Researchers at the University of Chicago have completed one of the largest microbiome studies ever. They used the opening of their new hospital, the Centre for Care and Discovery, to study bacterial diversity and interaction, including hospital-acquired infections. Two months before the hospital opened on February 23, 2013 and for 10 months afterwards, bacteria samples were collected from 10 patient care rooms, and two nursing stations on different floors.
More than 10,000 samples were ultimately collected with the aim of helping hospitals worldwide better understand the flow of microbes between staff, patients, and surfaces. Senior author Jack Gilbert, PhD, Director of the Microbiome Center and Professor of Surgery at the University of Chicago and group leader in Microbial Ecology at Argonne National Laboratory said, “We’ve created a detailed map, highly relevant to clinical practice, of microbial exchange and interaction in a large hospital environment. 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 micro-organisms enter and colonize a hospital environment.”
Patients, nurses, and room surfaces were swabbed daily. Samples were collected from patients’ skin, bedrails and faucets, as well as the floor and air filter. Cleaning was done daily and more extensively after a patient was discharged. The nursing staff was swabbed on their hands, gloves, shoes, shirts, pagers, computers, desk phones, cellphones, and countertops. Prior to the opening of the facility, researchers noted low diversity in the bacterial population. As soon as the hospital was open and full of staff and patients, the bacteria from their skin replaced the original bacterial organisms.
They also saw a pattern that occurred with each patient that was admitted to the hospital. On the first day of their stay, microbial movement was from surfaces such as bedrails, faucets and countertops to the patient. The direction reversed for the next day and every day thereafter. Movement of microbes was predominantly from the patient to the room surfaces, which added to their microbial diversity.
An important unanticipated finding was that treatments such as antibiotics and chemotherapy, whether given prior to or during admission, had minimal impact on the skin microbiome. Only topical antibiotic treatment wiped out the bacteria on the skin.
In the study, there were 92 patients who had extended stays in the hospital and researchers were able to analyze the samples from their rooms over a number of months. They found that some bacteria such as Staphylococcus aureus and Staphylococcus epidermidis changed over time by acquiring genes that made them more resistant to antibiotics. Gilbert said, “If it proves to be true then these genetic changes could affect the bacteria’s ability to invade tissue or to escape standard treatments.”
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