Computational tools help solve the mystery of infectious disease

12 October 2016

Using a combination of computers and laboratory work, Simon Fraser University bioinformatics and genomics professor Dr. Fiona Brinkman has made advances in developing more holistic and sustainable approaches for identifying, tracking and controlling infectious and immunological disease.

Brinkman and her team at the Fiona Brinkman Laboratory have taken an interdisciplinary approach to developing web-based computational tools to sequence and analyze the bacterial genomes of infectious diseases. By creating what Brinkman calls “the ultimate high-resolution DNA fingerprint”, researchers can track emerging clusters of related genomes and integrate with other information to sleuth out the origin and background of a particular bacteria. Such information provides clues about how an infectious disease outbreak occurred, how it’s spreading and the risk factors in further spread.

Increasingly, Brinkman’s methods are being applied to a more comprehensive approach to infectious disease control by identifying the environmental and social factors contributing to the occurrence of disease outbreaks. For example, integrated data analysis was used to track the origin of an unusual case of tuberculous in a Vancouver Island community. A combination of genomics and social-network surveys identified a link between an outbreak of TB and increased use of crack cocaine that was precipitating the spread of the disease in the community.

Her lab’s methods have also been used to study environmental contaminants, advancing research into allergy, asthma, and immune diseases and associated risk factors earlier in life. They can also be applied to food-borne illnesses caused by an infectious disease agent associated with food production. The ability to find clusters of related bacterial genomes sequenced from across Canada will help determine the source faster, allowing regulators to clamp down on the release of the food product responsible or initiate a recall. The ability to do so — rather than the traditional approach of waiting until a cluster of illnesses emerge — can potentially curtail the spread of a disease and avoid more people becoming ill.

By making the computational tools available to the research community on an open-source basis, Brinkman’s work is also facilitating a greater understanding of how microbes evolve and empowering others in their research. With more than 11,000 citations of her work (earning her recognition by Thomson Reuters as one of the world’s most influential scientific minds in 2014), both the tools developed and the insights gained from the analyses are being used in the development of new vaccines, drugs and diagnostics for infectious diseases.

“It’s been really gratifying seeing all the little outputs that occur in research as a result of this that are being used so widely in the community,” remarks Brinkman.