Friday, February 1, 2013

Update: Rapid DNA Sequencing Used with Clinical Laboratory Tests to Halt MRSA Outbreak in English Hospital


This may be a first for medical laboratory medicine. In England,  researchers used real-time advanced DNA sequencing to contain an infectious disease outbreak at a hospital. Rapid gene sequencing technology allowed them to bring the outbreak to a quick close. This saved other patients from harm and saved money for the hospital.

Clinical laboratory managers will be interested to learn that this ground-breaking episode occurred at Cambridge University Hospitals with the participation of the Wellcome Trust Sanger Institute and the University of Cambridge. Researchers from these institutions used insights gained from DNA sequencing to help stop a potentially deadly outbreak of Methicillin-resistant Staphylococcus Aureus (MRSA) at one of the Cambridge hospitals. The journal The Lancet Infectious Diseases  published the report.

A Step Closer for Clinical Use of Rapid Gene Sequencing by Medical Labs

Whole-genome sequencing was used to validate and expand findings from the hospital’s infection-control team after it had assessed the outbreak through conventional analysis, the research authors wrote in their abstract.

“What we’re working towards is effectively a ‘black box’,” stated clinical microbiologist and professor, Sharon Peacock, Ph.D., of Cambridge’s Departments of Medicine and Pathology. Peacock led the research team. She was quoted in a story published in Cambridge News.

MRSA Outbreak Occurs in Hospital’s Infant Unit

The outbreak of MRSA occurred in the Special Care Baby Unit of Cambridge University’s Rosie Hospital. Three infants tested positive for MRSA within a period of a couple of days, Cambridge News reported. Using insights gained from DNA sequencing, the researchers quickly identified the MRSA bacterial strains from their genomes.

Further, the team identified 12 infants who tested positive for MRSA within a six-month period in 2011. They suspected a link. However, a persistent outbreak could not be confirmed with conventional methods, according to the study authors.

Peacock stated that the MRSA isolated from all the babies were resistant to a nearly identical spectrum of antibiotics. The research team and the hospital epidemiologists tested 154 healthcare workers employed in the baby unit. They discovered one of the workers was a carrier of the MRSA strain that genetically matched the strain found in the infected babies, as well as some members of the greater community.

Reducing the Occurrence of Infectious Disease Outbreaks in Hospitals

The “black box” combines sophisticated DNA profiling and database analysis to produce real time results. Information on the genome sequence goes into the system. The device interprets the data. It then produces a report of the findings, Cambridge News reported. With further development, the researchers hope the device can be designed for routine use by hospital staff whom typically have no training in genetics.

Whole-genome sequencing holds great promise for rapid, accurate, and comprehensive identification of bacterial transmission pathways in hospital and community settings, the study authors wrote in the abstract. In turn, this means reductions in infections, morbidity, and costs.

Peacock elaborated on a number of potential capabilities of the “black box” in the Cambridge News story. These included the ability to:
  • determine the species of the bacterium;
  • determine antibiotic susceptibility;
  • provide information about which genes are present that are often associated with poor outcomes in patients; and,
  • provide information about how related an organism is to other organisms within the same setting, thus giving an indication of the capability of transmission from one patient to another.
The approach is much more accurate than current methods used by pathology laboratories, according to a story on the Cambridge University Hospitals NHS Foundation Trust website.

However, it is still several years away from routine clinical use.

Need Is for Automated Tools That Can Be Used by Clinical Laboratories

“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,” observed Peacock.

For pathologists and clinical laboratory managers, use of rapid gene sequencing as part of a hospital’s infection control effort should be considered a milestone. As has been long predicted, we are steadily approaching that time when next generation gene sequencing technologies will assume an important place in daily clinical use.

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