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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.



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