Scientists Sequence Largest Bacterial Genome Yet, And Open Door To Development Of New Antibiotics

A team of researchers at the University of Washington (UW) Genome Center and PathoGenesis Corporation, funded by the Cystic Fibrosis Foundation and PathoGenesis, collaborated to complete the genome sequence of P. aeruginosa. This bacterium is the most common source of chronic and fatal lung infections for those with CF, and also poses danger to burn and cancer patients and persons on respirators or those requiring catheters.

"This map of the genome provides scientists with a powerful tool that opens up new doors to develop innovative therapies that will make a difference in many lives," said Robert J. Beall, Ph.D., president and CEO of the Cystic Fibrosis Foundation. "In fact, researchers are already using knowledge about the genetic instructions of pseudomonas to identify targets for novel drug strategies."

P. aeruginosa causes chronic lung infections and lung damage, leading to lung failure in people with CF. The bacterium has a remarkable capacity to adapt to different environments and live even when nutrients are very limited. In CF lungs, P. aeruginosa develops a protective outer layer that shields it from antibiotics and the body's natural defenses.

Maynard V. Olson, Ph.D., lead scientist on the Nature study, who directs the UW Genome Center, explains. "We will now take the gene sequencing data and attempt to define the molecular mechanisms of infection for P. aeruginosa. We want to see which genes are needed for survival in its human host and which are needed for drug resistance."

P. aeruginosa is the largest of the 25 bacteria that scientists have sequenced so far. The largest previously sequenced bacterium was Escherichia coli (E. coli), which has 4.6 million base pairs and approximately 4,200 genes. P. aeruginosa, by contrast, has more than six million base pairs and approximately 5,500 genes. Preliminary work suggests that the high number of genes in P. aeruginosa allow it to adapt and survive in many different environments, whereas most bacteria live within a small niche. Indoor plumbing, in particular, is especially hospitable to P. aeruginosa. Typical disinfectants are not effective at eradicating it so P. aeruginosa can be found on nearly every shower curtain and drain pipe around the world.

"We have identified functions of P. aeruginosa that were previously unknown, suggesting new avenues for drugs to treat serious lung infections caused by this bacterium," said C. Kendall Stover, Ph.D., who led the research team which analyzed the genome at PathoGenesis. "For example, we now have a better understanding of why P. aeruginosa is naturally resistant to most antibiotics. As a result, we have new ideas on how to identify antibiotics that might circumvent some of the bacterium's intrinsic drug resistance mechanisms."

The UW Genome Center sequenced the bacterium based on one particular P. aeruginosa organism, or isolate, that is the standard in laboratories. The center is now examining variations that occur when the organism is taken from patients in the Cystic Fibrosis Foundation's Clinical Care Center at Children's Regional Hospital and Medical Center in Seattle. The scientists are looking for not only how P. aeruginosa differs from patient to patient, but also what happens to the organism inside the body.

"We want to figure out what is different about clinical isolates, and how these isolates change over time during chronic infection," Olson continued. With this information in hand, new windows of opportunity may arise, suggesting that certain biochemical pathways or proteins within P. aeruginosa are good targets for drug development. P. aeruginosa is difficult to overcome with antibiotics even in patients with new infections. Over time, treatment becomes progressively more difficult; this is not unique to P. aeruginosa. Therefore, results from studies in this organism may shed light on how other bacteria eventually acquire or develop antibiotic resistance.

Olson sees this genome-analysis project as already serving as a paradigm for similar work. "There are a lot of laboratories out there studying every aspect of pseudomonas biology," Olson said. "A genome sequence provides a way of organizing the known information about an organism and relating what you are doing to other relevant work in the same organism or even other organisms that are quite different."

The completion of the sequencing project represents a new level of collaboration between academia, industry and a non-profit voluntary health organization to move the science ahead at maximum speed. An unusual strategy to accelerate the project involved the scientific team posting the genetic data on the Internet, making the information available to the research community at large.

"A hallmark of CF research continues to be the sharing of data by researchers driven to move the field ahead quickly - and stop a fatal genetic disease," said Beall.

An innovative program designed to move science ahead quickly for the benefit of CF patients, has been funded by the Cystic Fibrosis Foundation, in cooperation with Affymetrix Corporation. The program will make DNA microarrays containing the P. aeruginosa genome widely available to researchers at a substantially reduced cost in the near future. By providing this resource to researchers, the Cystic Fibrosis Foundation wants to enable scientists to use new tools to discover novel targets for new drug strategies.

In addition, a contract was just awarded by Cystic Fibrosis Foundation Therapeutics, Inc, an affiliate of the Cystic Fibrosis Foundation, to the University of North Carolina at Chapel Hill School of Medicine. This contract, in cooperation with Informax, Inc. establishes the first comprehensive bioinformatics center for CF researchers. The center will be a key resource in exchanging data so that new CF therapeutics can be developed as efficiently as possible.

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Contacts:
Carolyn Habbersett
Cystic Fibrosis Foundation
(301) 951-4422

Walter Neary
University of Washington
(206) 685-3841

Maryellen Thielen
PathoGenesis Corporation
(847) 583-5424

Authors of the paper include Maynard V. Olson, Ph.D and C. Kendall Stover, Ph.D. as well as L. L. Brody, S. N. Coulter, A. L. Erwin, K. R. Folger, R. L. Garber, L. Goltry, M. J. Hickey, W. O. Hufnagle, D. J. Kowalik, M. Lagrou, S. D. Mizoguchi, E. Tolentino, P. Warrener, S. Westbrock-Wadman, and Y. Yuan, from PathoGenesis Corporation; A. Kas, R. Lim, X. Q. Pham, K. Smith, D. Spencer, and G. K.-S. Wong, Z. Wu from the University of Washington Genome Center; F. S. L. Brinkman and R. E. W. Hancock from the University of British Columbia and I. T. Paulsen, J. Reizer, and M. H. Saier from the University of California at San Diego.

The P. aeruginosa Genome Project was launched in 1997. Its Web site, at http://www.pseudomonas.com, posts the genomic information on the Internet for scientists to access free of charge. A tremendous number of laboratories have accessed the information.

Cystic fibrosis (CF) is a complex, genetic disease that affects about 30,000 children and adults in the United States. Despite the increasing lifespan for individuals with CF, now more than 32 years, CF remains fatal. CF is caused by a defective gene that causes the body to produce an abnormally thick, sticky mucus which clogs the airways, leading to fatal lung infections.

The mission of the Cystic Fibrosis Foundation is to assure the development of the means to cure and control cystic fibrosis and to improve the quality of life for those with the disease. For more information on cystic fibrosis, call (800) FIGHT CF or visit http://www.cff.org. The Cystic Fibrosis Foundation provided more than $1 million to the P. aeruginosa Genome Project.

The University of Washington Genome Center, Seattle, is internationally recognized for its large-scale production of genome mapping and sequencing data. (http://www.genome.washington.edu)

Seattle-based PathoGenesis Corporation develops and commercializes drugs to treat chronic infectious diseases - particularly serious lung infections, including those common in cystic fibrosis, bronchiectasis and ventilator patients. The company's first drug was approved for the management of cystic fibrosis patients with P. aeruginosa lung infections (http://www.pathogenesis.com). The title of the Nature paper is, "Complete Genome Sequence of P. aeruginosa PA01, an Opportunistic Pathogen."