Editor's note: Although BGI's press release states that a "draft assembly" of the new E. coli strain is available online, some readers have pointed out that these are only the raw sequence reads. This post has been updated to reflect that. Nick Loman at the Pathogens: Genes and Genomes blog has posted a first-pass de novo assembly using the BGI data.
The World Health Organization has declared the E. coli outbreak running rampant in Europe to be a new strain never before seen in people, says Scott Hensley at NPR's Shots blog. At least 18 people have died, and almost 1,500 people have been infected, Hensley says. Most of the deaths have occurred in people who live or have recently traveled to Germany, and officials believe they all ingested infected vegetables, though the source has not yet been identified. BGI has sequenced the bacterium and says it's a new type of E. coli never seen before, though it has a 93 percent similarity to a strain that appeared in the Central African Republic. The new bacterium has some different genes that seem to account for its virulence and high toxicity, Hensley says. It also appears to be resistant to antibiotics.
In a press release, BGI says it completed the sequencing within three days of receiving bacterial DNA samples, using the Ion Torrent sequencing platform. According to the sequence reads — which BGI has made available for download — the new strain's genome is about 5.2 million bases, and has a new serotype which the press release says has not previously seen in any E. coli outbreaks. "This new strain of E. coli has acquired specific sequences that appear to be similar to those involved in the pathogenicity of hemorrhagic colitis and hemolytic-uremic syndrome. The acquisition of these genes may have occurred through horizontal gene transfer," BGI adds.