TUESDAY, JUNE 19, 2018

Genome sequencing technology and social network analysis used to solve disease outbreaks

By combining social networking analysis and cutting-edge whole genome sequencing of bacteria, public health officials are now able to get a more detailed picture of disease outbreaks, helping epidemiologists to track and stop them.

The researchers discussed the combination of these two new tools at the 11th General Meeting of the American Society for Microbiology on Sunday. During an outbreak of tuberculosis in a medium-sized community in British Columbia, the researchers used these tools to determine the outbreak was due to increased usage of crack cocaine in the community.

"Public health agencies are now able to harness the power of genome sequencing, which, when combined with the detailed clinical and epidemiological data we have access to, allows us to reconstruct outbreaks and really understand how a pathogen moves through a population," Jennifer Gardy, of the British Columbia Center for Disease Control, said.

Whole-genome sequencing is the analysis of an entire microbe’s DNA and it has become cheaper and less time-consuming in the past few years.

"The complete genome sequence of a pathogen is the ultimate DNA fingerprint, and now, with the costs and time associated with genome sequencing dropping almost exponentially, it is possible to sequence most or all of the bacterial isolates taken from and outbreak," Gardy said.

Social network analysis takes epidemiology further by asking patients not just who they have been in contact with but also taking a detailed account of their time.

"Instead of getting a list of names, you are getting names, places and behaviors, and you can paint a much more detailed picture of the underlying structure," Gardy said. "Key people and places and certain behaviors that might be contributing to an outbreak's spread become much more apparent and allow you to adjust your outbreak investigation in real time as this new information becomes available."

The new technique also allowed the researchers to determine which individuals were superspreaders, usally those who are socially well connected and symptomatic for long periods of time. The information is now being used in outbreak investigation in which public health officials are trying to target socially popular people for screening as a priority.

"We took an outbreak that was an absolute mystery by traditional methods and solved it using genome sequencing and social network analysis," Gardy said, “[This is] a new and exciting direction for epidemiology and the study of infectious disease, particularly for public health agencies."