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Postdoc Profile: Emma Griffiths

November 16, 2015
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From Evolution to Epidemiological Outbreak Analysis, Emma Griffiths is Putting Genomics Research to Practical Use in Public Health

Some people read the Sports section first, others read about current events, entertainment or even check their horoscopes, when they pick up a newspaper or check the news online.

Not Dr. Emma Griffiths. She scans the headlines for food recalls and cases of food and waterborne infectious disease. Recently, the pickings have been easy: national reports included E. coli contamination of leafy vegetables and Niagara bottled water this past summer, as well as the Salmonella recall of certain types of frozen chicken fingers.

Her curious pastime is not because she has a morbid interest in intestinal upset – it’s because she’s studying the genes that cause disease in different pathogens and the strategies we can use to quickly detect them in order to improve public health and disease tracking.

Dr. Griffiths obtained a PhD in Comparative Genomics and Phylogeny at McMaster University, Ontario, followed by postdoctoral studies in fungal drug discovery and fungal genetics. Her field is called Pathogenomics, which utilizes genomic and metagenomics data gathered from high through-put technologies (e.g. DNA sequencing), to understand microbe diversity and interaction as well as host-microbe interactions involved in diseases.

At SFU, Griffiths is working with a leading Canadian researcher in the field. Dr. Fiona Brinkman, a professor in the Dept. of Molecular Biology and Biochemistry, is using next-generation sequencing technology and bioinformatics tools to create a platform for infectious disease outbreak investigation and disease tracking in collaboration with the BC Centre for Disease Control and the Public Health Agency of Canada. Griffiths was drawn to the Brinkman lab by the prospect of being able to put theoretical work in gene-disease research to practical use in public health.

Griffiths is part of a team developing Canada’s Integrated Rapid Infectious Disease Analysis (IRIDA) platform, a 1.56 million dollar project funded by Genome Canada. The IRIDA platform will equip public health workers with user friendly tools for incorporating whole-genome sequencing into isolate typing and epidemiological pipelines to support real-time infectious disease investigation (http://www.irida.ca).

“Putting research into practice to improve healthcare decisions is incredibly powerful.” says Griffiths about the IRIDA Project. “Translating research into a new technology or analytical platform that will affect the health of Canadians is really motivating.”

Whole genome sequencing (WGS) is a laboratory process that determines the complete DNA sequence of an organism's genome. WGS can provide more precise data that allows epidemiologists to determine which patients are sick with the outbreak strains, reducing the number of cases that require follow-up investigation.

“Reducing the amount of time required for investigation before a response is initiated will reduce the amount of time the disease has to spread, reducing the number of preventable cases of illness.” Griffiths explains.

Getting to the point where Canadian health care providers can use WGS to quickly identify disease outbreaks will take more work. In order to understand the practical requirements for implementing this platform within the Canadian health care network, Emma and the IRIDA team are interviewing public health stakeholders and domain experts. User activities, lab management software, national pathogen-tracking and reporting systems are being profiled to better characterize levels of user computational expertise, required functionalities and information flow within the network.

Another key task will be to create a standardized vocabulary for describing samples and cases (terms describing the host, symptoms and exposures, where the sample was taken from, and other types of information related to the case). Establishing these standardized hierarchical lists are important because they are both human readable and computer amenable, and will provide consistency in nation-wide outbreak analyses.

“For example,” explained Emma, “a High-Risk foods ontology (well-defined vocabulary) could be used to consistently describe what patients have eaten in a foodborne outbreak. By standardizing how food is described, the frequency of high-risk foods in different outbreaks can be assessed in an automated way. “

Griffiths has already authored 23 publications, 14 of which were first-author contributions, and she recognizes the importance of knowledge dissemination.

“An important skill for science researchers is without a doubt the ability to talk about your work with people outside of your field. I remember my mother was embarrassed by my first published paper because it had Chlamydia in the title and she said I was writing about “rude things”. That was when I realized I never really talked about the impacts of bacterial phylogeny (the evolutionary relatedness of bacteria) with my friends and family.”

To make up for this, Emma participates in Science outreach events and programs such as “Let’s Talk Science” and “Science Rendezvous”. Furthermore, as the first president of the Postdoc Association (PDA) at SFU (www.sfu.ca/postdocs), she knows learning to communicate well is critical for postdoc professional development.  This past May, Emma and other members of the PDA organized a campus-wide Postdoc Research Day to showcase PDF research excellence to the SFU community.

Griffiths and the PDA have also pioneered the Practice Job Talk program, which allows postdocs to try out their academic sales pitches on their peers prior to big interviews, providing an opportunity for valuable feedback.

Good communication is something Brinkman lab members learn well. Jennifer Gardy, a Brinkman lab alumni and currently a Senior Scientist at the British Columbia Centre for Disease Control, is also an occasional host of CBC's The Nature of Things. When asked if she had plans to host a tv show as well, Emma replied “The only “hosts” I see in my future are the ones that need some genome sequencing...”.

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