Real-time gene sequencing used to combat superbug

By Chris Wickham

LONDON | Wed Jun 13, 2012 5:11pm EDT

LONDON (Reuters) - Scientists have used genome sequencing technology to control an outbreak of the superbug MRSA in a study that could point to faster and more efficient treatment of a range of diseases.

The work adds to a burgeoning body of research into better techniques for diagnosing disease more quickly and at an earlier stage to allow more effective treatment and reduce healthcare costs.

Much of this is being driven by whole genome sequencing, which has enabled scientists to identify the genetic markers for a range of afflictions.

MRSA, or Methicillin-Resistant Staphylococcus Aureus, is a drug-resistant bacterial infection, or superbug, and major public health problem. When outbreaks occur in hospitals it can lead to the closure of whole wards and lengthy investigations.

The bug kills an estimated 19,000 people in the United States alone each year, and even when the infection is successfully treated it can double the average length of a hospital stay and thereby increase healthcare costs.

A team of scientists from the Wellcome Trust Sanger Institute, the University of Cambridge and genome sequencing company Illumina Inc, used samples from a 2009 MRSA outbreak in a hospital neo-natal intensive care ward to recreate and respond to it, as if in real time.

They found that genome sequencing produced results in roughly 24 hours, using the latest technology from Illumina, gave much more detailed information.

The researchers were able to identify the particular strain of MRSA causing the outbreak, and which strains were not, quickly enough to feed back into treatment and nip the outbreak in the bud faster than current clinical testing methods.

"I think we are at the very beginning of an explosion of evidence to support the use of whole genome sequencing in public health," Sharon Peacock of Cambridge University, who led the study, told Reuters.

The research, published in the New England Journal of Medicine, comes hot on the heels of similar work done on MRSA and Clostridium difficile by a team from Oxford University with Illumina and a group of hospitals in Britain.

That study was published earlier this month in the journal BMJ Open. Oxford microbiologist Derrick Crook, who worked on that project, said that as recently as two years ago "it would have taken months and thousands of pounds to process such informative sequence information on hospital infections."

Until recently, genetic analysis was more often done after outbreaks of MRSA and other infections to draw lessons for the future, but advances in sequencing have made the process much faster.

Experts say current techniques for analyzing MRSA do not give such detailed data meaning they are a blunt tool for dealing with an outbreak.

"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," said Julian Parkhill, who worked on the study at the Sanger Institute.

The researchers say this kind of fast genome sequencing could eventually form the basis for a regional or national infection surveillance program designed to head off MRSA outbreaks before they happen. It could also be used for outbreaks of food-borne infections like salmonella or E.coli.

Genome sequencing was used in an E.coli outbreak in Europe in 2011 but only in the latter stages to help identify the source.

But there are a number of hurdles before the new technique becomes a routine part of monitoring in hospitals.

Peacock says the next stage is to develop software that interprets the data in a way doctors can both understand and use in a hospital.

She also points out that while the study indicates this kind of sequencing is cheaper than existing, less detailed, tests, there will also need to be rigorous cost-benefit analysis.

Nevertheless, Illumina's senior director of research Geoffrey Smith, who co-led the study, said the results demonstrate "how advances in whole genome sequencing can provide essential information to help combat hospital outbreaks in clinically relevant turnaround times."

(Editing by Jon Hemming)

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