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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.

The Scan

And For Adolescents

The US Food and Drug Administration has authorized the Pfizer-BioNTech SARS-CoV-2 vaccine for children between the ages of 12 and 15 years old.

Also of Concern to WHO

The Wall Street Journal reports that the World Health Organization has classified the SARS-CoV-2 variant B.1.617 as a "variant of concern."

Test for Them All

The New York Times reports on the development of combined tests for SARS-CoV-2 and other viruses like influenza.

PNAS Papers on Oral Microbiome Evolution, Snake Toxins, Transcription Factor Binding

In PNAS this week: evolution of oral microbiomes among hominids, comparative genomic analysis of snake toxins, and more.