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Here are the microbes you can pick up at the hospital — and those you leave behind

‘People were shedding a ton of bugs into this environment’

Network map plotting different types of bacteria as interconnected nodes to illustrate changes in microbial community composition in samples taken from the floor of newly-opened hospital before (blue colors) and after (red colors) the facility became operational.
Image: Science Translational Medicine

I don’t like going to hospitals. I’m always wondering about what kind of bacteria are floating around and what pathogens I’m going to pick up. Well, my abstract fears have just gotten a little bit more real. A new study shows what kinds of organisms you encounter in hospitals — and how patients and the hospital rooms they’re in exchange these organisms with one another.

Researchers took thousands of samples from a hospital in Chicago for two months before it opened and for 10 months afterward. They swabbed floors, bedrails, pagers, and cellphones, as well as patients’ noses, hands, and armpits. They saw that the microbes changed dramatically after the hospital became operational. Patients picked up organisms already present in their rooms before their arrival, but over time, their own microbes took over. More bacteria were also being exchanged during the summer, and after months of the hospital running, more invasive organisms that might be antibiotic resistant were detected.

The findings, published today in Science Translational Medicine, show how microbial communities evolve in hospitals. That information could one day be used to build better health care facilities to try to avoid hospital-acquired infections. “We can now use this to design the most accurate intervention possible,” says study co-author Jack Gilbert, a microbial ecologist and professor of surgery at the University of Chicago.

Floor-plan of the newly opened hospital analyzed in the study.
Image: Science Translational Medicine

All of us are home to billions of bacteria, viruses, and fungi that live on our skin and inside our bodies — collectively called the microbiome. A building or place — like your office or house — has a microbiome, too. And like it or not, you’re constantly picking up microbes from the places you visit, and vice versa. We constantly shed skin and microbes from our bodies. This interaction can affect our health, and we’re just starting to understand how it all works.

Previous studies have looked at the microbiome of office spaces, as well as homes. But Gilbert says he wanted to look at the evolving microbiome of hospitals — and he had a unique opportunity that couldn’t be wasted. A new hospital was being built at the University of Chicago, and that gave his team the opportunity to analyze the organisms living in the facility before it opened, and how they changed after patients started coming in. “We got very lucky,” Gilbert says.

Starting in January 2013, he and his team began taking microbial samples of floors, countertops, computer mice, and phones. After the hospital became operational in late February 2013, they kept collecting samples — swabbing floors, bedrails, and people’s hands, noses, and armpits, for 10 months. Overall, they collected 6,523 samples in 10 patient rooms and two nurse stations on two floors. They also monitored the place’s humidity, temperature, and ventilation.

“We were able to build a very detailed map — a cartography if you will — of this new hospital environment and the role of the hospital itself in the transmission of microbes and how microbes were shaped by that environment,” Gilbert says.

Within 24 hours of the hospital’s opening, the bacteria and organisms changed dramatically, Gilbert says. Before patients moved in, the hospital was filled with “very hardy bugs” that were used to living in an environment where they were constantly purged and cleaned. But after patients moved in, they were almost completely swapped out by human skin bacteria, Gilbert says. Among them were Staphylococcus epidermidis, a skin colonizer that’s usually harmless, and Staphylococcus aureus, another bacterium found in the nose and skin that can cause food poisoning.

“People were shedding a ton of bugs into this environment,” he says. “It was like a microbial flood, entering into the hospital as the patients started to use this place.”

But the microbial exchange went both ways. Patients also picked up microbes already present in the rooms before their stay. In fact, the researchers were able to detect organisms left behind by a previous patient on the skin and inside the nose of the new patient — despite the fact that the rooms were cleaned in between stays. This sort of microbial transmission was known for years, Gilbert says, but “we didn’t know it was quite this prevalent.”

The researchers also saw that microbes were exchanged more easily during the summer months, possibly because of increased humidity. The diversity of a patient’s skin microbes didn’t change significantly based on whether the patient was undergoing chemotherapy, recovering from surgery, or taking antibiotics. Also, toward the end of the 10 months, the researchers began detecting organisms that had antibiotic-resistant genes and genes that boost the ability of these bugs to colonize human tissues. That could be because hospitals are constantly cleaned and people are taking antibiotics, so organisms evolve so that they’re “very well adapted to the constant stress of that environment,” Gilbert says.

The study has some limitations. It’s only an “observational” study, meaning it shows that people’s microbiome changed in a hospital, but it doesn’t allow researchers to draw a connection between, say, a microbe a patient picked up in a room and a health condition that person developed. Same goes for the organisms with the antibiotic-resistant genes the researchers detected: we don’t actually know if those organisms could have caused a drug-resistant infection.

Still, the findings make total sense and the research is important, says James Meadow, a senior data scientist at Cogitativo, who’s done microbiome research for a decade and was not part of the research. “I really like science like this where we just assume, yeah, I’m sure we give bacteria off to the room around us and I’m sure we get bacteria from the room around us,” Meadow says, “but it’s really important to actually go in and test these assumptions to make sure they’re right.”

In the future, this information could be used to make better hospitals where the risks of getting infections are reduced. In 2011, there were an estimated 722,000 hospital-acquired infections in the US, and about 75,000 patients died during their hospitalization, according to a 2014 survey. Understanding how microbial communities change in health care facilities, and how microbes are exchanged, is a step forward in finding a solution, Meadow says.

Next, Gilbert would like to get even more detailed information tracking where patients go in a hospital, and how that movement affects the number and type of microbes exchanged. I’m just afraid that after that data comes out, I won’t step into a hospital ever again. With bacteria and bugs, sometimes I just don’t want to know.