In the study, published Tuesday in the journal Nature Microbiology, the team applied this technique to the spread of drug-resistant E. faecium in a hospital setting.
“We’ve known for over two decades that patients in hospital can catch and spread drug-resistant E. faecium,” said Theodore Gouliouris from the Department of Medicine at the University of Cambridge and joint first author on the study. "Preventing its spread requires us to understand where the bacteria lives — its ‘reservoirs’ — and how it is transmitted.
“Most studies to date have relied on culturing the bacteria from samples. But as we’ve shown, whole genome sequencing — looking at the DNA of the bacteria — combined with detailed patient and environmental sampling can be a powerful tool to help us chart its spread and inform ways to prevent further outbreaks.”
Over a six-month period, the team followed 149 hematology patients. Researchers took stool samples from the patients and swabs from the hospital environment and cultured them for E. faecium.
Genomic analysis of the bacteria was much more effective at identifying hospital-acquired E. faecium: out of 101 patients who could be followed up, genomic analysis identified that two-thirds of patients acquired E. faecium.
Just fewer than half (48%) of the swabs taken from the hospital environment were positive for vancomycin-resistant E. faecium. This included 36% of medical devices, 76% of no-touch areas such as air vents, 41% of bed spaces and 68% of communal bathrooms tested.
“The researchers showed that even deep cleaning could not eradicate the bacteria. The hospital undertook deep cleaning on one ward over a three-day period during the study, when patients were moved elsewhere; however, when the team sampled locations prior to patients returning to the ward, they found that 9% of samples still tested positive for the bacteria. Within three days of patients returning to the ward, around half of the sampled sites tested positive,” the researchers wrote.
“Our study builds on previous observations that drug-resistant strains of E. faecium can persist in the hospital environment despite standard cleaning — we were still surprised to find how short-lasting was the effect of deep cleaning,” Gouliouris said.
“We found high levels of hospital-adapted E. faecium despite the use of cleaning products and procedures that have proven effective against the bug. It highlights how challenging it can be to tackle outbreaks in hospitals,” he added.