The National Infection Service – a first step to an integrated and system wide approach to implementing genomics?

Dr Leila LuheshiFriday, 25 September 2015

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Infectious disease genomics

Leila is responsible for the delivery of the scientific expertise and analysis that underpin our work.

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PHE annual conference played host last week to the head of the new PHE National Infection Service Prof. Derrick Crook. Prof. Crook set out his vision for a national infection service and provided an update on PHE’s ongoing work to pilot the implementation of whole genome sequencing for diagnosis, clinical and epidemiological management of tuberculosis.

The development of a national infection service in which pathogen genomics will play a central role is certainly to be welcomed, and I am delighted to see PHE taking the lead in delivering this potentially revolutionary innovation to the nation. Indeed, the clearest message to arise from the recent Pathogen Genomics into Practice report, published by the PHG Foundation, is that the community of clinical, public health and policy professionals engaged in delivering infectious disease management are looking to PHE for leadership and direction as they move towards implementing this technology in their own parts of the health system. This leadership needs to take many forms, ranging from the provision of vital national data infrastructure through which to collate and analyse genomic and clinical data to the sharing of expertise in the development of accredited methods for genomic sequencing and analysis.

However, the most important ‘ask’ to PHE in the report, and one that was re-iterated by several senior health service figures present at Prof. Crook’s presentation, was the need for PHE to work hand in hand with all the key stakeholders in the infectious disease management system, such as the NHS, APHA, FSA etc., to co-develop their national strategy for implementing genomics. It is absolutely vital that all parts of the health system are empowered to adopt pathogen genomics where it has the ability to improve the health of the patients and populations for whom they are responsible, and there is a strong onus on PHE to reach out across the health system to make sure this happens.

Failure to implement pathogen genomic services in an coordinated health system wide manner, and in particular failure to ensure that high quality and relevant genomic and clinical data are integrated and made available across the entire infectious disease management ecosystem (much of which is outwith the direct control of PHE) will dramatically blunt its effectiveness.

There are three keys reasons for this:

The delivery of effective genomic epidemiology and infection control relies entirely on timely access to the most accurate possible data and cannot be successful where there are significant geographical or institutional barriers.
The development of the wide range of possible future applications of genomics, for example in the field of antibiotic resistance detection and management and even in primary diagnosis of infection, depends entirely on the collation and analysis of phenotypic, genotypic and other clinical data from both research and clinical practice across the entire spectrum of infectious diseases and across the nation (and beyond)
Lack of integration and co-development of genomics strategy will perpetuate existing silos in the provision of microbiology services, leading to massive duplication of effort in service development as each lab strikes out on its own, failure to share expertise and learning, and ultimately variable quality of service provision and care for patients.

The Pathogen Genomics into Practice report provides both detailed recommendations, mostly devised by experts from within PHE and the other branches of our health system, and a clear strategic framework (in the form of our catalyst) to support an integrated approach to the implementation of pathogen genomics now, and the continued development of this technology for the future. This technology has immense potential and could transform the management of infectious disease in the UK and beyond. It is to be hoped that the new National Infection Service adopts an integrated and system wide approach to its development and use of genomics, and that they are provided by government with the financial support necessary to do this. The alternative is that the great progress made by the many world class researchers and clinicians in the UK developing applications of pathogen genomics risks being wasted as implementation proceeds slowly in a poorly coordinated, ineffective manner, and a golden opportunity to improve the health of our population is consequently squandered.