July 6, 2011

Pacific Biosciences Contributes Whole Genome Sequence Data for German E. Coli Outbreak Strain and 11 Related Strains for Comparative Analysis

Improved Chemistry and Software Provides Higher Accuracy Single

Molecule Reads and Longer Readlengths to Yield PacBio-only De Novo



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.

While not involved with the current E. Coli study, the Broad

Institute has been testing the new version of the sequencing enzyme in

development as part of Pacific Biosciences’ early access program. “We

are seeing significant increases in readlength, with high quality runs

producing reads with average 2,000 base readlengths or more,” said Chad

Nusbaum, co-director of the Genome Sequencing and Analysis program at

the Broad Institute. “The potential for even greater readlengths and the

possibility to trade off readlength to increase accuracy will be

important for bringing the PacBio RS to an increasing application

space. We have been impressed with the rapid progress PacBio has made in

improving their technology in a relatively short amount of time.”

Hugh Martin, Chairman and CEO of Pacific Biosciences stated: “Since this

collaboration employed an early version of our chemistry and software in

development for the next major upgrade of our product, we are taking

this opportunity to share some of the specifications that we expect to

reach for that planned Q4 upgrade. As demonstrated by the E. coli

project, we are already seeing a big step up from the specifications for

the first commercial release in April, and we expect to achieve even

more significant performance increases.” While not yet fully optimized,

the specifications are based on flexible parameters with the capability

to produce:

  • An average of 2,700 base pair reads, with 5% of the reads achieving

    5,100+ base pairs

  • Up to 90 megabases of mappable data per SMRT Cell

  • 1,350 base pair reads with 2X circular consensus sequencing single

    molecule accuracy of 93%

For more information about Pacific Biosciences, please visit

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About Pacific Biosciences

Pacific Biosciences’ mission is to transform the way humankind acquires,

processes and interprets data from living systems through the design,

development and commercialization of innovative tools for biological

research. The company has developed a novel approach to studying the

synthesis and regulation of DNA, RNA and proteins. Combining recent

advances in nanofabrication, biochemistry, molecular biology, surface

chemistry and optics, Pacific Biosciences has created a powerful

technology platform called single molecule, real-time, or SMRT™,

technology. SMRT technology enables real-time analysis of biomolecules

with single molecule resolution, which has the potential to transform

the understanding of biological systems by providing a window into these

systems that has not previously been open for scientific study.

Forward-Looking Statements

This press release contains forward-looking statements. Forward-looking

statements may contain words such as “believe,” “may,” “estimate,”

“anticipate,” “continue,” “intend,” “expect,” “plan,” the negative of

these terms, or other similar expressions, and include the assumptions

that underlie such statements. Such statements include, but are not

limited to, statements regarding the Company’s SMRT technology. These

statements are subject to known and unknown risks and uncertainties that

could cause actual results to differ materially from those expressed or

implied by such statements, including but not limited to risks discussed

from time to time in documents Pacific Biosciences of California, Inc.

has filed with the Securities and Exchange Commission, including the

risks identified under the section captioned “Risk Factors” in its

recently filed Quarterly Report on Form 10-Q. All forward-looking

statements are based on estimates, projections and assumptions as of the

date hereof. Pacific Biosciences undertakes no obligation to update any

forward-looking statements.

For Pacific BiosciencesNicole

Litchfield, 415-793-6468

BiosciencesTrevin Rard, 650-521-8450

Source: Pacific Biosciences

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