This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Spencer, D. H.
Right arrow Articles by Olson, M. V.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Spencer, D. H.
Right arrow Articles by Olson, M. V.

 Previous Article  |  Next Article 

Journal of Bacteriology, February 2003, p. 1316-1325, Vol. 185, No. 4
0021-9193/03/$08.00+0     DOI: 10.1128/JB.185.4.1316-1325.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.

Whole-Genome Sequence Variation among Multiple Isolates of Pseudomonas aeruginosa

David H. Spencer,1 Arnold Kas,1 Eric E. Smith,2 Christopher K. Raymond,1* Elizabeth H. Sims,1 Michele Hastings,3 Jane L. Burns,4,5 Rajinder Kaul,1 and Maynard V. Olson1

The University of Washington Genome Center, Department of Medicine,1 Molecular and Cellular Biology Graduate Program,2 Department of Genome Sciences,3 Division of Infectious Disease, Department of Pediatrics, University of Washington,4 Children's Hospital and Regional Medical Center, Seattle, Washington5

Received 24 June 2002/ Accepted 19 November 2002

Whole-genome shotgun sequencing was used to study the sequence variation of three Pseudomonas aeruginosa isolates, two from clonal infections of cystic fibrosis patients and one from an aquatic environment, relative to the genomic sequence of reference strain PAO1. The majority of the PAO1 genome is represented in these strains; however, at least three prominent islands of PAO1-specific sequence are apparent. Conversely, ~10% of the sequencing reads derived from each isolate fail to align with the PAO1 backbone. While average sequence variation among all strains is roughly 0.5%, regions of pronounced differences were evident in whole-genome scans of nucleotide diversity. We analyzed two such divergent loci, the pyoverdine and O-antigen biosynthesis regions, by complete resequencing. A thorough analysis of isolates collected over time from one of the cystic fibrosis patients revealed independent mutations resulting in the loss of O-antigen synthesis alternating with a mucoid phenotype. Overall, we conclude that most of the PAO1 genome represents a core P. aeruginosa backbone sequence while the strains addressed in this study possess additional genetic material that accounts for at least 10% of their genomes. Approximately half of these additional sequences are novel.

* Corresponding author. Mailing address: The University of Washington Genome Center, Box 352145, University of Washington, Seattle, WA 98195. Phone: (206) 221-6954. Fax: (206) 685-7344. E-mail: craymond{at}u.washington.edu.

