Pathogen genomics is an important tool in our mission to prepare for and respond to infectious disease threats.
Us new five-year Pathogen Genomics strategy will establish a unified program to improve and expand our excellence in this area. Using pathogen genomics, we will increase our understanding of the risks of infectious diseases and enable effective evaluation of interventions to limit them.
In this blog post we explore the role of pathogen genomics in UK biosecurity and how we are developing our genomic systems to better protect public health in Britain.
What is pathogen genomics?
Pathogenic genomics involves examining the genetic material of microorganisms that cause disease. We can analyze genomes to identify harmful mutations or variations in a pathogen compared to known strains. This will allow us to detect drug resistance or other characteristics, such as those related to severity, within a pathogen. By using genomic data we can track the spread of infections and outbreaks. Furthermore, pathogen genomics aids in the development and discovery of new vaccines and therapies, and plays a crucial role in fighting diseases and protecting our health.
How does pathogen genomics keep us safe?
Pathogen genomics is not new: the first bacteria were sequenced in 1995 and the pandemic brought genomics to public attention. It demonstrated the real-time impact of science on public health worldwide, by detecting and monitoring outbreaks; determining the effectiveness of interventions and by allowing us to adapt the global response to a pandemic.
Since 2014, more than 1 million samples taken from routine hospital samples, outbreak investigations, environmental and food samples and specific surveillance projects have been mapped by UKHSA and its existing organisations. To date, Britain has uploaded 3,138,941 SARS-CoV-2 genomes to GISAID through partnerships between UKHSA, public health authorities in the devolved nations, NHS, academic and industry partners. Proactively sharing genomic sequences in the public domain has made UKHSA an integral player in collaborative investigations into outbreaks between different agencies and countries. For example, last year global sequencing data was used to quickly identify a new COVID-19 variant with unusual mutations, and once identified we were able to quickly track and control local outbreaks.
The knowledge gained from the variant’s genomic profile allowed us to determine the continued effectiveness of Lateral Flow Device (LFD) testing and COVID-19 vaccines in our laboratories.
And automated data pipelines allowed us to quickly generate information through large-scale accessible genomic datasets, linked to local and national systems, which we could then share with scientists around the world.
Food Safety
Genomics also plays a key role in food safety by helping to monitor and prevent outbreaks in the food chain. UKHSA’s Gastrointestinal Bacteria Reference Unit (GBRU) pioneered the first service for genome-based surveillance and tracking of bacterial variants causing gastrointestinal infections. This marked an early shift from traditional laboratory methods to genomic analysis.
In April 2022, a separate type of salmonella in chocolate was identified using genomics. The early detection of this outbreak and routine surveillance with WGS helped link the outbreak to specific products, allowing for rapid and effective intervention. This technology has enabled quick and decisive actions, such as food recalls, that might previously have been delayed. Now, the results from WGS help provide a robust evidence base to quickly remove and recall hazardous products.
Individualized drug treatment
UKHSA supports the NHS and patients by providing WGS to identify the tuberculosis (TB) strain that causes disease in humans and using pathogen genomics to accurately predict the antibiotics that will effectively cure the individual with TB. This has halved the time between detecting tuberculosis and understanding the effective drugs, from 6 to 12 weeks to about 2 to 4 weeks in the vast majority of cases. This is especially important when individuals have drug-resistant infections, to both increase the individual’s chance of recovery and to prevent the spread of drug-resistant TB infections in the community by effectively targeting rapid public health interventions.
The next phase of pathogen genomics
Over the next five years, we will build on existing infrastructure, capacity and scientific capabilities in pathogen genomics, further benefiting public health and strengthening our mission to protect lives and livelihoods.
This enhanced approach to controlling infectious diseases will be supported by genomic data optimized for clinical and public health decision-making, with implications for local and global health situations.
And in practice, our enhanced capabilities will mean the early detection of new threats, a better understanding of how diseases spread through our population, and their application will deliver the most effective vaccines and treatments.
Genomic data will also drive advances in diagnostics, vaccines and therapeutics, enabling a more targeted and efficient response to infectious diseases.
Innovation in new methodologies and technologies, such as metagenomics, will give us an edge in detecting new and emerging infections. This drive for innovation will be balanced with building high-impact services that are economically efficient.
Equally important is workforce transformation within and beyond UKHSA. Through training and development, we will build a team well-versed in the complexities and capabilities of pathogen genomics.
By committing to openly sharing pathogen genomic data and promoting global collaboration, lessons and breakthroughs benefit a broader global community.
Our world is more connected than ever and infections and outbreaks can spread quickly.
Our genomics strategy represents a commitment to innovation, collaboration and excellence in addressing some of the most pressing health challenges of our time.
