In January 2024 the UKHSA published its Pathogen Genomics Strategy, which sets out a 5-year plan for the organisation’s role in the “wider delivery of pathogen genomics to prepare for and respond to infectious disease threats to public health”. Acknowledging the important of pathogen genomics on public health, particularly in the pandemic response to SARS-CoV-2, the UKHSA hopes to “integrate genomics into aspect of infectious disease control”. Priority will be given to areas of “vaccine-preventable disease, emerging infections, and antimicrobial resistance”, in which pathogen genomics has the “potential to yield substantial measurable benefits in health security”.
The strategy at a glance
The Strategy outlines the “direction” of investment in pathogen genomics to “mitigate public health threats from infectious diseases” and support delivery of the Science Strategy and organisational strategic plan.
“Over the next decade we aim to maximise the benefit of pathogen genomics for public health and health security, through a single co-ordinated programme across the agency working with the NHS, academic partners, industry, other Government Departments, and devolved administrations.”
The programme will “improve” understanding of pathogens that post the greatest risks to the UK population, “integrate genomics into every day public health decision making”, and “enhance the evidence base” for policy.
“We will improve health security, detecting and containing outbreaks, improving and protecting our vaccines and therapeutics, and building our capabilities to detect new pathogens and threats.”
Through seven strategic, “cross-cutting aims”, and three priority public health areas, the UKHSA outlines a “vision” for the next five years.
Strategic aim 1: use genomic data to optimise clinical and public health decision-making, from local to global settings
The following objectives are presented:
- Integrate pathogen genomic data into public health systems: we will ensure that pathogen genomic data is linked to epidemiological data and incorporated into clinical and public health systems to improve disease control and to quickly identify and respond to public health threats.
- Develop best practice guidelines for pathogen genomic data use: we will work with partners to develop consensus on genomic data standards and develop guidelines for how, when, and where pathogen genomic data should be used to inform clinical and public health decisions for all communities.
- Evaluate and implement metagenomic analysis: we will work with NHS England to investigate the utility of metagenomic analysis to quickly and accurately identify pathogens causing disease, including pathogens present in the environment, and design novel surveillance systems to enhance biosecurity.
Strategic aim 2: use genomic data to drive improvements in diagnostics, vaccines, and therapeutics.
The following objectives are presented:
- Use pathogen genomic data to inform vaccine development: we will use genomic data to help ensure that existing vaccines continue to be effective against current and emerging strains of pathogens, whilst using genomic data to inform development of new vaccines.
- Enhance therapeutic development and deployment using pathogen genomic data: we will use pathogen genomic data to understand the extent and evolution of antimicrobial resistance, enabling more effective treatments to be targeted to patients and informing future drug development.
Strategic aim 3: Provide a nationally coordinated, high-throughput pathogen genomics sequencing and analysis service
The following objectives are presented:
- Ensure that infrastructure and partnerships are in place to sequence and analyse large volumes of pathogen genomic data at pace to inform clinical decision-making: we will work to deliver scalable, robust, and standardised laboratory services, bioinformatic analysis pipelines and translational services for priority pathogens.
- Foster pathogen genomics system resilience and adaptability: working across UKHSA, we will build a system which is resilient, scalable, and rapidly adaptable to new public health challenges.
- Ensure equitable access nationally: working with stakeholders, including partners in the devolved nations, ensuring consistent, effective access to and use of pathogen genomics laboratory techniques, data, analysis, and infrastructure across the UK.
Strategic aim 4: Undertake a genomics workforce transformation within and beyond UKHSA
The following objectives are presented:
- Strengthen clinical and scientific genomics expertise and training: we will ensure there are clear pathways for the development of specialists in all aspects of pathogen genomics, from sequencing to policy applications.
- Improve genomic literacy across clinical and public health: working with stakeholders, we will develop training packages to improve the understanding and use of genomic data across all levels of the clinical, scientific, public health, and policymaker workforce.
