Deadly E. coli strain sequenced by HPA scientists

The deadly E. coli O104 strain that has killed dozens and hospitalised thousands across Europe has been sequenced using 454 Life Sciences’ benchtop GS Junior sequencing system to generate the “most accurate and detailed genetic analysis to date” of this particularly virulent strain.

The sequencing was performed by scientists at the UK’s Health Protection Agency 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 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 characterisation 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 is said to offer 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 ongoing 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.”