"For decades, we used pulsed-field gel electrophoresis to differentiate bacterial strains," said Tara N. Palmore, M.D., the NIH Clinical Center's deputy hospital epidemiologist who led the outbreak investigation. This test produces a barcode-like pattern of bacterial DNA that shows whether strains are genetically similar. In K. pneumoniae, however, 70 percent of the strains in the United States belong to one strain type with one pattern. "This test is not very helpful for that organism," she said.
As the outbreak began, the Clinical Center staff teamed up with NHGRI researchers led by Julie Segre, Ph.D., an NHGRI senior investigator. Dr. Segre had been working with the Clinical Center's Clinical Microbiology Department to study the evolution of bacterial antibiotic resistance when she heard about the outbreak.
"We were already trying to develop clinical molecular diagnostics tools," Dr. Segre said, "We thought we could use genome sequencing to tell whether the K. pneumoniae from the first patient was the same strain as the one that infected the second patient."
The hospital team sent samples of bacteria isolated from infected patients to the NIH Intramural Sequencing Center (NISC), a component NHGRI. NISC sequenced the DNA samples, and Dr. Segre's team analyzed the results. Where the pulse-field gel electrophoresis technique shows relatively crude patterns, genome sequence data shows precise differences, down to single genetic letters in the bacterial genome. This seque
|Contact: Raymond MacDougall|
NIH/National Human Genome Research Institute