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NGS Leaders Blog

Guest Post: International Crowdsourcing Initiative to Combat the E. Coli Breakout in Germany

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June 8, 2011 

Editor’s Note: In light of the recent E coli outbreak in Germany, NGS Leaders invited Joyce Peng from BGI to comment on the organization’s efforts to understand the culprit. Below Joyce describes BGI’s efforts to rally the international community in combating the outbreak. – Eric Glazergenome sequencing 

In response to the recent E. coli outbreak in Germany, BGI and its collaborators at the University Medical Centre Hamburg-Eppendorf have 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 ). The FTP site contains a file that provides the PCR primer sequences which researchers have used to create diagnostic kits for rapid identification of this highly infectious bacterium.

Bioinformatics analysis revealed that this E. coli is a new strain of bacteria that is highly infectious and toxic. BGI and its collaborators, as well as a growing number of researchers around the world “crowdsourcing” this data, are exploring in depth the European disease outbreak and helping to trace the origin and spread of the lethal E. coli strain. The latest evidence is that a previous 2001 German strain is the most likely ancestor of the current strain, perhaps suggesting that a fast evolution resulted in the gain of more genes over the last 10 years. Further comparisons between the genomes of these bacteria will clarify why the latest outbreak has been so exceptionally pathogenic, and help frontline healthcare workers fight to control this new global outbreak.

Unfortunately the 2001 German strain currently has no publicly available genome sequence, although it was preliminarily analyzed during the original outbreak and stocks and samples were hopefully stored. In the great strides already made in just a few days by the community from sharing original genomic data, BGI has made an appeal to any labs which have isolates of this key strain to share samples and respective data.

The international community “crowdsourcing” and analyzing BGI’s most up-to-date genomic data now has a repository for this preliminary data, and BGI encourages scientists to use its latest improved assembly (http://www.ncbi.nlm.nih.gov/bioproject/67657) and follow the repository and its Twitter feed (@BGI_Events) for announcements and data updates https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis 

BGI and the Beijing Institute of Microbiology and Epidemiology researchers have also 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-associated genes (more detailed protocol is available on the BGI FTP site). Diagnostic results can be obtained within 2–3 hours after receiving the sample, and thus will be extremely useful for epidemic surveillance and detection of the bacterium. The complete test protocol for E. coli O104 is available at ftp://ftp.genomics.org.cn/pub/Ecoli_TY-2482/Specific_primers_for_PCR_detection.pdf. In an effort to help control the spread of this lethal bacteria, BGI and the Beijing Institute of Microbiology and Epidemiology will provide the designed and synthesized primers free to any disease control and research agency worldwide.

This comparative work is now of the utmost urgency, so please contact BGI to collaborate in this effort by contributing samples or data from strain HUSEC041/01-09591 (contact caosujie@genomics.org.cn).

Joyce Peng, PhD is Marketing Director for BGI Americas Corporation (www.bgiamericas.com). She can be reached at joyce.peng@bgiamericas.com  

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