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How Open-Source Genomics helped defeat German E-coli outbreak

photo of Sepp Hasslberger

Sepp Hasslberger
11th September 2011


Opensource.com reports that a collaborative genomic investigation helped characterize and defeat the unusually violent mutated e-coli bacterium which, in May and June of this year, has infected thousands and killed some 50 people in Germany.

Open sourcing an outbreak investigation

Both publishing research groups working on this outbreak highlight the speed with which they obtained their results. This has been the fastest analysis of an outbreak-associated bacterial pathogen we know of, and now many believe this open source method of sharing data can (and should) play a significant role in public health emergencies.

BGI and its collaborators at the University Medical Centre Hamburg-Eppendorf, Beijing Institute of Microbiology and Epidemiology, and China’s Centers for Disease Control (CDC) (among others) sequenced the genome of E. coli isolate within three days, using the Ion Torrent Personal Genome Machine.

Dr. Junjie Qin, Principal Investigator at BGI and one of the co-leading authors of the collaboration’s study said, “In order to reveal the mechanisms of infection and control the spread of this epidemic as soon as possible, we together with our partners launched a rapid open-source genomics program for immediate data release and to provide more available genome data to the global researchers.”

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