Further Analysis on Improved Genome Assembly Indicates the Outbreak E. coli has Complex Genetics With Resistance to at Least Eight Antibiotics
-- Five additional antibiotic-resistant genes identified, including cephalosporin, monobactam, penicillin and streptomycin --
SHENZHEN, China, June 4, 2011 /PRNewswire/ -- To aid the fight of the deadly outbreak of E. coli O104 strain in Europe, BGI-Shenzhen and their collaborators at the University Medical Centre Hamburg-Eppendorf have released an updated draft genome assembly result built upon the sequencing data previously released and submitted to NCBI in the previous two days. As one of the first genomes assembled using the latest ion semiconductor sequencing technology, there were some initial difficulties assembling the genome, but a de novo assembly approach was applied first, and gene structures were refined with the assistance of genomic sequences from related strains.
This newly assembled draft genome is a large improvement on the previous version and is now freely accessible from the NCBI database (http://www.ncbi.nlm.nih.gov/bioproject/67657) and BGI website (ftp://ftp.genomics.org.cn/pub/Ecoli_TY-2482). The rapid release and dissemination of this data to the scientific community by the BGI, aided for the first time by new media forms such as Twitter (follow: @BGI_Events), has in less than 24-hours allowed researchers around the world to produce alternative genome assemblies, and now allows comparisons with additional, and potentially different isolates and strains (see: http://pathogenomics.bham.ac.uk/blog/2011/06/ehec-genome-assembly/). This data should also aid in the development of diagnostic tests, as well as help to resolve issues regarding the outbreak's origin.
While preliminary, considerable additional information has been derived from this latest dataset in addition to that announced previously (see: http://www.genomics.cn/en/news_show.php?type=show&id=644). Based on the draft assembly, the genome of this outbreak strain is a mosaic containing genes from a variety of strains. This data further confirms the serotype of the outbreak strain is O104, and while O104 E. coli strains have previously been implicated in outbreaks in the United States, BGI's initial results suggest that the current outbreak and the previous US O104 strain are genetically distinct. The sequences of seven housekeeping genes from the outbreak strain were also used in MLST (multi-locus sequences typing) analysis against 3,800 E. coli strains (http://mlst.ucc.ie/), and all seven genes were found to be different between the US and current outbreak strain.
BGI researchers also investigated whether previously reported E. coli virulence genes were present in the outbreak strains, and from its initial analysis only stx2 has been identified so far, and no previously described virulence gene has been detected in the outbreak strain. In contrast to this, a further five antibiotic-resistant genes have been identified on top of the three identified in the initial assembly, including cephalosporin, monobactam, penicillin and streptomycin, which provides further genetic evidence that the strain is at resistant to at least eight different types of antibiotics.
While the data released so far is only preliminary and should be used with that in mind, due to its great importance to public health the research group is making it immediately available to the community for download without restriction. The group will continue to improve the assembly with additional upcoming data, and will continue to release updated versions to facilitate the campaign against this deadly bacteria.
BGI (formerly known as Beijing Genomics Institute) was founded in 1999 and has become the largest genomic organization in the world. With a focus on research and applications in the healthcare, agriculture, conservation and bio-energy fields, BGI has a proven track record of innovative, high-profile research which has generated over 178 publications in top-tier journals such as Nature and Science. BGI's distinguished achievements have made a great contribution to the development of genomics in both China and the world. Our goal is to make leading-edge genomics highly accessible to the global research community by leveraging industry's best technology, economies of scale and expert bioinformatics resources. BGI and its affiliates, BGI Americas and BGI Europe, have established partnerships and collaborations with leading academic and government research institutions, as well as global biotechnology and pharmaceutical companies. At BGI, we have built the infrastructure and scientific expertise to enable our customers and collaborators to quickly migrate from samples to discovery. For more information, visit www.bgiamericas.com or www.bgisequence.com.
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