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Escherichia coli

Researchers used the PacBio system to sequence the O104;H4 strain of Escherichia coli responsible for a recent outbreak in Europe that resulted in thousands of illnesses and more than 50 deaths.

PacBio said it has extended its average read length to 2,900 bases and incorporated circular consensus sequencing to obtain a de novo assembly with 99.998-percent consensus accuracy.

In an online presentation, Illumina emphasized the higher throughput and accuracy of its system compared to the Ion Torrent 314 chip. Life Technologies, meantime, contests some of Illumina's claims, touting the Ion Torrent platform as being a "truly disruptive technology."

The outbreak genome has now been sequenced on four different platforms — the Ion Torrent PGM, Illumina's HiSeq and MiSeq, and Roche's 454 GS Junior.

OpGen has used its Argus Optical Mapping system to produce whole-genome optical maps of six of the isolates. Meantime, a UK team has used the 454 Junior to sequence and assemble the E. coli strain and BGI is continuing to publish draft assemblies.

Having sequenced the genome of Escherichia coli O104, separate teams from Life Technologies and BGI said this week that they have developed PCR-based tests to detect the bacterium and help public health officials identify and track future outbreaks.

According to Dag Harmsen, director of research at the University of Münster, the quick turnaround time of the instrument made it possible to obtain results within three days. "The biggest advantage [of the PGM] from my point of view as a public health official is that it's speedy, and speed is what is needed at the moment," he told In Sequence.

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