Journal of Bacteriology, February 2003, p. 1316-1325, Vol. 185, No. 4
0021-9193/03/$08.00+0     DOI: 10.1128/JB.185.4.1316-1325.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Parks, Q. M., Young, R. L., Poch, K. R., Malcolm, K. C., Vasil, M. L., Nick, J. A. (2009). Neutrophil enhancement of Pseudomonas aeruginosa biofilm development: human F-actin and DNA as targets for therapy. J Med Microbiol 58: 492-502 [Abstract] [Full Text]  
  • Winstanley, C., Langille, M. G.I., Fothergill, J. L., Kukavica-Ibrulj, I., Paradis-Bleau, C., Sanschagrin, F., Thomson, N. R., Winsor, G. L., Quail, M. A., Lennard, N., Bignell, A., Clarke, L., Seeger, K., Saunders, D., Harris, D., Parkhill, J., Hancock, R. E.W., Brinkman, F. S.L., Levesque, R. C. (2009). Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa. Genome Res 19: 12-23 [Abstract] [Full Text]  
  • Khan, N. H., Ahsan, M., Yoshizawa, S., Hosoya, S., Yokota, A., Kogure, K. (2008). Multilocus Sequence Typing and Phylogenetic Analyses of Pseudomonas aeruginosa Isolates from the Ocean. Appl. Environ. Microbiol. 74: 6194-6205 [Abstract] [Full Text]  
  • Upritchard, H. G., Cordwell, S. J., Lamont, I. L. (2008). Immunoproteomics To Examine Cystic Fibrosis Host Interactions with Extracellular Pseudomonas aeruginosa Proteins. Infect. Immun. 76: 4624-4632 [Abstract] [Full Text]  
  • Kukavica-Ibrulj, I., Bragonzi, A., Paroni, M., Winstanley, C., Sanschagrin, F., O'Toole, G. A., Levesque, R. C. (2008). In Vivo Growth of Pseudomonas aeruginosa Strains PAO1 and PA14 and the Hypervirulent Strain LESB58 in a Rat Model of Chronic Lung Infection. J. Bacteriol. 190: 2804-2813 [Abstract] [Full Text]  
  • Yang, L., Haagensen, J. A. J., Jelsbak, L., Johansen, H. K., Sternberg, C., Hoiby, N., Molin, S. (2008). In Situ Growth Rates and Biofilm Development of Pseudomonas aeruginosa Populations in Chronic Lung Infections. J. Bacteriol. 190: 2767-2776 [Abstract] [Full Text]  
  • Tralau, T., Vuilleumier, S., Thibault, C., Campbell, B. J., Hart, C. A., Kertesz, M. A. (2007). Transcriptomic Analysis of the Sulfate Starvation Response of Pseudomonas aeruginosa. J. Bacteriol. 189: 6743-6750 [Abstract] [Full Text]  
  • Ou, H.-Y., He, X., Harrison, E. M., Kulasekara, B. R., Thani, A. B., Kadioglu, A., Lory, S., Hinton, J. C. D., Barer, M. R., Deng, Z., Rajakumar, K. (2007). MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands. Nucleic Acids Res 35: W97-W104 [Abstract] [Full Text]  
  • Wiehlmann, L., Wagner, G., Cramer, N., Siebert, B., Gudowius, P., Morales, G., Kohler, T., van Delden, C., Weinel, C., Slickers, P., Tummler, B. (2007). Population structure of Pseudomonas aeruginosa. Proc. Natl. Acad. Sci. USA 104: 8101-8106 [Abstract] [Full Text]  
  • Earl, A. M., Losick, R., Kolter, R. (2007). Bacillus subtilis Genome Diversity. J. Bacteriol. 189: 1163-1170 [Abstract] [Full Text]  
  • Bragonzi, A., Wiehlmann, L., Klockgether, J., Cramer, N., Worlitzsch, D., Doring, G., Tummler, B. (2006). Sequence diversity of the mucABD locus in Pseudomonas aeruginosa isolates from patients with cystic fibrosis.. Microbiology 152: 3261-3269 [Abstract] [Full Text]  
  • Shen, K., Sayeed, S., Antalis, P., Gladitz, J., Ahmed, A., Dice, B., Janto, B., Dopico, R., Keefe, R., Hayes, J., Johnson, S., Yu, S., Ehrlich, N., Jocz, J., Kropp, L., Wong, R., Wadowsky, R. M., Slifkin, M., Preston, R. A., Erdos, G., Post, J. C., Ehrlich, G. D., Hu, F. Z. (2006). Extensive Genomic Plasticity in Pseudomonas aeruginosa Revealed by Identification and Distribution Studies of Novel Genes among Clinical Isolates. Infect. Immun. 74: 5272-5283 [Abstract] [Full Text]  
  • Smart, C. H. M., Walshaw, M. J., Hart, C. A., Winstanley, C. (2006). Use of suppression subtractive hybridization to examine the accessory genome of the Liverpool cystic fibrosis epidemic strain of Pseudomonas aeruginosa. J Med Microbiol 55: 677-688 [Abstract] [Full Text]  
  • Smith, E. E., Buckley, D. G., Wu, Z., Saenphimmachak, C., Hoffman, L. R., D'Argenio, D. A., Miller, S. I., Ramsey, B. W., Speert, D. P., Moskowitz, S. M., Burns, J. L., Kaul, R., Olson, M. V. (2006). From the Cover: Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients. Proc. Natl. Acad. Sci. USA 103: 8487-8492 [Abstract] [Full Text]  
  • Lamont, I. L., Martin, L. W., Sims, T., Scott, A., Wallace, M. (2006). Characterization of a Gene Encoding an Acetylase Required for Pyoverdine Synthesis in Pseudomonas aeruginosa.. J. Bacteriol. 188: 3149-3152 [Abstract] [Full Text]  
