Crowdsourcing Helps Tackle a Killer E. coli Outbreak
In 2011 scientists from across the world were mobilized to tackle one of deadliest E. coli outbreaks.
Biotechnology and Biological Sciences Research Councils (BBSRC), United Kingdom
E. coli (Escherichia coli) is a common bacterium that lives in the human gut. Most strains are harmless and some are beneficial, for example, by helping us to digest our food. Occasionally though these rod-shaped microbes can cause us a lot of trouble, and may even be fatal.
In 2011 an E. coli outbreak sickened thousands of Europeans and became one of the deadliest on record, killing 50 people.
There was an urgent need to track the source of the outbreak. The Beijing Genomics Institute in China put its DNA sequence of E. coli in the public domain, releasing it on the Internet to the international community.
This allowed anyone, no matter where they were based to join in the race to decode the organism’s DNA. Biologists across the world were mobilized to help and they hailed from numerous disciplines and institutes. The aims were to work out how, where and why this harmless microbe turned into a killer bacteria.
“The whole idea was to get an international community involved in the analysis just to do it really quickly,” said Dr Lisa Crossman of The Genome Analysis Centre (TGAC), Norwich, UK.
Dr Nick Loman from the University of Birmingham was the first person to post data of a reconstruction of DNA from the deadly E. coli strain, which he did on his pathogen blog. Within days scientists from four continents joined in with the analysis and it turned into a huge crowdsourcing effort.
Race against Time
“There was a huge sense of urgency while everyone was really keen to put in their analysis,” adds Crossman. “People were working on it round the clock, including people in Australia, Europe and America.”
Initially it was thought that the scientists were dealing with a strain that had never been seen before. But the genome data confirmed it was an already known strain that had acquired some virulence factors.
In comparing the DNA of the outbreak strain to existing strains scientists detected the presence of foreign genes in the deadly strain’s makeup. These belonged to Shiga toxin from a bacteriophage (a virus that attacks bacteria). It was this toxin that was conferring the virulence factors on E. coli and making it so deadly.
Benefits and Lessons Learned
One of the benefits of crowdsourcing is that information can be disseminated across the Internet very quickly, and people can work on projects in shared collaborative spaces, whether they are in Bulgaria or Botswana.
In this instance, scientists who are so used to working behind closed doors on projects with long time frames could discuss developments openly with everyone. The speed of responses was very high and collaboration occurred via websites, blogs and social networks.
By crowdsourcing the killer outbreak, scientists got to some of the answers very quickly, although the worst part of the outbreak had peaked by the time the project had started. But future outbreaks could be mitigated if scientists start analyzing data even earlier.
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