global community is facing an escalating threat: antimicrobial resistance (AMR). AMR is no longer a distant concern, with infections from resistant pathogens claiming more than a million lives worldwide each year. In England alone, over 58,000 people suffered from antibiotic-resistant infections in 2022, a 4% increase from the previous year.

To prevent outbreaks and facilitate early intervention, it is imperative that the research community understand where AMR is emerging, how it evolves and how it spreads. Genomic sequencing will prove fundamental in meeting this goal – by strengthening global surveillance of AMR, protecting existing antimicrobial therapies and safeguarding the health of communities worldwide.

Genomic sequencing in pandemic preparedness

Genomic sequencing allows scientists to gain a comprehensive and accurate picture of pathogens’ inner workings and evolution. To combat AMR effectively, national biosurveillance programs can employ genomics to help identify emerging threats early.

The NCTC 300 Project, led by the UK’s National Collection of Type Cultures (NCTC), is a perfect example of how sequencing plays a pivotal role in early pathogen detection and monitoring the evolution of resistance. In partnership with the Wellcome Sanger Institute, to date NCTC has sequenced 3,000 historical bacterial strains to create high-quality reference genomes. These reference genomes provide invaluable insights into what bacterial genomes looked like before the advent of antibiotics and how their genomes have changed, including the development of resistance traits.

Recent advances in sequencing technology have opened up even more opportunities to establish large-scale disease surveillance networks, enabling a preventative approach to pandemics. The cost of sequencing has reduced significantly, while the number of samples available for analysis has increased. Researchers can now track the spread of resistant pathogens through populations and across species while they are still localized. These insights can then be applied to prepare for – and ultimately prevent – large-scale outbreaks.

Surveillance and monitoring: pathogen detection in livestock

In addition to monitoring human pathogens, the involvement of non-healthcare bodies like the UK’s Department for Environment, Food & Rural Affairs (DEFRA) and the Environment Agency in AMR surveillance is paramount.

Expanding the genomic characterization and surveillance of pathogens affecting livestock is an important step toward comprehensive biosurveillance. Many pandemics have zoonotic origins, meaning they arise from infections crossing from animals to people. Although some livestock pathogens are currently monitored in the UK, there is still more that can be done. For example, more than 16 strains of bird flu have been identified in the UK, but only four are extensively monitored.

Governments are taking steps to expand the genomic characterization and surveillance of pathogens affecting livestock. However, AMR knows no borders. Collaboration and data sharing at a global level are essential to bridge gaps in monitoring, enhance preparedness strategies and establish effective early warning systems.

Tracking pathogens through wastewater analysis

Beyond animals, the misuse of antibiotics and other environmental factors also contribute to AMR. Wastewater surveillance, facilitated by genomic sequencing, is a valuable strategy for tracking resistance rates among microbes in local populations.

While many countries recognize the value of wastewater analysis in early disease outbreak detection, the challenge lies in understanding the genetic characteristics of circulating pathogens. The DNA in wastewater samples is often degraded and exists amidst background noise, requiring sequencing technologies with high specificity and sensitivity for accurate analysis – and many countries lack access to such sequencing capabilities.

Modern sequencing technologies, such as sequencing by binding (SBB), offer a solution to this challenge. They are up to 15 times more accurate than legacy methods, enabling early detection of new resistant strains in wastewater. This data can provide a comprehensive understanding of antimicrobial use and exposure in local populations, helping inform public health strategies and powering research into effective treatments.

Towards a global approach to AMR surveillance

The clock is ticking in addressing the AMR threat, and global collaboration is imperative. A standardized approach to AMR surveillance, where genomic and epidemiological information is collated in a database, can uncover high-risk areas and global trends. These insights can then inform pandemic preparedness strategies. Take, for example, the Global Microbial Identifier (GMI) project, which has harnessed genomic sequencing for global disease surveillance and response.

What is needed next is coordination across health, agriculture and environmental departments at an international level. This will underpin a shift towards a preventative approach to pandemics, where we recognize and respond to emerging threats before they become crises. The battle against AMR necessitates a multifaceted approach, and genomic sequencing stands at the forefront of our efforts.

By understanding the spread of resistance – from farm to gutter – we can shape effective strategies to contain the spread of resistant infections.