High speed bench-top sequencing to revolutionise hospital infection control

11 June 2012

A new generation of bench-top DNA sequencers can quickly and cheaply map the entire genetic codes of bacteria causing life-threatening infections. This technology has the potential to revolutionise the speed and accuracy with which potential outbreaks of MRSA, Clostridium difficile and other infections are detected and investigated.

This was shown by study published this month in BMJ Open, by researchers from Oxford, Leeds, Brighton and the Health Protection Agency.

For the study, samples were obtained from potential outbreaks of MRSA and Clostridium difficile causing problems in three UK hospitals. The samples were sequenced with a new bench-top sequencer. The study showed that obtaining the genetic codes of bacteria were useful in resolving otherwise puzzling clusters of infections and that the information could be made available within 5 days, fast enough for local infection-control teams to use it in planning the management of outbreaks.

Knowing the DNA sequences of bacteria causing healthcare-associated infections can help to identify the route and timing of person-to-person transmission. If this information can be made available quickly enough, hospital infection control teams may be able to step in and eliminate further spread. These sequencing technologies are rapidly becoming cheaper, faster, more accurate and simple enough to use that within a few years local hospitals are likely to be using them every day.

Professor Derrick Crook, infection control doctor at the Oxford University Hospitals NHS Trust and professor of microbiology at the University of Oxford said: “This is the first illustration of how rapid sequencing technology could play a huge role in managing hospital infections such as MRSA and C. difficile. Our findings provide several good examples of how rapid and precise sequencing could transform identification of outbreaks of healthcare-associated infection, and therefore improve hospital infection control and patient outcomes in routine clinical practice. In one example we monitored the genetic code of all new cases and compared them to the genetic code of previous cases thereby identifying new outbreaks.”

“As recently as two years ago it would have taken months and thousands of pounds to process such informative sequence information on hospital infections; now with high speed sequencing it can take as little as days and tens of pounds. Soon it may take only hours and just a few pounds. We can realistically begin to think ahead to a time when we can create a database of genetic codes for many kinds of germ, to continuously track the spread of infections within and between hospitals.”

Further information

The organisations involved in the study were:

  • The Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford;
  • Department of Statistics, University of Oxford, Oxford;
  • Oxford University Hospitals NHS Trust, Oxford;
  • Health Protection Agency Centre for Infections, Staphylococcus Reference Unit, London;
  • Illumina, Inc., San Diego, California;
  • Ashford and St Peter's NHS Foundation Trust, Department of Microbiology, Surrey;
  • Health Protection Agency, Royal Sussex County Hospital, Brighton;
  • Leeds Teaching Hospitals & University of Leeds, Microbiology, Leeds General Infirmary, Leeds.

The Modernising Medical Microbiology Consortium

UK CRC Modernising Medical Microbiology Consortium is a UK wide consortium funded by the Wellcome Trust and MRC, between the University of Oxford, Health Protection Agency (HPA) and the Wellcome Trust Sanger Institute; to establish how revolutionary new technologies can be optimally integrated into microbiology research and service strategic vision. Website: www.modmedmicro.ac.uk

The Health Protection Agency

The Health Protection Agency is an independent UK organisation that was set up by the government in 2003 to protect the public from threats to their health from infectious diseases and environmental hazards. In April 2013, subject to the usual approvals procedures for establishing new bodies, the Health Protection Agency will become part of a new organisation called Public Health England, an executive agency of the Department of Health. Website: www.hpa.org.uk 


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