Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:


International Team Collaborates on Sequence Data for German E. Coli Outbreak

Pacific Biosciences of California, Inc. (NASDAQ: PACB) announced that it has completed a de novo sequence assembly of the Escherichia coli O104:H4 strain responsible for the recent outbreak in Germany using its Single Molecule Real Time (SMRT™) technology, and sequenced 11 related bacterial strains (including six previously unsequenced strains of the same serotype) for comparative analyses.

An international team of scientific experts on E. coli collaborated on the rapid sequencing project to provide more comprehensive information about the origins of the strain that gave rise to the deadly outbreak. The data were generated using an early version of chemistry and software in development at Pacific Biosciences for the next major PacBio RS product upgrade, planned for the fourth quarter of 2011.

The data provided to the public domain includes a complete assembly of the German outbreak strain, alignment to assemblies from other outbreak isolates, and sequences for 11 related Enteroaggregative E. coli strains. The project demonstrates the ability to produce a PacBio-only de novo assembly for a complex microbial pathogen, and the power of rapid sequencing of multiple genomes with the PacBio RS to elucidate the evolutionary history of a pathogenic microbe. A summary of the project appears on the company’s website at

The Pacific Biosciences scientific team, led by Chief Scientific Officer Eric Schadt, Ph.D., is collaborating with some of the world’s leading experts on E. coli and infectious diseases for this project. The collaborators include:

In Europe:
• Karen Angeliki Krogfelt, Ph.D., Professor, Head of Unit, Gastrointestinal Infections, Statens Serum Institut (SSI), Denmark
• Flemming Scheutz, Ph.D., Head of the WHO Collaborating Centre for Reference and Research on Escherichia and Klebsiella, SSI, Denmark
In the U.S.:
• James P. Nataro, M.D., Ph.D., Professor and Chair, Pediatrics, University of Virginia School of Medicine
• David A. Rasko, Ph.D., Assistant Professor, University of Maryland School of Medicine, Institute for Genome Sciences and Department of Microbiology and Immunology
• Nadia Boisen, Ph.D., Research Scientist, Department of Pediatrics, University of Virginia School of Medicine

• Matthew K. Waldor, M.D., Ph.D., Professor of Medicine at Harvard Medical School, Brigham and Women’s Hospital, and HMMI

“Using samples provided by our collaborators, we rapidly sequenced each strain using a standard PacBio RS protocol that took on average less than eight hours from sample preparation to sequencing results,” said Dr. Schadt. “The ability to sequence the outbreak strain with reads averaging 2,900 base pairs and our longest reads at over 7,800 bases, combined with our circular consensus sequencing to achieve high single molecule accuracy with a mode accuracy distribution of 99.9%, enabled us to complete a PacBio-only assembly without having to construct specialized fosmid libraries, perform PCR off the ends of contigs, or other such techniques that are required to get to similar assemblies with second generation DNA sequencing technologies.”

Dr. Krogfelt commented: “These high quality data will provide scientists with more information about the genomic features of this strain that could provide new markers for predicting the higher degree of pathogenicity we are seeing with this outbreak. A more comprehensive evolutionary view of this pathogen may also help identify markers for antibiotic drug resistance that could be used in the future should other related strains emerge. The complexity of this case proves that international collaborations and communications are important in the achievement of detailed scientific information.”

The data are available for the bioinformatics community at the PacBio developer’s network (DevNet) web site (, where a suite of open source tools and other resources designed for SMRT sequence data are available to analyze the information. The data have also been submitted to the National Center for Biotechnology Information (NCBI) SRA database.

Sarah Pick | Newswise Science News
Further information:

More articles from Life Sciences:

nachricht First time-lapse footage of cell activity during limb regeneration
25.10.2016 | eLife

nachricht Phenotype at the push of a button
25.10.2016 | Institut für Pflanzenbiochemie

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Etching Microstructures with Lasers

Ultrafast lasers have introduced new possibilities in engraving ultrafine structures, and scientists are now also investigating how to use them to etch microstructures into thin glass. There are possible applications in analytics (lab on a chip) and especially in electronics and the consumer sector, where great interest has been shown.

This new method was born of a surprising phenomenon: irradiating glass in a particular way with an ultrafast laser has the effect of making the glass up to a...

Im Focus: Light-driven atomic rotations excite magnetic waves

Terahertz excitation of selected crystal vibrations leads to an effective magnetic field that drives coherent spin motion

Controlling functional properties by light is one of the grand goals in modern condensed matter physics and materials science. A new study now demonstrates how...

Im Focus: New 3-D wiring technique brings scalable quantum computers closer to reality

Researchers from the Institute for Quantum Computing (IQC) at the University of Waterloo led the development of a new extensible wiring technique capable of controlling superconducting quantum bits, representing a significant step towards to the realization of a scalable quantum computer.

"The quantum socket is a wiring method that uses three-dimensional wires based on spring-loaded pins to address individual qubits," said Jeremy Béjanin, a PhD...

Im Focus: Scientists develop a semiconductor nanocomposite material that moves in response to light

In a paper in Scientific Reports, a research team at Worcester Polytechnic Institute describes a novel light-activated phenomenon that could become the basis for applications as diverse as microscopic robotic grippers and more efficient solar cells.

A research team at Worcester Polytechnic Institute (WPI) has developed a revolutionary, light-activated semiconductor nanocomposite material that can be used...

Im Focus: Diamonds aren't forever: Sandia, Harvard team create first quantum computer bridge

By forcefully embedding two silicon atoms in a diamond matrix, Sandia researchers have demonstrated for the first time on a single chip all the components needed to create a quantum bridge to link quantum computers together.

"People have already built small quantum computers," says Sandia researcher Ryan Camacho. "Maybe the first useful one won't be a single giant quantum computer...

All Focus news of the innovation-report >>>



Event News

#IC2S2: When Social Science meets Computer Science - GESIS will host the IC2S2 conference 2017

14.10.2016 | Event News

Agricultural Trade Developments and Potentials in Central Asia and the South Caucasus

14.10.2016 | Event News

World Health Summit – Day Three: A Call to Action

12.10.2016 | Event News

Latest News

VDI presents International Bionic Award of the Schauenburg Foundation

26.10.2016 | Awards Funding

3-D-printed magnets

26.10.2016 | Power and Electrical Engineering

Advanced analysis of brain structure shape may track progression to Alzheimer's disease

26.10.2016 | Health and Medicine

More VideoLinks >>>