Collaborating to deliver pathogen genomics - share the risks and reap the rewards

By Sobia Raza

11 November 2015


A number of initiatives to integrate genomics into microbiological investigations, from the Global Microbial Identifier to the recent guidance from the ECDC, all provide a clear indication that genomics can increasingly play a vital role in the management of infectious diseases. Indeed the chief question is shifting from ‘if’ genomics can add value, to ‘how’ to ensure its benefits can be realised most effectively across health systems and for both patients and populations alike. Our own report ‘Pathogen Genomics into Practice’, details 35 recommendations for the implementation of microbial genomics into the English Health system. The number and scope of these recommendations are emblematic of the complexity of the systems required, as well as the diversity of the stakeholders involved in national infectious disease management. 

Last month the PHG Foundation hosted a summit “Pathogen Genomics - the future of infectious disease management?” to discuss our report and its recommendations with representatives from government departments and their agencies (Public Health England; the Department of Health; NHS; Department for Environment, Food and Rural Affairs; the Animal and Plant Health Authority; and the Food Standards Agency), as well as leading academic researchers, commercial groups developing genomic sequencing solutions, public health experts, infectious disease physicians, clinical microbiologists, and bioinformaticians. 

No risk no reward

Discussions focused on the key recommendation of our report - the development of a catalyst; a set of real or virtual structures to amplify and integrate the current activities in pathogen genomics to accelerate and increase the effectiveness of their impact on patient and population health. The four overarching functions of this catalyst are (i) collaboration, (ii) standardisation (iii) strategic coordination and, (iv) repository development for data, tools, samples, and knowledge. 

Opening the October event Deputy Chief Medical Officer - Professor John Watson welcomed our report, and acknowledged that realising the benefits of pathogen genomics requires taking a calculated risk to build and operate the catalyst. The other speakers at the event, Professor Sharon Peacock, Professor Paul Kellam and Dr Nick Loman, echoed this view and endorsed the catalyst as they shared their own experiences of deploying pathogen genomics both in their local hospitals and further afield – most recently in Western Africa to track the transmission of the deadly Ebola virus. Nick Loman explained the paradox of relying on evidence for implementation in the context of genomic based disease surveillance; where an understanding of its full utility and value will only be realised if the risk is first taken to establish genomic surveillance through commitment to collate and share data for this purpose. 

Collaboration – the key to enabling impact

Developing and operating the catalyst will ultimately require strong leadership and direction to organise, oversee and establish collaborative working across the wide range of organisations and professional groups involved in infectious disease management. Currently PHE are at the forefront of developing genomic services and are therefore best positioned to assume this leadership role. In the immediate term this will involve the support of the Department of Health and close collaboration with NHSE given the extent of convergence in patient and public health priorities.  

To assist PHE, NHSE and the Department of Health in identifying which of our recommendations they most urgently need to respond to we have distilled our report down to the five or six most fundamental actions each must take in order to ensure the most effective and equitable implementation of pathogen genomics. Cooperation, coordination, collaboration are the recurring themes across these three organisational policy notes. The Department of Health has a crucial role to play in supporting strategic and operational coordination between PHE and NHSE; PHE are integral to developing the functions of the catalyst; and they should expect to support and to be supported in these endeavours by NHSE. 

During our meeting last month representatives from other government agencies s such as the Food Standards Agency and Animal and Plant Health Agency relayed how they are keen to utilise genomics, for example in resolving foodborne outbreaks. Indeed in some cases these organisations are already collaborating with scientific colleagues within PHE on the development of genomic epidemiology services. What is needed now is for this ‘grass roots’ collaboration between frontline providers to be matched by strategic co-operation between these organisations to develop truly integrated approaches to the use of genomics. As one delegate pointed out - the current economic environment heightens the need for improved integration and coordination of services across governmental departments and agencies.  

It is our view that a collaborative multi-agency effort underpinned by strong leadership by PHE will be critical in realising the full potential of pathogen genomics for health, and positioning the UK at the forefront of genomic medicine. 

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