Methicillin resistant Staphylococcus aureus or MRSA is an ongoing problem in hospitals around the world. Standard infection control procedures use cultures of swabs from patients and comparison of the antibiotic resistance profile of the bacteria to see how related they are. This information along with epidemiological analysis usually allows identification of outbreaks from a common source. However in a recent outbreak in a special care baby unit in a UK hospital, conventional analysis could not determine whether there was a common source for the infections or whether it was due to repeated introductions of MRSA into the unit by patients or relatives who had acquired the MRSA in the outside community. Part of the reason for this was the fact that the clusters of infections were separated in time and antibiotic resistance profiles erroneously indicated that some isolates were different from the majority.
Researchers at the University of Cambridge and the Sanger Institute used whole-genome sequencing to study all the MRSA strains isolated from the special care baby unit and also some isolates from other parts of the hospital. They were able to show that nearly all the isolates were from one source and to show transmission chains both within the hospital and also from the hospital to people outside the hospital who came in contact with infants or mothers who had picked up the bug in the hospital. Finally the researchers were able to deduce that there was likely to be a healthy carrier among the staff and they swabbed and checked all 154 members of staff who were possibilities. This allowed them to identify a carrier of the specific strain of MRSA involved and treat that staff member to clear the bacteria from their system.
Since bacterial genomes are relatively small it is now possible to carry out whole genome sequencing both quickly and relatively cheaply. Outbreaks of MRSA within hospitals are not only bad for the patients, they also generate high costs in managing their effects and trying to eradicate them. Thus this new approach to infection control is likely to be cost-effective.
The BBC website quotes Dr Julian Parkhill from the Sanger Institute; "We think this is the first case where whole genome sequencing has actually led to a clinical intervention and brought the outbreak to a close."
Prof Sharon Peacock, from the University of Cambridge who was also involved in the study said she wanted to develop a simple system that could be used easily by hospitals. "It could, for example, determine the species of the bacterium; it could determine antibiotic susceptibility, and it could provide information about what genes are present that are often associated with poor outcomes in patients."
Commenting on the research, Prof Ross Fitzgerald, from the Roslin Institute at the University of Edinburgh, told the BBC: "The study clearly highlights the power of whole genome sequencing for resolving the source and the spread of an epidemic of hospital acquired infection such as MRSA. It will ultimately, within a small number of years, be standard practice for any hospital outbreak. I fully expect this to be rolled out as a standard approach in UK hospitals in the very near future."
Sir Mark Walport, director of the Wellcome Trust, said: "This is a dramatic demonstration that medical genomics is no longer a technology of the future - it is a technology of the here and now."
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