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Sequencing to Follow the Transmission Chain

Standard approaches could only determine that the Klebsiella pneumoniae infections spreading through a Denver hospital were related, but not how the bug was passed from patient to patient, the Wall Street Journal reports.

The hospital turned to scientists at the US Centers for Disease Control and Prevention who then sequenced the isolates, determining sub-clusters within the hospital as well as transmission events between different units of the hospital.

Similar techniques, the Journal notes, have been used determine the source — cheese — of a listeria outbreak and other food-borne outbreaks.

"With next-generation sequencing, you can really see the person has the same isolate [sample] as came from that lettuce. It's a much better tool to be able to say what the source was for an outbreak," Jill Taylor, the interim director of New York State's public-health lab, the Wadsworth Center, tells the Journal.

The Journal adds that the Obama administration in the US has asked for $40 million for fiscal year 2014 for an "advanced molecular detection" initiative that would improve the CDC's ability to sequence and analyze such bugs. However, it says that it isn't certain that Congress would approve this request, noting that the CDC's budget was cut this year by $580 million.