Genomic medicine steps closer to the clinic

The Lancet

“Gene detectives find new tool to contain deadly bacteria” and “CSI Bethesda: Sleuths used sequenced genome to track down killer” were just some of the newspaper headlines sparked by an early online publication in Science Translational Medicine last week. The research article details a medical mystery that led to the novel tracking of a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing.

In July last year, the US National Institutes of Health (NIH) Clinical Center admitted a patient with carbapenem-resistant K pneumoniae whose care included strict infection control measures such as isolation. The patient was eventually discharged after successful treatment. However, 3 weeks later a second case of the drug-resistant bacterium emerged at the centre in a patient who had never been in the same location as the first. The outbreak continued over a 6 month period—18 patients were affected in total, 11 of whom died (six from the infection).

To find out how transmission occurred, the NIH researchers used whole-genome sequencing to compare patients' bacterial strains. Most strains of K pneumoniae in the USA belong to the same clone and are difficult to distinguish with traditional methods such as pulsed field gel electrophoresis. However, sequencing revealed that despite the 3 week gap, the infection in the index patient had triggered the outbreak and transmission occurred from three different sites on the patient's body. Tracking of the transmission using genomic and epidemiological data gave other insights, such as the emergence of colistin resistance, and led to broadened infection control efforts that eventually stopped the outbreak.

The authors suggest that real-time application of this technology could guide hospital infection-control measures in the future. Although most hospitals do not yet have the resources to sequence bacterial genomes, the technology is rapidly becoming more affordable (from US$2000 per sequence in 2011 to $500 this year). Its use in controlling difficult hospital infections, such as K pneumoniae, certainly has the potential to become invaluable. The promise of genomic medicine has been a long time coming, but this latest research brings it tantalisingly close to reality.