Pathogen Genomics Into Practice: from potential to reality

Dr Sobia RazaThursday, 9 July 2015

Related project

Infectious disease genomics

Sobia has experience in data-handling, interpretation, and the management challenges faced in the 'omics era.

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Infectious diseases are a persistent threat to the health of the nation and have an estimated economic burden in England alone of £30 billion a year. Genomics presents exciting potential opportunities to transform the investigation, control and treatment of infectious disease. Whole genome data can be used to discriminate between pathogens with greater sensitivity and often specificity than current methods, enabling better outbreak management. Moreover genomic data can provide essential clues about the clinically relevant characteristics of a pathogen. This ‘multi-use’ attribute of pathogen genomic data has the potential to transform microbiology services by replacing multiple processes that occur across diagnostic and reference laboratories with a single technology.

The current picture

A wealth of world-class translational research and service development activities to capitalise on the powerful advantages of pathogen genomic technologies over existing microbiological methods are already underway in the UK. However, there remain significant gaps in the evidence base, and limitations in current knowledge and technology that could be considered barriers to implementation; the current clinical and public health utility of pathogen genomics being limited to outbreak management, with just a few exceptions including tuberculosis diagnostics. Therefore transforming pathogen genomics from a promising technology used in small-scale studies, into the reality of improved patient and population health outcomes requires a strategy for accelerating and expanding service development and delivery.

A road towards implementation

In our major new report Pathogen Genomics Into Practice, we examine the potential for genomics to improve infectious disease management, and set out the steps essential to support ‘the development and delivery of genomics informed infectious disease services that are evidence based, high quality, available population-wide, and on an equitable basis’.

We have confined the scope of our research to infectious diseases in human health, and the English health system. Our recommendations are therefore intended for key organisations involved in the protection of the public’s health in England; namely Public Health England, NHS England and the Department of Health. We present these recommendations within the framework of a roadmap directed at achieving two key objectives:

Ensuring effective genomics service implementation and delivery, where this is justifiable on the basis of evidence, in the short term
Driving innovation and expansion in the range of genomics informed / enabled services that can be developed and delivered in the long term

Embedded within the roadmap is a catalyst - a set of real or virtual structures to integrate and amplify the range of current activity in pathogen genomics.

Achieving effective implementation now and driving future innovation

Taken together our recommendations, roadmap and catalyst cover the spectrum of considerations for achieving the above. These range from very practical considerations such as establishing validly and utility, assessing needs, configuring, accrediting, quality assuring and evaluating services – to the wider ‘systems-level’ considerations around implementation and enabling future expansion in services. These include building the evidence base for clinical utility and cost effectiveness, ethical legal and social implications of using pathogen genomics, delivering sa fe and effective services in a dynamic technology environment, and maximising the utility of pathogen genomic data. In the full report we detail and provide evidence for over 30 recommendations in these different areas. We also focus on data integration and strategic coordination and leadership as crucial areas for delivering the patient and population level benefits of pathogen genomics.

Why is data integration needed?

Put simply, individual pathogen genomes cannot be usefully analysed in isolation. The timely collation, integration and sharing of genomic, clinical and epidemiological metadata across all parts of the health system is essential both for delivering services effectively now - e.g. national surveillance and outbreak monitoring - and for driving innovation and expansion of services in the future, by improving the knowledgebase and understanding of pathogen genomes, for example how genome variation relates to a pathogens antimicrobial resistance profile.

Why is strategic coordination needed?

Managing infectious diseases and their impact on human health demands the input of a wide range of organisations and professional groups. Effective development and delivery of services at a national level, can only succeed if there is strategic coordination of policy across these organisations and if there are mechanisms to support professional groups to work together to share and develop best practice, expertise and knowledge.

Establishing the necessary systems and infrastructure to deliver the above will require the direction, investment and support of health service leaders. If accomplished we could be looking at a future where genomics is an effective frontline tool in the analysis and management of most (if not all) of the pathogens that represent a threat to human health.