Moving pathogen genomics out of the ‘too difficult’ pile

By Leila Luheshi

9 March 2016


Infectious disease management: the status quo is not OK

Infectious diseases - and their impact on our health - are never far from the headlines these days. Recent outbreaks of Ebola and Zika infections overseas, and the ongoing debate about access to vaccines for Meningitis B and the threat posed by antimicrobial resistance closer to home, are constant reminders that infectious diseases remain a significant threat to health, wherever you live.

Given how difficult it is to treat many infections, and how prudent we need to be about the use of the treatments we do have, prevention – through vaccination, infection surveillance and control measures – is a vital component of the ongoing battle against infectious disease. It is widely acknowledged that until recently the methods available for the early detection, investigation and resolution of outbreaks were often insufficiently accurate to provide public health and clinical microbiologists and epidemiologists with the information they need to bring life-threatening disease outbreaks under control quickly.

Pathogen genomics: the possibilities…

This situation has now changed. Using pathogen whole genome sequencing it is possible to detect, investigate and resolve infectious disease outbreaks in both healthcare and community settings with a degree of accuracy and effectiveness not previously achievable. It is possible to do this not only in high income countries such as the UK, but also in low and middle income countries. Possible? Yes, but is it actually happening? Even when we look at the high income countries, such as those in the Europe and the US who have pioneered pathogen genomics in translational clinical research, progress towards delivering fully operational and integrated systems for surveillance and investigation of infections using pathogen whole genome sequencing remains painfully and frustratingly slow.

It looks a bit tricky. Maybe we’ll come back to it later…

Part of the explanation for the slow pace of implementation of this potentially transformative technology can be found by looking back to our own Pathogen Genomics Into Practice report (all 230 odd pages of it!). As we set out, following consultation with world leaders in this field, there are significant infrastructure and strategic challenges to be faced head on if, both nationally and globally, we are to realise the benefits of this technology. Achieving a high degree of coordination between multiple organisations and professional groups and harnessing a continually evolving technology and knowledge base is not straightforward. But it can be done. None of these challenges are unsolvable or even particularly unique experiences for healthcare practitioners. As programmes such as the 100,000 Genomes Project are beginning to show, where there is organisational (and political) commitment and investment, complex transformation of our health systems is entirely achievable.

Admittedly, it will remain difficult to deliver all the benefits of this technology to less well-resourced nations until much of the heavy lifting is done by the better resourced early adopter nations, such as the UK, who have the capacity to develop the necessary knowledge base and systems to deliver genomics-enabled infectious disease management. It is true that recent examples of using portable sequencing in low resource settings show that it is possible to sequence a pathogen almost anywhere, and with remarkably little equipment and infrastructure. However, it remains the case that transforming sequence data into reliable clinical and public health insights that routinely produce meaningful improvements in health for individuals or populations requires a level of expertise, infrastructure and organisation that even the most advanced health systems are currently struggling to deliver.

Sadly, this slow pace of progress and the apparently bumpy road ahead appears to be discouraging all but the most ardent of pathogen genomics ‘fans’ from throwing their political, organisational and financial weight behind this game changing technology in the way that has been done for ‘human’ genomics, at least in the UK.

A beginner’s guide to implementing pathogen genomics in your health system

With the challenges outlined above very much in mind, our latest briefing note, Delivering an effective infectious disease genomics service, sets out in simple terms what it would currently take for a health system to develop an integrated and effective approach to the use of pathogen genomics in the management of infectious disease. We hope that by providing an accessible introduction to what can appear an overwhelmingly complex technology to implement, this briefing note will help frontline professionals, health system managers and policy makers to grasp the nettle and begin to think about how they could deliver the benefits of pathogen genomics to their population.

Yes, it is true that pathogen genomics is not a simple ‘plug and play’ technology, but as this briefing and the report it complements show, much of the heavy lifting to develop the policies and practices necessary for implementation has already been done by the experts in the UK and elsewhere who are waiting, ready and able to enact their own recommendations. What they, and more importantly their patients, need is the organisational commitment and leadership to make this happen, now.

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