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Video transcript: Crowdsourcing killer outbreaks

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February 2013

Video show cells dividing continuously to the sound of sinister background music

Dr Nick Loman, University of Birmingham
This outbreak was one of the most serious E.coli outbreaks in recent history over 5000 people were affected by this outbreak at the last count there was over 50 deaths.

Dr Lisa Crossman, The Genome Analysis Centre (TGAC)

The outbreak with E.coli, that's Escherichia coli

Video shows a computer animation of the bacteria spreading inside a gut

…and this is the common gut bacteria which lives in all our guts and normally helps us digest food and so on but in certain circumstances E.colis can cause disease and this was a particularly severe disease involved with HUS syndrome which is hemolytic uremic syndrome which causes fatal kidney failure. So obviously this is of high concern to the international community and in fact the Beijing Genomics Institute in China decided to place their sequence as fast as possible out on the internet and the whole idea was really to get an international community involved in the analysis just to do it really quickly.

Dr Nick Loman, University of Birmingham
I became involved in the E.colis outbreak because we were fortunate enough to be in procession of a new sequencing instrument called an Ion Torrent and during the outbreak the Chinese Genomics Centre (The BGI) released reeds from the outbreak which I was able to download and start analysing while the outbreak was going on.

So initially there was about a day's lull after I posted an assembly of the genomics sequence on my blog and then after that it just went crazy, within a few days a number of people from four different continents had started analysing the data and by two weeks there were over 50 pieces of independently produced analysis on the genomic sequence posted on blogs and disseminated via Twitter.

Dr Lisa Crossman, The Genome Analysis Centre (TGAC)
There was a huge sense of urgency while everyone was really keen to put in their analysis and people working on it round the clock and especially help with people working on it in Australia as well as in Europe and slightly in America.

Dr Nick Loman, University of Birmingham
The use of crowdsourcing where the aim is to get information out in a timely fashion using the internet is really a very novel idea in science where often the pressure is to get published papers in this case it was because there was an on-going outbreak which was effecting thousands of people and it was absolutely imperative to get that information into the public domain as quickly as possible and that drove that analysis.

Dr Lisa Crossman, The Genome Analysis Centre (TGAC)
We became much more heartily involved with the downstream analysis from that so the annotation where we actually call what the genes are and attempt to place a function onto the gene and the downstream analysis from that again which is comparative genomics where we can pair the different genomes.

Dr Nick Loman, University of Birmingham
Some of the early press releases suggest that this was an entirely novel strain never seen before but the genomic sequence data confirmed that this was a variant of an existing type of strain which had acquired some variance facts which were probably significant in the severity of this outbreak.

Dr Lisa Crossman, The Genome Analysis Centre (TGAC)
The crowdsourcing really brought the first analysis in terms of what sort of genes were involved I mean particularly pinpointing this bacterial phase which is a bacterial virus which carried the Shiga toxin and the Shiga toxin is something which you can really put your finger on and say this was causing the HUS, the hemolytic uremic syndrome which could arise to the fatal kidney failure.

Dr Nick Loman, University of Birmingham
The study of bacterial genomics shows us that bacteria consequently engaged in sex and combination with each other…

Video show a computer animation of the bacteria invading cells

…exchanges genetic material and under selection by humans like antibiotics we are encouraging the development of more resistant strains and this strain was particularly antibiotic resistance. There was an interesting combination of collaboration and competition during the crowdsourcing because people wanted to get their curiosity driven analysis out there first but of course there was also quedos for being the first to do it.

Dr Lisa Crossman, The Genome Analysis Centre (TGAC)
So it was great to be involved with kind of friend also like a family kind of thing. There was also a touch of competition involved in who was going to get out the various data first.

Dr Nick Loman, University of Birmingham
What we have learnt from this crowdsourcing effort is that it can be done and we are not limited by technological communications issues now, what we need to do is try and harness the power of these types of technologies in routine surveillance of pathogens and during outbreaks and this provides a model for how that can be done.

Video show cells dividing continuously to the sound of sinister music

ENDS

Credits

Produced in collaboration with TGAC and University of Birmingham.