Using genomics to combat infectious disease

Case study


We were approached by senior experts to lead a national strategic review of  how the genomics of microbes was being used in the UK to prevent and manage infectious disease and the policy actions needed to maximise the benefits more widely.

In our landmark 2015 report, Pathogen genomics into practice, we highlighted the status of the science and its uses within healthcare, and set out a practical plan to build on this excellence for increasing health protection capacity.

What we did

In addition to extensive review of the fast-moving science, we brought together a wide range of experts to help us fully understand infectious disease genomics, and discuss needs, priorities and challenges for the future.

Our report, the first ever description of the UK landscape of infectious disease genomics, concluded that genomic technologies had ‘the power to transform the management of infectious disease in England’. It was clear they could be used to detect and manage many different forms of health threats in hospitals, communities and by directing responses to public health crises such as serious epidemics or pandemics.

To get the most out of genomics for infectious diseases, we recognised that national leadership was urgently needed to implement a comprehensive strategy and coordinated delivery to enable new tests and technologies to move smoothly into routine public health and healthcare practice. Our strategic roadmap set out the priority policy actions needed for the UK to achieve this.


Our findings were welcomed by policy-makers in several countries, where they were used to guide development of local and national services. In the UK, infectious diseases formed a critical element of national genomics policy initiatives from 2016 onwards, beginning with the Generation Genome report of the Chief Medical Officer. By 2020, with the publication of the government's Genome UK report,  pathogen genomics was firmly embedded in the national genomic healthcare strategy.

“This timely report from the PHG Foundation provides an insight into the importance of this work. I welcome it and think it is an excellent contribution to the future debate”


Professor Dame Sally Davies, 2015 Chief Medical Officer for England (now UK Special Envoy on Antimicrobial Resistance)

The value of infectious disease genomics – and the exceptional UK expertise in this area – was been widely recognised in the wake of the COVID-19 pandemic. From 2021, a new National Institute for Health Protection in the UK is to provide strategic leadership and oversight of public health protection with a ‘rigorous science-led approach’ and a special focus on infectious disease surveillance and control.

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