Deadly E. Coli Strain Sequenced with Roche GS Junior System by HPA Scientists
Provides Community Most Complete Assembly to Date
The results suggest that the strain has a unique combination of features containing genes from two different types of E. coli as well as its own genes. The sequencing assembly shows that the strain contains two extrachromosomal elements or plasmids which may factor into its pathogenicity. In essence, this strain of E. coli may have ‘picked up’ some extra genetic material along the way.
“Despite the availability of short read sequencing data from this E. coli outbreak strain for over a week, the short fragmented assembly has offered only limited information on gene order and gene composition,” said Chinnappa Kodira, Director of Genomics at 454 Life Sciences. “This long contiguous assembly enables much better characterization of genome structure, horizontal gene transfer and pathogenic islands which are crucial for understanding the emergence of new virulent bacterial strains.” The addition of this new long read sequence data from the GS Junior System offers the community the most contiguous sequence to date, and provides a comprehensive assembly on which subsequent genomic analysis can be performed.
The long shotgun reads generated using the 454 Sequencing System allowed the HPA scientists to assemble almost the entire genome into a comprehensive and detailed genomic map of this pathogen within hours. The sequence data will assist in on-going efforts to identify the source of the outbreak, and understand how the strain may have evolved.
“The combination of fast turnaround time and high-quality, long sequencing reads makes the GS Junior an ideal research platform for rapid and comprehensive whole genome analysis in novel pathogen outbreak situations,” said Christopher McLeod, President and CEO of 454 Life Sciences. “We are gratified that 454 Life Sciences is helping to improve health care by enabling a quick response to shed some light on potential epidemics.”
Other news from the department science
Get the life science industry in your inbox
From now on, don't miss a thing: Our newsletter for biotechnology, pharma and life sciences brings you up to date every Tuesday and Thursday. The latest industry news, product highlights and innovations - compact and easy to understand in your inbox. Researched by us so you don't have to.