Researchers at the Wellcome Trust Sanger Institute, University of Cambridge, and Illumina used whole-genome sequencing to retrospectively analyse patient isolates of MRSA from a previous hospital outbreak.
Professor Sharon Peacock, lead author from the University of Cambridge, explains: “The purpose of our study was to see if whole-genome sequencing of MRSA could be used to distinguish between related strains at a genome level, and if this would inform and guide outbreak investigations.”
MRSA is a type of bacteria that is resistant to many common types of antibiotic and is a major public health problem. Even when the disease is treated, MRSA infections double the average length of hospital stay and increase healthcare costs. The fast and accurate detection of bacterial transmission is crucial for the better control of healthcare-associated infection.
The team focused on an outbreak in a neonatal intensive care unit that had already ended. They took the samples and sequenced them as if they had been working in real time.
They found they could distinguish between strains that were part of the outbreak and strains that were not, something that cannot be achieved with current laboratory techniques. They also found that they could have identified the outbreak earlier than current clinical testing, potentially shortening the outbreak.
Dr Geoffrey Smith, co-lead author and Senior Director of Research at Illumina, added: “This study demonstrates how advances in whole-genome sequencing can provide essential information to help combat hospital outbreaks in clinically relevant turnaround times.
“As sequencing has become increasingly accurate and comprehensive, it can be used to answer a wide range of questions. Not only could we distinguish different MRSA strains in the hospital, we were also able to rapidly characterise antibiotic resistance and toxin genes present in the clinical isolates.”
The team constructed a list of all the MRSA genes that cause antibiotic resistance. Rapidly identifying drug resistance in MRSA strains will guide healthcare professionals to give each infected patient the most appropriate treatment possible. This also provides a powerful tool for the discovery of new drug resistance mechanisms.
MRSA produces numerous unique toxins that can inflict severe clinical syndromes, including septic shock, pneumonia, and complicated skin and soft tissue infections. The team created a list of toxin genes to rapidly identify those present in the MRSA strains, which currently can only be identified with multiple assays in reference laboratories.
“Distinguishing between strains is important for infection control management,” says Dr Julian Parkhill, lead author from the Wellcome Trust Sanger Institute. “Quick action is essential to control a suspected outbreak, but it is of equal importance to identify unrelated strains to prevent unnecessary ward closures and other disruptive control measures. Healthcare needs better, more efficient ways of identifying an outbreak and then processing the data.”
“The next stage is to develop interactive tools that provide automated interpretation of genome sequence and provide clinically meaningful information to healthcare workers, a necessary advance before this can be rolled out into clinical practice,” added Professor Peacock.
The findings are published today in the ‘New England Journal of Medicine’.
Image: Clusters of methicillin-resistant Staphylococcus aureus (MRSA) bacteria. Credit: Annie Cavanagh, Wellcome Images.
Köser CU et al. A neonatal MRSA outbreak investigation using rapid whole genome sequencing. New Engl J Med 2012;366(24):21-9.