  • Silo-Suh, L., Suh, S.-J., Phibbs, P. V., Ohman, D. E. (2005). Adaptations of Pseudomonas aeruginosa to the Cystic Fibrosis Lung Environment Can Include Deregulation of zwf, Encoding Glucose-6-Phosphate Dehydrogenase. J. Bacteriol. 187: 7561-7568 [Abstract] [Full Text]  
  • Walker, T. S., Tomlin, K. L., Worthen, G. S., Poch, K. R., Lieber, J. G., Saavedra, M. T., Fessler, M. B., Malcolm, K. C., Vasil, M. L., Nick, J. A. (2005). Enhanced Pseudomonas aeruginosa Biofilm Development Mediated by Human Neutrophils. Infect. Immun. 73: 3693-3701 [Abstract] [Full Text]  
  • Winstanley, C., Kaye, S. B, Neal, T. J, Chilton, H. J, Miksch, S., Hart, C A., and the Microbiology Ophthalmic Group, (2005). Genotypic and phenotypic characteristics of Pseudomonas aeruginosa isolates associated with ulcerative keratitis. J Med Microbiol 54: 519-526 [Abstract] [Full Text]  
  • Sadikot, R. T., Blackwell, T. S., Christman, J. W., Prince, A. S. (2005). Pathogen-Host Interactions in Pseudomonas aeruginosa Pneumonia. Am. J. Respir. Crit. Care Med. 171: 1209-1223 [Abstract] [Full Text]  
  • Tummler, B., Cornelis, P. (2005). Pyoverdine Receptor: a Case of Positive Darwinian Selection in Pseudomonas aeruginosa. J. Bacteriol. 187: 3289-3292 [Full Text]  
  • Smith, E. E., Sims, E. H., Spencer, D. H., Kaul, R., Olson, M. V. (2005). Evidence for Diversifying Selection at the Pyoverdine Locus of Pseudomonas aeruginosa. J. Bacteriol. 187: 2138-2147 [Abstract] [Full Text]  
  • Mohd-Zain, Z., Turner, S. L., Cerdeno-Tarraga, A. M., Lilley, A. K., Inzana, T. J., Duncan, A. J., Harding, R. M., Hood, D. W., Peto, T. E., Crook, D. W. (2004). Transferable Antibiotic Resistance Elements in Haemophilus influenzae Share a Common Evolutionary Origin with a Diverse Family of Syntenic Genomic Islands. J. Bacteriol. 186: 8114-8122 [Abstract] [Full Text]  
  • Curran, B., Jonas, D., Grundmann, H., Pitt, T., Dowson, C. G. (2004). Development of a Multilocus Sequence Typing Scheme for the Opportunistic Pathogen Pseudomonas aeruginosa. J. Clin. Microbiol. 42: 5644-5649 [Abstract] [Full Text]  
  • Finnan, S., Morrissey, J. P., O'Gara, F., Boyd, E. F. (2004). Genome Diversity of Pseudomonas aeruginosa Isolates from Cystic Fibrosis Patients and the Hospital Environment. J. Clin. Microbiol. 42: 5783-5792 [Abstract] [Full Text]  
  • Morales, G., Wiehlmann, L., Gudowius, P., van Delden, C., Tummler, B., Martinez, J. L., Rojo, F. (2004). Structure of Pseudomonas aeruginosa Populations Analyzed by Single Nucleotide Polymorphism and Pulsed-Field Gel Electrophoresis Genotyping. J. Bacteriol. 186: 4228-4237 [Abstract] [Full Text]  
  • Ghysels, B., Dieu, B. T. M., Beatson, S. A., Pirnay, J.-P., Ochsner, U. A., Vasil, M. L., Cornelis, P. (2004). FpvB, an alternative type I ferripyoverdine receptor of Pseudomonas aeruginosa. Microbiology 150: 1671-1680 [Abstract] [Full Text]  
  • Arora, S. K., Wolfgang, M. C., Lory, S., Ramphal, R. (2004). Sequence Polymorphism in the Glycosylation Island and Flagellins of Pseudomonas aeruginosa. J. Bacteriol. 186: 2115-2122 [Abstract] [Full Text]  
  • He, J., Baldini, R. L., Deziel, E., Saucier, M., Zhang, Q., Liberati, N. T., Lee, D., Urbach, J., Goodman, H. M., Rahme, L. G. (2004). The broad host range pathogen Pseudomonas aeruginosa strain PA14 carries two pathogenicity islands harboring plant and animal virulence genes. Proc. Natl. Acad. Sci. USA 101: 2530-2535 [Abstract] [Full Text]  
  • Klockgether, J., Reva, O., Larbig, K., Tummler, B. (2004). Sequence Analysis of the Mobile Genome Island pKLC102 of Pseudomonas aeruginosa C. J. Bacteriol. 186: 518-534 [Abstract] [Full Text]  
  • Head, N. E., Yu, H. (2004). Cross-Sectional Analysis of Clinical and Environmental Isolates of Pseudomonas aeruginosa: Biofilm Formation, Virulence, and Genome Diversity. Infect. Immun. 72: 133-144 [Abstract] [Full Text]  
  • Lu, S.-E., Soule, J. D., Gross, D. C. (2003). Characterization of the argA Gene Required for Arginine Biosynthesis and Syringomycin Production by Pseudomonas syringae pv. syringae. Appl. Environ. Microbiol. 69: 7273-7280 [Abstract] [Full Text]  
  • Gibson, R. L., Burns, J. L., Ramsey, B. W. (2003). Pathophysiology and Management of Pulmonary Infections in Cystic Fibrosis. Am. J. Respir. Crit. Care Med. 168: 918-951 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»