TGAC helps in crowd-sourcing analysis of E. coli strain
8 June 2011
Scientists from The Genome Analysis Centre (TGAC), which receives strategic funding from BBSRC, have identified several genes which may be key factors in the recent E.coli outbreak of strain 0104:H4. The strain has now been implicated in a number of hospitalisations and deaths, particularly in Germany. The outbreak has also had a high economic impact on the fresh vegetable market, particularly in Spain and across the EU. The studies have been made possible by the public release of genome sequence data from BGI, China last week.
A comparison between different E.coli strains including O157:H7 responsible for a previous food poisoning outbreak in the UK. (click for larger version). The coloured blocks represent regions of the sequence in common with other E.coli strains. The outbreak E.coli is second from the base, red lines on this sequence show where the sequence is still in pieces that need to be joined before we can make sense of the genes in this region. Image: TGAC
TGAC is contributing to the 'Crowd–sourcing' analysis of the genome analysis involving an unprecedented level of scientific cooperation across the globe on the internet to uncover the secrets of this E.coli genome and find out what is making it so dangerous to health.
Many antibiotic resistance genes have been found in this draft sequence, as well as at least part of a gene known to be involved in attachment and uptake into human cells. There are several other genetic factors that, taken together, are likely to contribute to this organism's serious impact on human health. Several of these implicated genes are found in key areas of the genome which may have been gained from other E.coli strains.
Genes for outer cell structures have been found, known as pili, that are involved in attachment to surfaces, and could potentially be involved in attachment to vegetable skins or plastic packaging. This bacterium also has a number of genes associated with survival under stress conditions, that could improve its tolerance of adverse conditions such as acid, heavy metals such as copper, low iron, low oxygen and UV light.
Dr. Lisa Crossman, TGAC Microbial Genomes Project Leader said "By studying the genetic factors involved in the survival of this bacterium on surfaces we hope to get an angle on how this organism has been able to get a foothold in the global food chain."
So far the 'crowd–sourcing' analysis has identified that the closest related E.coli strain is one which was isolated several years ago in the Central African Republic and linked with serious diarrhoea. However, the new outbreak strain is believed to have gained genes from a different E.coli not previously involved with food poisoning, which now allows the outbreak strain to induce the life–threatening haemorrhagic uraemia symptoms.
TGAC has been established in Norwich by the Biotechnology and Biological Sciences Research Council (BBSRC) in partnership with regional economic development partners – The East of England Development Agency (EEDA), Norfolk County Council, South Norfolk Council, Norwich City Council and the Greater Norwich Development Partnership. The centre represents an investment by all the partners in the capital infrastructure of £13.5M.
BBSRC is the UK funding agency for research in the life sciences. Sponsored by Government, BBSRC annually invests around £470M in a wide range of research that makes a significant contribution to the quality of life in the UK and beyond and supports a number of important industrial stakeholders, including the agriculture, food, chemical, healthcare and pharmaceutical sectors.
BBSRC provides institute strategic research grants to the following:
- The Babraham Institute
- Institute for Animal Health
- Institute of Biological, Environmental and Rural Sciences (Aberystwyth University)
- Institute of Food Research
- John Innes Centre
- The Genome Analysis Centre
- The Roslin Institute (University of Edinburgh)
- Rothamsted Research
The Institutes conduct long-term, mission-oriented research using specialist facilities. They have strong interactions with industry, Government departments and other end-users of their research.