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Scientists turn DNA detectives to track spread of hospital superbugs as the equivalent of a barcode

From The Times
January 4, 2010

  The genetic fingerprints of germs are to be mapped to open a new front in the battle against hospital superbugs.
  Scientists have embarked on an ambitious project to read the complete genetic codes of pathogens taken from hundreds of people, so that DNA can be used to track the spread of infection and to identify the source of outbreaks of disease. Much as detectives use DNA to place suspects at crime scenes, the database will help doctors to determine the route by which patients with MRSA and Clostridium difficile have picked up these bacteria, and thus to control infection.
  When a patient falls ill with MRSA, the germ’s DNA will be sequenced, and compared with samples in the database. This should help to determine whether the infection was present when the patient was admitted to hospital or whether it was acquired on the ward. The information will help doctors to decide what must be done to stop the outbreak. This approach could even allow scientists to establish whether individual nurses or doctors are spreading disease through poor hygiene, by matching DNA from patients’ germs to samples from the skin or clothing of staff.
  Large databases of genetic information about germs will also provide powerful insights into their biology, which promise to help the development of diagnosis and treatment.
  Derrick Crook, a clinical microbiologist at the John Radcliffe Hospital in Oxford, who is leading the Modernising Medical Microbiology initative, said that it could transform infection control in hospitals and the community. “We want to forensically describe how germs are transmitted, and work out better ways of intervening and interrupting that transmission,” he said.
  “This will help us to identify emerging threats, and may give us an understanding of which genetic changes in germs are harmful and which are not. We’ll be using the genomic sequence data as the equivalent of a barcode, which tells us what we’re dealing with and where it might have come from.”
  Peter Donnelly, of the Wellcome Trust Centre for Human Genetics at the University of Oxford, said: “If someone gets a bug in hospital, you want to know whether they’ve brought it in with them or picked it up on the ward. Genomics should be able to tell us.”
  The £6 million initiative is funded by the UK Clinical Research Collaboration. It also involves the Health Protection Agency and the Wellcome Trust Sanger Institute near Cambridge. It is concentrating on Staphylococcus aureus, the bacterial species that includes antibiotic-resistant MRSA strains; C. difficile; norovirus, which causes winter vomiting sickness; and tuberculosis.
  Work has begun on sequencing 300 different samples of S. aureus and C. difficile, and the tuberculosis research will start this year. The norovirus project has been held up because there was not a significant outbreak in 2009.
  The aim is to use the genetic mutations that each of these organisms acquire to construct their family trees. “The hope is that this will give us exquisitely detailed information with which to track infection and learn about patterns of transmission,” Professor Donnelly said. “In a sense, it is like genetic fingerprinting.
  “When someone gets sick, you will sequence the bug and see whether it looks like something in the hospital or elsewhere. If you can determine enough about the pattern of spread — is it patient-to-patient, or via a worker on the ward — you can direct containment efforts much more effectively.”
  Advances in DNA sequencing technology have made it practical to read the genetic code of hundreds of examples of the same germs at low cost. The differences between strains and lineages can then be mapped in a database, against which new samples can be compared to track their likely origins. Professor Donnelly added: “It could start to tell us the factors in the genome of a bug that influence virulence. It’s a huge opportunity to learn about the biology of these organisms, and why they make us sick.”