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Something New: Jun 2, 2011

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.

The Scan

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Breast Cancer Risk Gene Candidates Found by Multi-Ancestry Low-Frequency Variant Analysis

Researchers narrowed in on new and known risk gene candidates with variant profiles for almost 83,500 individuals with breast cancer and 59,199 unaffected controls in Genome Medicine.

Health-Related Quality of Life Gets Boost After Microbiome-Based Treatment for Recurrent C. Diff

A secondary analysis of Phase 3 clinical trial data in JAMA Network Open suggests an investigational oral microbiome-based drug may lead to enhanced quality of life measures.

Study Follows Consequences of Early Confirmatory Trials for Accelerated Approval Indications

Time to traditional approval or withdrawal was shorter when confirmatory trials started prior to accelerated approval, though overall regulatory outcomes remained similar, a JAMA study finds.