The deadly E.coli O104 strain has been sequenced using 454 Life Sciences' bench-top GS Junior sequencing system, generating an accurate genetic analysis of this particularly virulent strain.
The sequencing was performed by scientists at the UK's Health Protection Agency (HPA) and the data has been uploaded onto the National Centre for Biotechnology Information (NCBI) website for use by the scientific community.
The results suggest that the strain has a unique combination of features containing genes from two types of E.coli as well as its own genes.
The sequencing assembly shows that the strain contains two extrachromosomal elements or plasmids that may factor into its pathogenicity.
In essence, this strain of E.coli may have 'picked up' some extra genetic material along the way.
Chinnappa Kodira, director of genomics at 454 Life Sciences, said: 'Despite the availability of short-read sequencing data from this E.coli outbreak strain for more than a week, the short fragmented assembly has offered only limited information on gene order and gene composition.
'This long, contiguous assembly enables the much better characterisation of genome structure, horizontal gene transfer and pathogenic islands, which are crucial for understanding the emergence of new virulent bacterial strains,' added Kodira.
The addition of this new long-read sequence data from the GS Junior system offers contiguous sequence 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 detailed genomic map of this pathogen within hours.
The sequence data will assist in 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 chief executive officer of 454 Life Sciences.
