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Panning for patterns

July 21, 2015

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Using hospital data to map and fight antimicrobial resistance

By Betty Zou

Mining is something that Annie Wang knows well. As an engineering student at the University of Calgary, she spent her internship helping optimize oil mining operations in Alberta’s oil sands. This summer, she is mining data from hospitals across Canada and the U.S. to look for geographic trends in antimicrobial resistance, a phenomenon whereby bacteria, viruses and fungi become impervious to antimicrobial compounds. The spread of these so-called “superbugs” threatens the usefulness of these drugs in preventing and treating infections.

Wang, who just completed her first year of medical school at the University of Toronto, is one of the students taking part in the D+H SRI Summer Student Research Program at Sunnybrook Research Institute. She is working with a team led by Dr. Nick Daneman, a scientist in Trauma, Emergency and Critical Care program, to develop an open source database of antibiograms. Antibiograms are the results of laboratory tests that determine how sensitive an isolated bacteria strain is to different antibiotics. Collected over a period of time, they can provide information about local resistance rates and help monitor trends.

“Most hospitals collect antibiograms but no one uses that data,” says Wang. “We’re not generating [the data]. We’re just putting it together in a meaningful way and analyzing it.” As of right now, their team has collected antibiogram data from about 150 hospitals in Canada and the U.S. The first part of Wang’s project is to determine whether hospitals that are close together geographically share similar patterns of antimicrobial resistance. “It seems intuitive but no one has really looked at it,” she says.

The database will be housed online on an open access website that is scheduled to launch in early August of this year. While most of the data are publicly available, they can be difficult to find and even more difficult to interpret, as there is no agreed-upon way for hospitals to collect and present their antibiogram data. Wang hopes that by compiling all of the data into a central database and standardizing their presentation format, physicians will use it more readily as a tool to guide their clinical decisions. “A lot of the time, a physician may have an intuitive idea of which bacteria are resistant to which medications,” she says. “But to move toward an evidence-based approach, you need to have the numbers to back up what you’re doing.”

Wang says that her engineering background provided her with the necessary skills and experience to take on the project. In particular, her experience working with large datasets and using the statistical and analysis skills she learned in her undergraduate classes have helped her to tease out significant trends from the data.

For Wang, this foray into epidemiology and public health research is a marriage of the aspects she likes most about medicine and engineering. “The attraction of medicine for me was the personal relationship with patients and the one-to-one impact that you have. Engineering was [appealing] to me [because] you get to have an impact over large populations,” she says. “I’ve come to realize that I need both—working with individual patients clinically, and also seeing the bigger picture and working on a systems-level problem.”

For students applying for research positions, Wang advises them to think carefully about what they want to get out of the experience, as well as what the supervisor is looking for. “Be very upfront about that, so you can establish clear expectations early on about what both sides want,” she says.

And if you don’t succeed at first, keep trying. If you really want to work with a certain professor, then take the initiative and reach out to him or her on your own, Wang urges. There are often other ways of getting involved with a professor’s research, but it’s up to you to find and create those opportunities, she says.

Annie Wang received a D+H Summer Studentship Award. 

Annie Wang