CAMBRIDGE, Mass. and SHENZHEN, China, June 7, 2011 /PRNewswire/
— Scientists worldwide have been working on the publicly available
genomic sequences of the deadly E. coli O104 strain, which
is causing the current health crisis in Germany and now spreading
throughout Europe. To continue to speed the ongoing international
efforts of researchers to assess and halt this growing epidemic,
BGI and their collaborators at the University Medical Centre
Hamburg-Eppendorf have now released their third version of the
assembled genome, which includes new data from this E. coli
O104. (
ftp://ftp.genomics.org.cn/pub/Ecoli_TY-2482/Escherichia_coli_TY-2482.contig.20110606.fa.gz).
In addition, the FTP site contains a file that provides the PCR
primer sequences BGI and its collaborators have used to create
diagnostic kits for rapid identification of this highly infectious
bacterium.
The new assembly includes more than 200x single-end reads from
the Illumina HighSeq Platform, which allowed BGI to provide a more
complete genome map and to correct any assembly errors from the
previous version. More importantly, this version is a completely
de novo assembly, whereas the previous versions by BGI and
others used a reference-based assembly method to obtain a consensus
sequence. The new assembly continues to support the finding that
this infectious strain carries disease-causing genes from two types
of pathogenic E. coli: enteroaggregative E. coli
(EAEC) and enterohemorrhagic E. coli (EHEC).
Taking advantage of this genomic feature, BGI and the Beijing
Institute of Microbiology and Epidemiology researchers have
developed a straightforward PCR diagnostic protocol for rapid
identification of the outbreak strain. The diagnostic method
consists of two pairs of amplification primers that target the
enteroaggregative- and hemorrhagic-a
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