[D66] .. up against something unusual . . .

[Henk Elegeert]

*DNA Sequence Yields Clues to Germany's 'Super Toxic' E. coli
Outbreak*<http://news.sciencemag.org/scienceinsider/2011/06/sequence-yields-clues-to-germany.html>

"
Just from the high number of deaths and severe cases, scientists and public
health experts battling Germany's massive *E. coli* outbreak knew they were
up against something unusual. Now, early results from sequencing projects of
the enterohemorrhagic *Escherichia coli* (EHEC) strain appear to confirm
that a never-before-seen hybrid, combining the worst of several bacterial
strains, is causing the havoc.

The Beijing Genomics Institute (BGI), in Shenzhen, China—which today
announced <http://www.genomics.cn/en/news_show.php?type=show&id=644> that it
has sequenced the microbe's entire 5.2-million-base-pair genome—says that
its acquisition of several virulence genes make this EHEC strain
"supertoxic."

The outbreak, which has caused mayhem in European trade relations, is still
growing; so far, more than 16 patients have died. The origin of the microbe
remains a riddle; cucumbers from Spain, originally fingered as the potential
source<http://news.sciencemag.org/scienceinsider/2011/05/cucumbers-may-be-culprit-in-mass.html?ref=hp>,
were acquitted on Tuesday and have not been replaced by other suspects. All
researchers know is that raw vegetables are the most likely carrier.

Scientific results announced in two press releases today—both also intended
to tout the extraordinary speed of today's sequencing technology—suggest
that within the microbe's DNA lie clues to its aggressive nature.

The second came from Life Technologies Corporation, which manufactures
so-called third-generation sequencing machines. Today, the company
announced<http://www.lifetechnologies.com/news-gallery/press-releases/2011/dna-sequencing-data-reveals-new-hybrid-e.html>that
sequencing at its lab in Darmstadt, Germany, in collaboration with the
nearby University of Münster, "strongly suggests that the bacterium … is a
new hybrid type of pathogenic *E. coli* strains." Spokespeople for the
company in the United States and Germany could not provide details today.
"Further analyses on Ion PGMT"—the company's flagship sequencing
machine—"will confirm [the] data," the press release promised.

BGI, meanwhile, says that the microbe's genome—which it says took just 3
days to sequence, also using Life Technologies equipment—reveals that it
shares 93% of its sequence with EAEC 55989 *E. coli*, a strain isolated in
the Central African Republic and known to cause serious diarrhea. It appears
to have acquired several genes that make it more pathogenic, however,
probably in a process called horizontal gene transfer, by which microbes
exchange bits of genetic information.

In an e-mail to *Science*Insider, Yang Bicheng, director of BGI's marketing
department, wrote that one gene fragment appears to have come from another
food-borne pathogen, *Salmonella enterica*, while other genes are highly
homologous to those found in other, phylogenetically distinct *E.
coli*strains, including a strain called O25:H4-ST131.

BGI, which has made the sequence
available<http://www.genomics.cn/en/news_show.php?type=show&id=644>for
researchers to download, says the analysis also confirmed that the
microbe is resistant to many antibiotics. These include aminoglycoside, the
macrolides, and the beta-lactams—"all of which makes antibiotic treatment
extremely difficult," according to the press release. However, German EHEC
patients aren't treated with antibiotics; most scientists believe they make
matters worse, because killing EHEC results in the release of more toxin.

Yang acknowledged that finding the resistance genes may not be clinically
relevant, but says they may help understand how the strain arose. "The
evolutionary process … of this very strange hybrid strain may be a very
interesting scientific story," Yang wrote in his e-mail.

Microbial genomicist Frederick Blattner of the University of Wisconsin,
Madison—who worked for almost 15 years to sequence the first *E.
coli*strain<http://www.genome.wisc.edu/aboutus.htm>and finished in
1997—says the results have to be considered preliminary;
it's not clear whether BGI assembled the entire genome from its sequenced
pieces, he notes, and usually in such efforts, a number of stretches need to
be resequenced. Still, "they did this at an amazing speed, and it looks like
they found some very intriguing information," Blattner says

"

... (is) het begin van het failliet van de EU?

Voor nu al - 27 - EU-burgers komt alle hulp te laat. Voedsel veiligheid
blijkt schijn, en kan zelfs niet voorkomen dat handel in onbesmette
producten geen doorgang kan vinden, en uitgerekend Nederland - een van de
oprichters van de EU - zoekt de oplossing buiten de EU om.

Henk Elegeert
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