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Journal of Bacteriology, October 2008, p. 6881-6893, Vol. 190, No. 20
0021-9193/08/$08.00+0     doi:10.1128/JB.00619-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates{triangledown} ,{dagger}

David A. Rasko,1* M. J. Rosovitz,3,{ddagger} Garry S. A. Myers,1 Emmanuel F. Mongodin,1 W. Florian Fricke,1 Pawel Gajer,1 Jonathan Crabtree,3 Mohammed Sebaihia,4 Nicholas R. Thomson,4 Roy Chaudhuri,5 Ian R. Henderson,6 Vanessa Sperandio,2 and Jacques Ravel1

Department of Microbiology, University of Texas Southwestern Medical Center at Dallas, 6000 Harry Hines Blvd., Dallas, Texas 75235,2 J. Craig Venter Institute, 9712 Medical Center Drive, Rockville, Maryland 20850,3 The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom,4 Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, United Kingdom,5 University of Birmingham, Birmingham, B15 2TT, United Kingdom,6 Institute for Genome Sciences, Department of Microbiology & Immunology, University of Maryland School of Medicine, 20 Penn Street, Baltimore, Maryland 212011

Received 4 May 2008/ Accepted 21 July 2008

Whole-genome sequencing has been skewed toward bacterial pathogens as a consequence of the prioritization of medical and veterinary diseases. However, it is becoming clear that in order to accurately measure genetic variation within and between pathogenic groups, multiple isolates, as well as commensal species, must be sequenced. This study examined the pangenomic content of Escherichia coli. Six distinct E. coli pathovars can be distinguished using molecular or phenotypic markers, but only two of the six pathovars have been subjected to any genome sequencing previously. Thus, this report provides a seminal description of the genomic contents and unique features of three unsequenced pathovars, enterotoxigenic E. coli, enteropathogenic E. coli, and enteroaggregative E. coli. We also determined the first genome sequence of a human commensal E. coli isolate, E. coli HS, which will undoubtedly provide a new baseline from which workers can examine the evolution of pathogenic E. coli. Comparison of 17 E. coli genomes, 8 of which are new, resulted in identification of ~2,200 genes conserved in all isolates. We were also able to identify genes that were isolate and pathovar specific. Fewer pathovar-specific genes were identified than anticipated, suggesting that each isolate may have independently developed virulence capabilities. Pangenome calculations indicate that E. coli genomic diversity represents an open pangenome model containing a reservoir of more than 13,000 genes, many of which may be uncharacterized but important virulence factors. This comparative study of the species E. coli, while descriptive, should provide the basis for future functional work on this important group of pathogens.

* Corresponding author. Mailing address: Institute for Genome Sciences, Department of Microbiology & Immunology, University of Maryland School of Medicine, 20 Penn Street, HSF-II, Room 445, Baltimore, MD 21201. Phone: (410) 706-6774. Fax: (410) 706-1482

{triangledown} Published ahead of print on 1 August 2008.

{dagger} Supplemental material for this article may be found at http://jb.asm.org/.

{ddagger} Present address: Midwest Research Institute, 1330 Piccard Dr., Rockville, MD 20850.

Journal of Bacteriology, October 2008, p. 6881-6893, Vol. 190, No. 20
0021-9193/08/$08.00+0     doi:10.1128/JB.00619-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.



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