Year-Long Survey Tracks Microbiome of Newly Opened Hospital

Potentially harmful bacteria acquire antibiotic-resistance genes

Results from a 12-month study mapping bacterial diversity within a hospital—with a focus on the flow of microbes among patients, staff, and surfaces—should help hospitals worldwide better understand how to promote beneficial microbial interactions and reduce potentially harmful contact.

“The Hospital Microbiome Project is the single biggest microbiome analysis of a hospital performed, and one of the largest microbiome studies ever,” said author Jack Gilbert, PhD, director of the Microbiome Center and professor of surgery at the University of Chicago.

“We’ve created a detailed map, highly relevant to clinical practice, of microbial exchange and interaction in a large hospital environment,” he said. “This describes the ecology of a building, a thriving microbial ecosystem that regularly interacts with patients in a seemingly benign way––at least most people don’t appear to be negatively affected. It gives us a framework, something we can build on, showing how microorganisms enter and colonize a hospital environment.”

The study began two months before the University of Chicago Medicine opened its new hospital, the Center for Care and Discovery, in February 2013 and continued for 10 months afterward. The researchers collected more than 10,000 samples and were able to detect microbial DNA in 6,523 of them. These came from 10 patient-care rooms and two adjoining nursing stations––one caring for surgical patients and the other, on a different floor, for cancer patients.

The investigators swabbed each patient’s hand, nostril, and armpit, as well as the surfaces patients may have touched, such as bedrails or faucet handles. They collected additional room samples from multiple surfaces, including the floor and the air filters. Each room was cleaned daily, with a more-extensive cleaning after each patient’s discharge.

The researchers also gathered samples from each unit’s nursing staff, swabbing their hands, gloves, shoes, nursing-station countertops, pagers, shirts, chairs, computers, land lines, and cell phones.

The most obvious change came when the hospital opened, which followed extensive cleaning efforts. Bacterial organisms such as Acinetobacter and Pseudomonas, abundant during construction and pre-opening preparations, were quickly replaced by human skin-associated microbes, such as Corynebacterium, Staphylococcus, and Streptococcus, brought in by patients.

A second, and ongoing, set of changes followed each patient’s hospital admission. On a patient’s first day in the hospital, microbes tended to move from surfaces in the patient’s room—bedrails, countertops, and faucet handles—to the patient. But by the next and every subsequent day, the preponderance of microbes moved in the other direction, from the patient to the room, steadily adding to the microbial diversity of the surfaces in the room.

“By the second day of their stay,” Gilbert said, “the route of microbial transmission was reversed. Within 24 hours, the patient’s microbiome takes over the hospital space.”

The researchers made two unanticipated findings. First, when the heat and humidity increased during the summer, staff members shared more bacteria with each other. Second, when they measured the impact of treatments—such as antibiotics before or during admission, chemotherapy during admission, surgery, or admission to the hospital though the emergency department—the impact was minimal.

“We consistently found that antibiotics given intravenously or by mouth had almost no impact on the skin microbiome,” Gilbert said. “But when a patient received a topical antibiotic, then, as expected, it wiped out the skin microbes.”

Samples from the rooms of 92 patients who had longer hospital stays, measured in months, revealed a trend. Some potentially harmful bacteria, such as Staphylococcus aureus and Staphylococcus epidermidis, faced with continual selective pressure, managed to acquire genes that could boost antibiotic resistance and promote host infection.

“This requires further study,” Gilbert said, “but if it proves to be true, then these genetic changes could affect the bacteria’s ability to invade tissue or to escape standard treatments.”

Source: Medical Xpress; May 24, 2017.