Revolutionary 'black box' genome sequencing system traces root of MRSA outbreaks and advises on best treatment options
Hospitals are stepping up infection control measures following the Pseudomonas outbreak in Northern Ireland
British researchers have made a breakthrough in the fight against MRSA, finally cracking the lethal superbug’s genetic code in a move that will enable them to identify and destroy the source of the infection.
The discovery paves the way for the eradication of the life-threatening bacteria from hospitals around the world.
The research, led by Professor Sharon Peacock of Cambridge University, explored a technique known as whole genome sequencing - a process that maps an organism’s entire genetic code - to analyse MRSA bacteria taken from 12 affected babies.
Information on the genome sequence goes into the system and is interpreted and what comes out the other end is a report to the healthcare worker
By quickly identifying the specific bacterial strains from their genetic codes, experts were able to target the transmission path of the infection and cut it off.
The system has already been successfully tested, halting an outbreak of the superbug at the special care baby unit at the Rosie Hospital in Cambridge.
The researchers studied the hospital after infection rates rose significantly from 100 a year in the 1990s to 7,700 in 2003 and 2004. Even after the Government’s Clean Your Hands campaign, while rates fell steadily, more than 1,000 people were still affected in 2011/12.
A report on how the outbreak was controlled is published in the latest issue of the journal, The Lancet Infectious Diseases.
It shows that standard investigations had failed to show whether a genuine outbreak had occurred at the hospital, or whether the babies had all coincidentally been exposed to MRSA.
Using the new technique, provisionally dubbed ‘the black box’, scientists were quickly able to determine that 10 babies were part of an outbreak involving a previously unknown strain of the bacteria. And they quickly discovered that the bug had also spread outside the hospital and into the community.
Despite deep cleaning interventions and antibiotic treatment, two months later a new case was diagnosed at the unit. DNA sequencing showed it was caused by the same strain identified in the earlier outbreak and was carried to the ward by one of 154 screened healthcare workers.
It could 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
Co-author of the report, Dr Julian Parkhill, said of the discovery: “The staff member was decolonised and went back to work and we believe this brought the outbreak to a close.”
The researchers are now planning to develop the concept into a new system that could be used by hospital staff with minimal training.
There are also hopes it could be further enhanced to protect against other common bacteria, rapidly detecting the source of the infection and the best options for treatment.
The technology, which could be available on the market in just a few years, combines DNA profiling and database analysis.
What we have glimpsed through this pioneering study is a future in which new sequencing methods will help us to identify, manage and stop hospital outbreaks and deliver even better patient care
Professor Peacock said: “What we’re working towards is effectively a ‘black box’.
“Information on the genome sequence goes into the system and is interpreted and what comes out the other end is a report to the healthcare worker.
“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.
“It will also give information about how related that organism is to other organisms within the same setting, giving an indication of the capability of transmission from one patient to another.”
The outbreak at the Rosie Hospital cost the NHS around £10,000. It is expected the ‘black box’ system will cost around £50 per sample, effectively saving the taxpayer hundreds of thousands of pounds.
The discovery has been welcomed by infection experts. Dr Nick Brown, a consultant microbiologist at the Health Protection Agency (HPA), and an infection control lead at Addenbrooke’s Hospital in Cambridge, said: “What we have glimpsed through this pioneering study is a future in which new sequencing methods will help us to identify, manage and stop hospital outbreaks and deliver even better patient care.”
HPA figures show that currently around 6% of hospital patients in England acquire an infection during their stay.