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--A recent study uses a new approach to investigate the shiga toxin producing bacteria responsible for a serious
disease outbreak in Germany in 2011. The real culprits behind the outbreak are the viruses that carry
the gene for shiga toxin and transfer it to otherwise harmless bacteria --
What’s
harder than finding a needle in a haystack? Finding the bacterial genome you’re
looking for in a diarrhea sample. A recent study
published on April 10, 2013 in the Journal of the American Medical Associaton (JAMA)
made this task seem relatively easy. The bacteria being searched for was a rare shiga toxin producing
bacteria that causes bloody diarrhea and other severe complications in
humans upon infection. This study was done by an international team of
researchers coordinated by Mark
J. Pallen who recently became the head of Warwick Medical School’s new Division
of Microbiology and Infection. The bacterial strain that caused an outbreak in Germany was especially rare making it hard to identify. Because of this, researchers employed a new method to
identify the genome sequence of this highly pathogenic bacteria. Their method of detection was to sequence all the genetic
material present in fecal samples from patients with diarrhea during the outbreak
and sort through this genetic information to find the sequence of the disease causing strain.
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The source of the outbreak in Germany during the summer of 2011 is believed to be from the consumpton of raw
sprouts contaminated with the dangerous bacteria strain (2). This outbreak affected
thousands of people in a wealthy, modern, industrialized society, causing more
than 50 deaths (4). In times like this, quick identification of
the causative pathogen (in this case a shiga toxin producing bacterial strain)
is critical for the management of the outbreak. Traditionally, the standard for identifying
pathogens in clinical samples is to isolate the disease causing bacteria from
other microbiota in the samples and then sequence it once it is in pure
culture. This study's approach is different becuase they directly sequenced the mixed communities of bacteria and anything else present within the feces sample and then analyzed the sequence data to find
the disease causing bacteria. The sequencing of mixed microbial communities is called metagenomics
and allows identification independent of laboratory isolation and culture of the causative
bacteria.
