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Pacific Biosciences DNA Sequencing Technology Yields New Insights into Virulence and Evolution of German E. coli Pathogen

Wednesday, July 27, 2011

International Team Publishes Comprehensive DNA

Analysis of Outbreak Strain and 11 Related Strains in New England

Journal of Medicine

MENLO PARK, Calif.–(BUSINESS WIRE)–

An international team of scientists has successfully employed single

molecule, real-time (SMRT™) DNA sequencing technology from Pacific

Biosciences of California, Inc. (NASDAQ:PACB) to provide valuable

insights into the pathogenicity and evolutionary origins of the highly

virulent bacterium responsible for the German E. coli outbreak.

Published online today in the New England Journal of Medicine, the

results provide the most detailed genetic profile to date of the

outbreak strain, including medically relevant information.

The researchers determined the outbreak strain was a member of the

enteroaggregative pathotype of E. coli (EAEC) with serotype

O104:H4. The outbreak isolates are distinguished from other O104:H4

strains because they contain genes encoding Shiga toxin 2 (Stx2) and a

distinct set of additional virulence and antibiotic resistance factors.

In addition, the team found that expression of the stx2 gene was

increased by certain antibiotics including ciprofloxacin, suggesting

caution should be used before using certain classes of antibiotics to

counteract this newly emerged pathogen.

By sequencing the outbreak strain and 11 related strains with the PacBio RS,

the team concluded that horizontal genetic exchange with the Shiga

toxin-producing enterohemorrhagic E. coli (EHEC) strain enabled

the emergence of the highly virulent Shiga toxin-producing O104:H4 EAEC

strain. The genetic analysis also indicates that evolution of this new

form was a relatively recent event.

The team identified many virulence factor genes commonly found in EAEC.

Furthermore, the exceptionally long sequencing reads that are

characteristic of PacBio SMRT DNA sequencing technology enabled the team

to also detect larger-scale deletions, insertions, inversions and other

structural variation between the O104:H4 outbreak samples and the other

O104:H4 EAEC samples that were sequenced. Several of these structurally

divergent regions house genes that encode virulence factors. Another

feature in which the current outbreak diverges from common EAEC isolates

is in the number and nature of SPATE proteases. Taken together, the

results provide a possible explanation for the increased virulence of

the German E. coli outbreak strain.

The authors included scientists in the U.S. and Denmark from Pacific

Biosciences, the University of Maryland School of Medicine, the

University of Virginia School of Medicine, the World Health Organization

Collaborating Centre for Reference and Research on Escherichia coli

and Klebsiella, the Statens Serum Institut, Hvidovre University

Hospital, Brigham and Women’s Hospital and Harvard Medical School.

“This multi-strain sequencing data and analysis significantly increases

the amount of scientific information available for the study of this new

deadly form of E. coli and has yielded critical insights into its

causative agent,” said co-author, David A. Rasko, Ph.D., Assistant

Professor, University of Maryland School of Medicine, Institute for

Genome Sciences and Department of Microbiology and Immunology. “Our

results provide the most complete published genome of this strain to

date and highlight the importance of DNA sequencing to understanding how

the plasticity of bacterial genomes facilitates the emergence of new

pathogens.”

Whole genome sequencing involves decoding the precise order of

nucleotide bases that make up an organism’s complete set of DNA and

provides more comprehensive information than other analysis methods such

as DNA fingerprinting or arrays. With advances in technology and

decreasing cost, whole genome sequencing is emerging as the gold

standard method for identifying and classifying infectious agents. SMRT

technology is the latest advance in DNA sequencing, capable of

generating long sequence reads to resolve structural variations and

complex genomes at ultra-fast speeds by ‘eavesdropping’ on DNA

replicating in real time.

Eric Schadt, Ph.D., Chief Scientific Officer of Pacific Biosciences and

co-author of the paper commented: “We have reached a new era in which

communities of researchers can rapidly share large-scale data sets and

analyses vital for public health. Sequencing genomes in hours, as

opposed to days or weeks, with unprecedented read lengths is the

emerging hallmark of third generation DNA sequencing. The long PacBio RS

reads enabled a PacBio-only de novo genome assembly, a key

component of new pathogen characterization, as well as deeper insights

into structural variants.”

The paper is available at www.nejm.com.

The data are available for the bioinformatics community at the PacBio

developer’s network (DevNet) web site (www.pacbiodevnet.com),

where a suite of open source tools and other resources designed for SMRT

sequence data are available to analyze the information. A summary of the

sequencing project appears on the Pacific Biosciences website at https://blog.pacificbiosciences.com.

More information about SMRT technology is available at www.pacificbiosciences.com.

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 (Media)
nicole@bioscribe.com
or
Pacific

BiosciencesTrevin Rard, 650-521-8450 (Investors)
ir@pacificbiosciences.com

Source: Pacific Biosciences

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