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Published online on December 5, 2002, 10.1073/pnas.252529799
PNAS | December 24, 2002 | vol. 99 | no. 26 | 17020-17024


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Microbiology
Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli

R. A. Welch *, V. Burland {dagger} {ddagger}, G. Plunkett, III {dagger}, P. Redford *, P. Roesch *, D. Rasko §, E. L. Buckles ¶, S.-R. Liou {dagger} ||, A. Boutin {dagger} **, J. Hackett {dagger} {dagger}{dagger}, D. Stroud {dagger}, G. F. Mayhew {dagger}, D. J. Rose {dagger}, S. Zhou {dagger}, {ddagger}{ddagger}, D. C. Schwartz {dagger}, {ddagger}{ddagger}, N. T. Perna §§, H. L. T. Mobley §, M. S. Donnenberg ¶, and F. R. Blattner {dagger}

*Department of Medical Microbiology and Immunology,{dagger} Laboratory of Genetics, {ddagger}{ddagger}Genome Center of Wisconsin, and §§Animal Health and Biological Sciences, University of Wisconsin, Madison, WI 53706; and§ Department of Microbiology and Immunology, Division of Infectious Diseases, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201

Edited by John J. Mekalanos, Harvard Medical School, Boston, MA, and approved October 24, 2002 (received for review August 30, 2002)

We present the complete genome sequence of uropathogenic Escherichia coli, strain CFT073. A three-way genome comparison of the CFT073, enterohemorrhagic E. coli EDL933, and laboratory strain MG1655 reveals that, amazingly, only 39.2% of their combined (nonredundant) set of proteins actually are common to all three strains. The pathogen genomes are as different from each other as each pathogen is from the benign strain. The difference in disease potential between O157:H7 and CFT073 is reflected in the absence of genes for type III secretion system or phage- and plasmid-encoded toxins found in some classes of diarrheagenic E. coli. The CFT073 genome is particularly rich in genes that encode potential fimbrial adhesins, autotransporters, iron-sequestration systems, and phase-switch recombinases. Striking differences exist between the large pathogenicity islands of CFT073 and two other well-studied uropathogenic E. coli strains, J96 and 536. Comparisons indicate that extraintestinal pathogenic E. coli arose independently from multiple clonal lineages. The different E. coli pathotypes have maintained a remarkable synteny of common, vertically evolved genes, whereas many islands interrupting this common backbone have been acquired by different horizontal transfer events in each strain.


{ddagger} To whom correspondence should be addressed at: Laboratory of Genetics, University of Wisconsin, 445 Henry Mall, Madison, WI 53706. E-mail: val{at}genome.wisc.edu.

|| Present address: Department of Ecology and Evolution, State University of New York, Stony Brook, NY 11794.

** Present address: Department of Biology, University of California at San Diego, La Jolla, CA 92093.

{dagger}{dagger} Present address: Department of Biology, University of Iowa, Iowa City, IA 52242.

This paper was submitted directly (Track II) to the PNAS office.

Data deposition: The sequence reported in this paper has been deposited in the GenBank database (accession no. AE014075).


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