Unleashing the potential of infectious disease genomics

Leila Luheshi

6 July 2017

Understandably, much of the fanfare (and hot air) surrounding the release of Generation Genome, the CMO’s report into genomics, focused on the current importance of genomic medicine in the diagnosis of rare disease and its emerging role in personalising cancer care. However, the report itself was commendably broad, and covered a far wider range of medical applications of genomics, including in the field of infectious diseases.

Ever since we published our Pathogen Genomics into Practice report in 2015, the PHG Foundation has advocated strongly for the acceleration of the implementation of genomics for infectious disease. It is great to see the key conclusions of our report are echoed in the CMO’s report, in particular the recognition that overcoming the obstacles to implementation will “require a major development programme in its own right, necessitating commitment analogous to a major infrastructure project that is mostly beyond the resources of a single laboratory or commercial enterprise”.

The case for investing in infrastructure

We have long argued that while technology companies and researchers have significant roles to play in bringing the necessary sequencing and analytical capabilities to the table to deliver rapid, low cost and accurate clinical genomic analysis for infectious disease, the health system itself must take responsibility (as it has for ‘human’ genomic medicine) for leading and co-ordinating the many organisations that need to be involved. The health system - including public health, healthcare and animal health organisations – must also accept that, as with human genomic medicine, they will need to invest in establishing the infrastructure to underpin the necessary sharing of genomic and clinical data, development of an evidence base for clinical interpretation and delivery of both local and national level services.

It is great to see that the authors of the chapter of the CMO’s report on pathogen genomics agree with these conclusions, however, given that they are not new (indeed the CMO welcomed our report in 2015 in which they were originally articulated) and can hardly come as a surprise to those policy makers we hope are diligently reading the report, one has to wonder whether they will stimulate change on the scale that the realisation of the CMO’s ‘genomic dream’ would seem to require?

The bottom line is as ever about money. The public health budget from which our national infectious disease management services are being funded is continuing to be squeezed, and so the speed with which our world-leading public health microbiologists can develop and implement genomic services has slowed to a snails pace. Similarly, NHS diagnostic microbiology laboratories have precious little capacity to undertake the development and evaluation of new genomic tests, let alone to undertake the substantial changes to their ways of working required to deliver the genomic data analysis and exchange with public health upon which much of the benefits of pathogen genomics will rely.

From dream to reality

So, how do we make the pipe dream of pathogen genomics a reality? Do we sit back and wait for technology companies to come up with a solution that can be effortlessly plugged in to the existing systems? Or do we take the approach that has worked so well for the 100,000 Genomes Project, and adopt a risk and reward sharing approach between public and private sector that can accelerate progress towards earlier patient benefit?

Admittedly, pathogen genomic data does not have the ‘resale’ value to pharma and other industries of human genome data. A couple of years ago this could have been used to argue that the ‘spill over’ benefits to the economy of investing public money in accelerating the development of pathogen genomics were small, and so pitching for the investment of tax-payers money in this area was futile. However, the O’Neill Review on Antimicrobial Resistance (commissioned by the prime minister) has surely blown that excuse out of the water? Whether or not you believe the precise figures placed on the future cost of the global crisis posed by ever increasing antimicrobial resistance, it is abundantly clear that for an absolutely tiny fraction of that potential cost to the global economy (and our health!) we could unleash the power of our scientific knowledge and genomic technologies to tackle this threat.

The dangers of delayed action

The slow progress towards implementation of pathogen genomics underlined in the CMO’s report, which talks mainly about future aspirations rather than currently active services – is just one tiny drop in the ocean of consequences arising from the failure of politicians and policy makers to recognise the long term return on investing in health innovations that will protect us from diseases both today and in the future. The CMO herself acknowledged that much of the current investment in human genome sequencing will be for the benefit of future rather than current generations. We can only hope that policy makers will eventually see fit to apply this logic not only to patients with cancer and rare disease, but also to those afflicted by infectious diseases, many of which are getting harder, not easier to treat.