Strategic aim 5: Commit to pathogen genomic data sharing and global collaboration
The following objectives are presented:
- Enable rapid public data sharing: we will support the development of national and global policies, systems, and infrastructure to ensure that pathogen genomic data is quickly and fully shared with the global public health community and researchers.
- Foster collaborative networks: building on existing networks and working with key multilateral agencies, we will foster partnerships between organisations and countries to enhance the sharing of genomic data and scientific knowledge and improve global health security and response capabilities.
Strategic aim 6: Drive innovation in pathogen genomics
The following objectives are presented:
- Set priorities for health protection and security research and development in pathogen genomics: we will work across government, develop priorities with academic funders, work with academic partners thrgouh NIHR HPRU, joint grants and academic partnerships, and promote collaboration and knowledge exchange with a focus on improving the evidence base for linking human and pathogen genomics, developing methodologies and cost-effectiveness estimates.
- Develop innovation hubs: we will work to connect academic, NHS England Centres of Excellence, and industry partners to find pragmatic solutions for priority public health challenges.
- Develop industry partnerships: we will work with companies who develop sequencing technologies, bioinformatic tools, diagnostic platforms to leverage resources and support the UK ambition to enhance productivity across the economy, and in turn bring jobs, growth, and prosperity to all parts of the UK.
Strategic aim 7: Build high-impact services that are good value for money
The following objectives are presented:
- Develop and conduct rigorous health economic evaluation: we will embed evaluation of public health impact and value for money into our services, and build the evidence base for the value of pathogen genomics for public health.
- Ensure long-term sustainability: through improvements in laboratory efficiency, we will work to ensure that our genomic services are sustainable and continue to deliver value over the long-term. We will also improve flexibility to keep pace with advances in technology and the expanding role of pathogen genomics.
Three key areas
The strategic aims “cut across” three areas that are “directly aligned” with UKHSA’s strategic priorities, chosen for their population health impact and because “investment in pathogen genomics and its application in these areas offers evidence-based public health benefits”.
- AMR: Pathogen genomics applied to AMR will provide detailed understanding of resistance mechanisms and transmission patterns, enabling healthcare practitioners and policymakers to implement targeted infection control interventions and antimicrobial stewardship programmes, ultimately preserving the efficacy of antibiotics and protecting public health.
- Emerging infections and biosecurity: Pathogen genomics will serve as an early-warning system for emerging infections, facilitating the detection and rapid and precise identification of new or variant pathogens. This capability will guide timely public health responses and strengthen biosecurity, and mitigate the impact of public health threats.
- Vaccine-preventable diseases and elimination programmes: The application of pathogen genomics to vaccine-preventable diseases will inform vaccine development and deployment, support the identification and interruption of disease transmission chains, and play a role in achieving disease elimination targets, ultimately contributing to improved vaccine efficacy and enhanced population immunity.
The experts weigh in
Dr Meera Chand, Deputy Director for Emerging Infections and Clinical Lead for the Genomics Programme at UKHSA, commented that pathogen genomics is an “essential component of world’s ability to respond quickly to infectious disease threats”.
“The new UKHSA Pathogen Genomics Strategy will provide a framework for us to build on our already substantial capacity in this area, and to implement genomics across all our work to keep the public safe from threats to their health.”
UKHSA Chief Executive, Professor Dame Jenny Harries, emphasised the “vital contribution” pathogen genomics experts in the COVID-19 pandemic response.
“Pathogen genomics remains central to the national and international effort to keep the public safe from many other types of infectious disease threats.”
It will be “even more important” for the future, suggested Professor Harries, who hopes that the new strategy will “ensure that UKHSA continues to be at the forefront of implementing this technology to keep our communities safe, save lives, and protect livelihoods.”
We look forward to welcoming senior representatives of the UKHSA to our Congress in Washington once again; will you join us to learn more? To check out their sessions on the agenda, click here. Don’t forget to subscribe for weekly updates like this.
