26 September 2014
‘Pathogens don’t carry passports’ and know no boundaries, as outbreaks of infectious diseases such as the H1N1 ‘flu virus (2009), E.coli in beansprouts (2011), and more recently the spread of Ebola across Western Africa (2014), have demonstrated. The ever-present threat of disease spread across international borders is to a large extent an upshot of a globalised world. Increasing levels of international trade and travel carry the risk of transnational exchange of rather more unwelcome visitors: pathogens. Managing and containing infectious diseases of a global significance therefore requires global cooperation and coordination, as epitomised by the efforts underway to tackle the Ebola virus.
Earlier this month the 7th Global Microbial Identifier (GMI) Meeting took place at the Food & Environment Research Agency in Sand Hutton, York, UK. GMI are described as an 'informal global, visionary taskforce of scientists and other stakeholders who share the aim of making novel genomic technologies and informatics tools available for improved global patient diagnostics, surveillance, research and public health response'. The initiative first started in September 2011 with the vision of developing a global system to aggregate, share, mine and use microbiological genomic data to address global public health and clinical challenges. The meeting in York comprised a series of presentations, and working group discussions.
Mapping the bugs
Academic, government, and industry representatives shared their experience with deploying pathogen sequencing for detection and surveillance purposes, and described the analytic tools being developed to enable the aforementioned. Amongst the eye-catching tools showcased were supraMAP, presented by Daniel Janies (University of North Carolina at Charlotte). The application integrates genomic data with evolutionary, geo-spatial and temporal information, and overlays this onto Google Earth. The projection is akin to a weather map for infectious disease, tracking how a pathogen has spread from its geographical origin and host species. Similarly, David Aanensen (Sanger Institute / Imperial College London), demonstrated the latest tools from his group, wgsa.net and spatialepidemiology.net, which also provide Google Map-based interfaces for the display and analysis of infectious disease data.
Sarah O’Brien (University of Liverpool), presented an elegant example of plans to use real-time disease detection in the community. Patients with diarrhoeal disease are to provide clinical samples following their primary care telephone consultations. Genomic data from the samples is to be integrated with geo-spatial information collected during the telephone calls to analyse patterns of infection and assess whether or not a disease outbreak is occurring.
Lessons from experience
Despite the impressive examples of how the use of genomic data can be utilized for monitoring and managing infectious diseases, the widespread and successful application of pathogen genomics at a global and arguable even national level, faces a number of practical challenges. Keynote speaker on day-1 of the event, Paul Flicek (European Bioinformatics Institute) underscored the importance of robust informatics infrastructure and support, without which the full potential of genomic data and the sophisticated analytic tools being developed, cannot be realised. Attempting to maximise the utility of genomics data, in the absence of appropriate infrastructure, was likened to "driving a Ferrari on a dirt road".
Steve Musser of the Food and Drug Administration shared their learnings from their Genome Trakr Network, a pilot network of U.S. state and federal public health laboratories collecting and sharing genomic data from foodborne pathogens. Communication, coordination, data storage, analytics, and real time reporting of data, were highlighted as some of the most essential elements needed for the network to function effectively.
Tackling the challenges ahead
A significant portion of the meeting to was dedicated to focussed working group sessions for discussing the challenges to, and requirements for delivering the GMI vision in terms of (1) political challenges and outreach, (2) storage of sequence data, (3) analytic approaches, (4) quality assurance, and (5) pilot projects. Open access and free exchange of microbial genomic data and related metadata (data about data), formed a key highlight of the discussions. International cooperation on mechanisms for open data sharing is fundamental to delivering the GMI vision, and indeed effective global management of infectious disease. Yet ‘open’ public release of data is a mammoth undertaking, particularly given the complex local and international legal frameworks regarding data ownership, privacy and release. A more practical consideration being the variable levels of reliable infrastructure, including informatics (electricity, internet access, band width) in low, middle and high income countries, which will impact on the ability to both generate and share data.
At time of initiation (2011), the GMI had envisaged that within ten years there could be a global-coordinated microbial genomics systems in place. The taskforce are now planning a ‘landscape analysis’, of global microbial genomics, to include assessments of the pathogen sequencing initiatives underway, health economics, bioinformatics needs, ethical- legal, and social barriers to data sharing. The challenge of delivering such a wide-spanning and worldwide analysis is not one to be underestimated. However apposite solutions can only be developed by evaluating the current landscape and barriers.
The PHG Foundation is currently embarked on a major project assessing the impact of pathogen genomics on health services, specifically in the UK, and developing policy recommendations to support implementation. The project includes landscape analysis of pathogen genomics initiatives in England, and the final report will be available in early 2015.