Genomic technologies have the potential to transform the care and control of infectious diseases caused by pathogenic microorganisms, such as viruses and bacteria. We have led a national strategic review of the potential impact on public health and health services, working in consultation with leading stakeholders. This informed development of an implementation plan for policy-makers - published as our major report Pathogens Genomics into Practice -  setting out actions needed to transform pathogen genomics from a promising technology and discrete service pilots, into mainstream national infectious diseases services.

Central to our recommendations is the call for all stakeholders to engage with addressing the challenge of adopting a whole system approach that, just as pathogens cross barriers between species, will cut across national and international barriers and the specialism and organisational silos. We therefore convened a summit of expert representatives of the main stakeholders involved in delivery of infectious disease services in England, to receive and review our findings and consider the way forward.

We were delighted that the Deputy Chief Medical Officer Professor John Watson was able to open our discussion, held in the illustrious surroundings of the library of the Royal College of Physicians. He welcomed the report, noting that it covered areas of great importance for current Department of Health research and service priorities for infectious diseases.

“I welcome this PHG Foundation report because it faces head on some of these challenging issues.”

Prof John Watson MBBS, MSc, FRCP, FFPH

Deputy Chief Medical Officer for England


Three leading experts in some of the most ground-breaking work in pathogen genomics discussed their visions for the future: Dr Nick Loman (University of Birmingham), Professor Paul Kellam (Wellcome Trust Sanger Institute / UCL) and Professor Sharon Peacock (Bloomsbury Research Institute).

The work that you do is going to be instrumental in getting genomics into the NHS.”

Professor Sharon Peacock CBE, FMedSci 

Director of the Bloomsbury Research Institute


We provided three specially tailored briefings for the principal organisations involved in infectious disease services in England:

Pathogen genomics into practice – Department of Health briefing (June 2015)

Pathogen genomics into practice – NHS England briefing (June 2015)

Pathogen genomics into practice – Public Health England briefing (June 2015)

The full report Pathogen Genomics into Practice includes an overview of these proposals:

Pathogen Genomics Into Practice - Executive Summary

Pathogen Genomics Into Practice - Full Report

Interactive policy map for infectious disease

In addition we have had two articles published:

Luheshi L, Raza S and Peacock SJ. Moving pathogen genomics out of the lab and into the clinic: what will it take? Genome Med. 2015:7:132.

Raza S and Luheshi L. Big data or bust-realising the microbial genomics revolution. Microbiology Society. 2015 Dec 18; published ahead of print.

The value of pathogen genomics

The advantages of using genomics to understand pathogens is that their genome sequences are much shorter and therefore cheaper and quicker to sequence than human genomes. The sequence data is of immense value, allowing precise identification of pathogen species and strains, and characterisation of virulence factors such as antibiotic resistance, with important applications including tackling outbreaks and drug resistance, personalising treatments, vaccine and drug design and novel threat detection. 

Finally, PHG Foundation project leader Dr Leila Luheshi summarised the strategic recommendations of the report and delegates discussed issues surrounding the systematic, co-ordinated national delivery of pathogen genomics to front-line health services.


To find out more about this important event, read our Storify round-up:
The future of infectious disease management - stakeholder meeting(October 2015)

Our messages to key stakeholders are:

Health policy makers
Implemented effectively in the English health system, pathogen genomics has the potential to make the UK a world leader in this area. The roadmap is an essential tool to successful implementation.

Frontline practitioners (providers and users)
By following our recommendations on service configuration and linking to the catalyst, this will ensure effective service development within your branch of the health system.

Frontline health service managers / commissioners (purchasers)
Be aware that this technology is almost ready for implementation, start to assess your needs and consider how its use can benefit you in managing nosocomial infections and in future, a much wider range of frontline diagnostic applications too.