Those familiar with my ‘infectious thoughts’ will know that I’m following the deadly European E. coli outbreak with great interest. Earlier this week, it was announced that the genome of the culprit strain had been sequenced by BGI (formally the Beijing Genomics Institute) in collaboration with the University Medical Centre Hamburg-Eppendorf. A really interesting development has been release of the genomic data to the international community for ‘crowdsourcing’ alongside a site for people to download up-to-date analyses and a Twitter feed (@BGI_Events). This is how science should be done!
BGI and the Beijing Institute of Microbiology and Epidemiology have taken advantage of the genome data to develop a PCR-based diagnostic protocol (using two specific genes) to rapidly identify the outbreak strain. When tested computationally against publicly available whole-genome sequences from over 4,500 strains covering more than 2000 species, the protocol was found to be highly specific for the outbreak strain. This was confirmed experimentally using 323 DNA samples (from 93 species, including 55 E. coli strains). They have released a detailed protocol of the method and will provide the designed and synthesised primers free to any disease control and research agency worldwide. Amazing.