DNA sequencing controls MRSA outbreak for the first time

Researchers from the Wellcome Trust Sanger Institute (Hinxton, England), the University of Cambridge, and Cambridge University Hospitals (both in Cambridge, England) turned to advanced DNA sequencing technologies to confirm the presence of an ongoing outbreak of methicillin-resistant Staphylococcus aureus (MRSA) in a special care baby unit in real time. The investigators note that this approach assisted in stopping the outbreak earlier, saving possible harm to patients.

The team revealed that the outbreak had extended into the wider community, a conclusion that could not be reached with available methods. They also used sequencing to link the outbreak to an unsuspecting carrier, who was treated to eradicate the MRSA.

“Our aim is to prevent outbreaks, and in the event that they occur to identify these rapidly and accurately and bring them under control,” explains Nick Brown, MD, an author on the paper and consultant microbiologist at the Health Protection Agency and an infection control doctor at Addenbrooke’s Hospital Cambridge. “What we have glimpsed through this pioneering study is a future in which new sequencing methods will help us to identify, manage, and stop hospital outbreaks and deliver even better patient care.”

Over a six-month period, the hospital infection control team used standard protocols to identify 12 patients who were carrying MRSA. However, this standard approach alone could not give enough information to confirm or refute whether or not an ongoing outbreak was actually taking place.

In this study, the researchers analyzed MRSA isolates from these 12 patients with DNA sequencing technology—a MiSeq instrument from Illumina (San Diego, CA)—and demonstrated clearly that all the MRSA bacteria were closely related and that this was an outbreak. They also revealed that the outbreak was more extensive than previously realized, finding that over twice as many people were carrying or were infected with the same outbreak strain. Many of these additional cases were people who had recent links to the hospital but were otherwise healthy and living in the community when they developed a MRSA infection.

While this sequencing study was underway, the infection control team identified a new case of MRSA carriage in the special care baby unit, which occurred 64 days after the last MRSA-positive patient had left the same unit. The team used advanced DNA sequencing to show in real time that this strain was also part of the outbreak, despite the lack of apparent links between this case and previous patients. This raised the possibility that an individual was unknowingly carrying and transmitting the outbreak MRSA strain.

The infection control team screened 154 healthcare workers for MRSA and found that one staff member was carrying MRSA. Again using DNA sequencing, they confirmed that this MRSA strain was linked to the outbreak. This healthcare worker was quickly treated to eradicate their MRSA carriage and thus remove the risk of further spread.

“Our study indicates the considerable potential of sequencing for the rapid identification of MRSA outbreaks,” explained Sharon Peacock, Ph.D., lead author from the University of Cambridge and clinical specialist at the Health Protection Agency. “What we need before this can be introduced into routine care is automated tools that interpret sequence data and provide readily understandable information to healthcare workers. We are currently working on such a system. If we have a robust system of this type in operation when the outbreaks occur, we predict that we will be able to stop them after the first few cases, as we will rapidly find clear connections.”

In their next step, the team will study all MRSA carriers and infected patients over the next year in Addenbrooke’s Hospital and surrounding hospitals and the community to understand transmission events with the aim of improving infection management.

The study was published online in Lancet Infectious Diseases; for more information, please visit www.thelancet.com/journals/laninf/article/PIIS1473-3099(12)70268-2/fulltext#.

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