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Decoding DNA

June 6, 2011

In a DW interview, a UK bioinformatician says he's part of a group 'crowdsourcing' E. coli analysis. They are using public data made available from Chinese researchers as a way to better understand the new strain.

E. coli
Researchers are rapidly try to reveal this E. coli's secretsImage: Robert Koch Institut

On Sunday, German health authorities identified German-grown bean sprouts as the most likely potential source of the deadly E. coli. The bacteria has so far killed 22 people and made more than 2,000 ill across Europe since being detected in northern Germany more than three weeks ago.

German scientists and their colleagues at the Beijing Genomics Institute in China have been working on uncovering secrets of the outbreak. BGI scientists revised their draft genetic sequence of the E. coli strain and have been sharing their data with dozens of scientists around the world as a way to "crowdsource" this data. By publishing their data publicy and freely, these other scientists can have a look at the genetic structure, and try to sort it out for themselves.

To learn more, Deutsche Welle spoke with one of those people participating in this crowdsourced research, David Studholme, a bioinformatician and lecturer at the University of Exeter in the UK.

You've been doing some of your own research on this new E. coli strain here in Germany?

Yes. That's right. The really exciting thing here is that the Chinese institute, the BGI, released a complete genome sequence for this strain. Within hours of them releasing that, people like myself, and lots of other people around the world have taken this data that was publicly released by the BGI and have done our own analysis on it. Then, we've shared our results with each other, and it's all made public. It's very exciting to be able to do this.

David Studholme
Studholme normally studies pathogens that affect plants but volunteered during this crisisImage: David Studholme

What exactly have you been able to determine from the results you've gotten from the genetic sequence?

So probably the most important thing is that having the complete genetic sequence of this particular outbreak strain. We can then compare that against the complete gene sequences of other E. coli strains from other outbreaks in the past, so we can get a clue as to how similar this strain is to other outbreaks. It can give us some clues to the origin of this particular outbreak. It can also tell us some more interesting biology of this particular strain that make it particularly aggressive or antibiotic resistant, or those kind of features. So we can learn a lot about the strain by looking at its gene sequence.

What we've learned in this particular case is that this strain, the German strain, for the current outbreak, is very very similar to a couple of other strains that have been studied previously. One of those is one that occurred in an outbreak in Africa from 2001. But also very interestingly the current outbreak strain is one is also similar to an outbreak in Germany. If you have a look at the BGI's website, they actually speculate that the current outbreak is derived from this previous outbreak.

The other thing that I specifically found here is that I identified several genes that are in this current outbreak, and these are genes that are not found in any previously studied E. coli strain.

But these new gene sequences that you've identified, do you know what they do?

For some of them, yes, or at least we can make a good guess. So most of them look as though they are derived from a bacteriophage. This is a virus that infects the bacteria, or like a parasite on a parasite. They may be of some significance. There is also a gene in there that looks like it might be involved in breaking down or overcoming antibiotic.

So it has antibiotic resistance?

Yes, there are several genes in there that look like antibiotic resistant genes. And one of them looks pretty unique, not previously seen in E. coli. It's specifically called a microswin esterase, if you care to know what it's called.

Interview: Cyrus Farivar
Editor: Stuart Tiffen