Navigation Links
BGI releases a complete de novo E. coli O104 genome and details of their detection kit

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. ( In addition, the FTP site contains a file that provides the PCR primer sequences BGI and their 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-associated genes (more detailed protocol is available on the BGI FTP site). Diagnostic results can be obtained within 2𔃁 hours after receiving the sample, and thus will be extremely useful for epidemic surveillance and detection of this bacterium.

BGI has assessed the specificity and sensitivity of this kit and protocol through computational analyses of 4,547 strains (from 2,183 species) using publicly available whole-genome sequences, and through experimental analyses of 323 DNA samples (from 93 species, including 55 E. coli strains that have different phenotypes and the current infectious strain). The findings demonstrated that the kit and protocol have high specificity: no bacterial strain other than E. coli O104 had positive amplification results of both target regions. Sensitivity testing indicated that the kit and protocol could detect this bacterium using a DNA concentration as low as ~1 picogram (10-12 g) in the PCR. Additional validation tests on more patient isolates will be carried out within the week.


Contact: Bicheng Yang
Beijing Genomics Institute at Shenzhen

Related biology news :

1. Techne Corporation Releases Unaudited Third Quarter Results for Fiscal Year 2011
2. India releases tiger numbers as experts convene
3. WCS releases Birds of Brazil
4. U of Minnesota center releases nations first long-term framework for statewide water sustainability
5. Snow from space: University of Leicester releases satellite images of snow-bound UK
6. Structural Genomics Consortium releases 1,000th protein structure
7. 1000 Genomes Project releases pilot data
8. ADA releases updated position paper on nutrition assistance programs for children
9. National Center for Secure and Resilient Maritime Commerce releases annual report
10. NASS releases new geospatial data products
11. AMP releases statement on oversight of laboratory tests
Post Your Comments:
(Date:11/16/2015)... 2015  Synaptics Inc. (NASDAQ: SYNA ), ... announced expansion of its TDDI product portfolio with ... and display driver integration (TDDI) solutions designed to ... TDDI products add to the previously-announced TD4300 ... resolution), and TD4322 (FHD resolution) solutions. All four ...
(Date:11/11/2015)... --  MedNet Solutions , an innovative SaaS-based eClinical technology company ... to announce that it will be a Sponsor of the ... be held November 17-19 in Hamburg , ... iMedNet , MedNet,s easy-to-use, proven and affordable ... been able to deliver time and cost savings of up ...
(Date:11/9/2015)... JOSE, Calif. , Nov. 9, 2015  Synaptics ... human interface solutions, today announced broader entry into the ... vehicle-specific solutions that match the pace of consumer electronics ... and biometric sensors are ideal for the automotive industry ... vehicle. Europe , ...
Breaking Biology News(10 mins):
(Date:11/24/2015)... LUMPUR, Malaysia , Nov. 24, 2015 /PRNewswire/ ... global contract research organisation (CRO) market. The trend ... result in lower margins but higher volume share ... increased capacity and scale, however, margins in the ... Research Organisation (CRO) Market ( ), ...
(Date:11/24/2015)... Halozyme Therapeutics, Inc. (NASDAQ: HALO ) will be presenting at ... on Wednesday, December 2 at 9:30 a.m. ET/6:30 a.m. PT ... provide a corporate overview. th Annual Oppenheimer Healthcare ... ET/10:00 a.m. PT . Jim Mazzola , vice president ... --> th Annual Oppenheimer Healthcare Conference in ...
(Date:11/24/2015)... (PRWEB) , ... November 24, 2015 , ... ... event of the year and one of the premier annual events for pharmaceutical ... ran from 8–11 November 2015, where ISPE hosted the largest number of attendees ...
(Date:11/24/2015)... PUNE, India , November 24, 2015 ... to a new market research report "Oligonucleotide Synthesis Market ... Equipment), Application (PCR, Gene Synthesis, Diagnostic, DNA, RNAi), End-User ... to 2020", published by MarketsandMarkets, the market is expected ... 1,078.1 Million in 2015, at a CAGR of 10.1% ...
Breaking Biology Technology: