Online epidemic tracking tool embraces open data and collective intelligence to understand outbreaks
Researchers from the Wellcome Trust Sanger Institute and Imperial College London have developed Microreact, a free, real-time epidemic visualisation and tracking platform that has been used to monitor outbreaks of Ebola, Zika and antibiotic-resistant microbes
The team have collaborated with the Microbiology Society to allow any researcher around the world to share their latest information about disease outbreaks. Details of the platform are published in the journal Microbial Genomics today (30 November).
Until now, disease data and geographic information about the movement of an infection or disease as it evolves and spreads has been locked up in databases that are often out of people’s reach. Researchers have been left to rely on published information in research papers, which may be many months out of date, containing static visuals which show only a small part of the whole disease or infection threat.
Microreact is a cloud-based system that combines the power of open data and the web, to provide real-time global data sharing and visualisation, allowing anyone to explore and examine outbreak information with unprecedented speed and detail. This is becoming increasingly important in the race to monitor and control fast-developing outbreaks like Ebola or Zika, or the growing threat of anti-microbial resistance.
Microreact allows data and metadata sets to be uploaded via a web browser, which can then be visualised, shared and published in a research paper via a permanent web link. The partnership with Microbial Genomics allows the journal to make data from prospective publications available through Microreact. This promotes open availability and access while also starting to build a unique resource for global health professionals and scientists.
“Until now, the global research community has been hamstrung because results are generally only shared in static pictures or tables in publications. Microreact allows everyone to explore the information dynamically – across both time and space – letting them see the whole picture. Using Microreact takes disease tracking out the hands of a privileged few and gives it to everyone who wants to understand disease evolution.”
Dr David Aanensen Director of the Centre for Genomic Pathogen Surveillance (a joint initiative between Imperial College London and the Sanger Institute) and one of Microreact’s creators
One example of how Microreact can democratise genomic data and resulting insights is the work of Dr Kathryn Holt and Professor Gordon Dougan. They have recently published two papers on the global distribution of typhoid bacteria around the world, showing the epidemic spread of a multidrug resistant strain. But they also published their data to Microreact to help others build on their work.
“We gathered together data from almost 2000 samples Salmonella Typhi bacteria collected by 74 collaborators in 63 countries. By comparing the different strains and mapping them to when and where they were ‘caught’ we were able to show that a new drug-resistant strain emerged in Asia and has spread across that continent and into Africa. We have put all this information on Microreact and now anyone can see exactly what we saw – both scientists and those public health professionals tasked with controlling such outbreaks.”
Dr Kathryn Holt From the University of Melbourne
By putting this information on Microreact, the researchers have ensured that the data continues to live on – allowing others to learn from their work and to use the information as a basis of comparison or foundation for future work. Microreact also allows individual researchers to share information globally and in real-time – crowdsourcing new discoveries and insights that could have immediate impact.
“We are delighted that our open-access, open-data journal Microbial Genomics is partnering with Microreact. All Microreact projects that appear in Microbial Genomics papers will be highlighted on the journal’s website to increase the discoverability and accessibility of researchers’ datasets.”
Leighton Chipperfield Director of Publishing at the Microbiology Society
Microreact visualisation and tracking platform:
View the Microreact website at: http://microreact.org
View a video of Microreact: Open data for genomic epidemiology video from the Centre for Genomic Pathogen Surveillance at: https://vimeo.com/193252797
Wong et al. (2016) An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid. Nature Communications http://www.nature.com/articles/ncomms12827
Global typhoid distribution in Microreact – https://microreact.org/project/styphi
The Centre for Genomic Pathogen Surveillance is a joint initiative between Imperial College London and The Wellcome Trust Sanger Institute. The centre seeks to provide data and tools to allow researchers, doctors and governments worldwide to track and analyse the spread of pathogens and antimicrobial resistance. http://www.pathogensurveillance.net/
The Microbiology Society is a membership organisation for scientists who work in all areas of microbiology. It is the largest learned microbiological society in Europe with a worldwide membership based in universities, industry, hospitals, research institutes and schools. For more details, please visit www.microbiologysociety.org
Imperial College London is one of the world’s leading universities. The College’s 16,000 students and 8,000 staff are expanding the frontiers of knowledge in science, medicine, engineering and business, and translating their discoveries into benefits for society.
Founded in 1907, Imperial builds on a distinguished past – having pioneered penicillin, holography and fibre optics – to shape the future. Imperial researchers work across disciplines to improve health and wellbeing, understand the natural world, engineer novel solutions and lead the data revolution. This blend of academic excellence and its real-world application feeds into Imperial’s exceptional learning environment, where students participate in research to push the limits of their degrees.
Imperial collaborates widely to achieve greater impact. It works with the NHS to improve healthcare in west London, is a leading partner in research and education within the European Union, and is the UK’s number one research collaborator with China.
Imperial has nine London campuses, including its White City Campus: a research and innovation centre that is in its initial stages of development in west London. At White City, researchers, businesses and higher education partners will co-locate to create value from ideas on a global scale. www.imperial.ac.uk
The Wellcome Trust Sanger Institute is one of the world’s leading genome centres. Through its ability to conduct research at scale, it is able to engage in bold and long-term exploratory projects that are designed to influence and empower medical science globally. Institute research findings, generated through its own research programmes and through its leading role in international consortia, are being used to develop new diagnostics and treatments for human disease. https://www.sanger.ac.uk
Wellcome exists to improve health for everyone by helping great ideas to thrive. We’re a global charitable foundation, both politically and financially independent. We support scientists and researchers, take on big problems, fuel imaginations and spark debate. http://wellcome.org
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