Hospital bacterial colonization tracked by supercomputers
Researchers will feed 12,000 swabs of bacteria to supercomputers that will sequence DNA in the swabs.
Mon, Nov 19, 2012 at 11:32 AM
After the new wing of the University of Chicago hospital opens in 2013, it'll slowly get colonized by bacteria and other microscopic creatures. It matters little how clean the staff keep the hospital; where people live and work, so do bacteria. Now one team of researchers plans to track that colonization, collecting so much data that the team will need a supercomputer to analyze it all.
Over the course of a year, engineers, doctors and biologists from all around the U.S. will track bacteria in patient rooms and nursing stations, and on the hands and in the noses of patients and nurses. They hope that by discovering how bacteria get introduced to a new building and set up shop, they'll learn more about infections people acquire just from being in the hospital, according to the project's website, Hospital Microbiome. Five percent of hospital patients catch such hospital-acquired infections, which can be fatal, according to Hospital Microbiome.
The researchers may even find that many bacteria in the hospital are beneficial and shouldn't be scrubbed away. "Ninety-nine percent of bacteria are good, even in a hospital," Jack Gilbert, a microbiologist with the University of Chicago and Argonne National Laboratory, said in an interview with the University of Chicago. "We're going to determine how good and bad bacteria co-exist in a hospital, and how the good can keep out the bad."
Gilbert and his colleagues plan to eventually rub 12,392 Q-tip-style swabs around 187 locations in a University of Chicago hospital pavilion slated to open Jan. 31, 2013. They'll test some locations every day and some every week. They want to see how bacterial populations move in, interact with each other and change over time. Temperature, humidity and other sensors will keep track of the environments the bacteria live in.
To identify the bacteria they gather, Gilbert and his team will sequence the bacterial DNA they find on their swabs. That effort will require help from the high-powered computers at Argonne, which is home to Mira, the fourth most powerful supercomputer in the world. "To process 13,000 samples takes an experienced and high-throughput facility such as the one at Argonne," Gilbert said.
Gilbert's study will be the first to systematically analyze where bacteria live in hospitals, Hospital Microbiome says.
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