Researcher Tracks Hospital Bacteria that Stay Long After Patients Leave

By Sam Cholke on December 13, 2012 6:24am | Updated on December 13, 2012 8:57am

 Jack Gilbert and his team will take thousands of samples of bacteria at the University of Chicago's new hospital over the coming year.
Jack Gilbert and his team will take thousands of samples of bacteria at the University of Chicago's new hospital over the coming year.
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Arete/University of Chicago

HYDE PARK — Disease can enter a hospital with each new patient, and one University of Chicago researcher is trying to figure out what pathogens remain hospitalized after their host is discharged.

Marine ecologist Jack Gilbert and a team of researchers are mapping the microscopic biome in the University of Chicago’s new hospital to find out which harmful bacteria stay to breed after the patient leaves.

The Hospital Microbiome Project will take thousands of samples from the hospital and its staff over the next year to document the fierce ecosystem of bacteria that live in the Center for Care and Discovery.

“We want to know what’s stopping pathogens from becoming abundant on certain surfaces,” Gilbert said in a Dec. 7 interview.

Gilbert admits he’s never had much interest in hunching over a lab bench. But during a long, cold research expedition to Antarctica to collect bacteria for his doctoral research, he was overwhelmed by intellectual puzzles of the microscopic ecosystems. Even in the deep freeze, bacteria survived and colonized.

Gilbert now rarely uses words such as sanitary.

“There are bacteria that can survive even in bleach — but not for very long,” Gilbert said. “Bacteria have infinite ability to adapt to any ecosystem. They’ve survived for billions of years.”

This film of bacterial life coating our environment does not disgust Gilbert, he sees instead a potential path to reducing hospital-associated infections.

Every year, approximately 1.7 million people contract an infection while hospitalized. Six percent of patients die from hospital-associated infections, the sixth leading cause of deaths in hospitals, ahead of diabetes and pneumonia, according to the National Center for Health Statistics.

“There’s nothing in there we can’t stop from happening, we just don’t know how to stop it from happening,” Gilbert said.

He thinks we may have sanitized our way into poorer health, saying "99.999 percent of bacteria are totally harmless."

 The University of Chicago's Center for Care and Discovery will be the first hospital ever to have it's bacterial tenants thoroughly mapped.
The University of Chicago's Center for Care and Discovery will be the first hospital ever to have it's bacterial tenants thoroughly mapped.
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DNAInfo/Sam Cholke

He mused about coating the surface with harmless bacteria, creating a rainforest that would make it difficult for harmful bacteria to get a foothold and reproduce. “This rainforest can outcompete any of the bad bacteria that come later,” he said.

Before Gilbert’s idea could become a reality, he must better understand the hospital’s bacterial terrain. Such a map has never been created before and it is unknown how many species of bacteria inhabit a hospital and how harmful bacteria enter the system.

“The pathogens may not be finding reservoirs in the hospital, it may be that it’s all person-to-person transmission,” Gilbert said, admitting that result would be the most novel of the possible outcomes.

Gilbert and his team will start collecting samples this month while the hospital is closed. The real work begins on Feb. 23, when Gilbert’s team will begin a year of sampling of countertops, keyboards, nursing stations — and the nurses. The samples will then be analyzed using rapid genomic sequencing and recombined with data about the light, oxygen and humidity levels from sensors in the hospital.

Gilbert admits the expected data set will be overwhelming and the largest task will be combing through it and searching for insights.

“We are helping humanity by conducting this research, we are not just doing this for our own bizarre interest,” Gilbert said. “This next century — the century we’re now in — is the microbial century.”

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