The pangenome structure of Escherichia coli: Comparative genomic analysis of E. coli commensal and pathogenic isolates

Rasko, DA; Rosovitz, MJ; Myers, GSA; Mongodin, EF; Fricke, WF; Gajer, P; Crabtree, J; Sebaihia, M; Thomson, NR; Chaudhuri, R; Henderson, IR; Sperandio, V; Ravel, J

The pangenome structure of Escherichia coli: Comparative genomic analysis of E. coli commensal and pathogenic isolates

Rasko, DA Rosovitz, MJ Myers, GSA

Mongodin, EF Fricke, WF Gajer, P Crabtree, J Sebaihia, M Thomson, NR Chaudhuri, R Henderson, IR Sperandio, V Ravel, J

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Publication Type:: Journal Article
Citation:: Journal of Bacteriology, 2008, 190 (20), pp. 6881 - 6893
Issue Date:: 2008-10-01

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Field	Value	Language
dc.contributor.author	Rasko, DA	en_US
dc.contributor.author	Rosovitz, MJ	en_US
dc.contributor.author	Myers, GSA https://orcid.org/0000-0002-4756-4810	en_US
dc.contributor.author	Mongodin, EF	en_US
dc.contributor.author	Fricke, WF	en_US
dc.contributor.author	Gajer, P	en_US
dc.contributor.author	Crabtree, J	en_US
dc.contributor.author	Sebaihia, M	en_US
dc.contributor.author	Thomson, NR	en_US
dc.contributor.author	Chaudhuri, R	en_US
dc.contributor.author	Henderson, IR	en_US
dc.contributor.author	Sperandio, V	en_US
dc.contributor.author	Ravel, J	en_US
dc.date.issued	2008-10-01	en_US
dc.identifier.citation	Journal of Bacteriology, 2008, 190 (20), pp. 6881 - 6893	en_US
dc.identifier.issn	0021-9193	en_US
dc.identifier.uri	http://hdl.handle.net/10453/39749
dc.description.abstract	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. Copyright © 2008, American Society for Microbiology. All Rights Reserved.	en_US
dc.relation.ispartof	Journal of Bacteriology	en_US
dc.relation.isbasedon	10.1128/JB.00619-08	en_US
dc.subject.classification	Microbiology	en_US
dc.subject.mesh	Animals	en_US
dc.subject.mesh	Rabbits	en_US
dc.subject.mesh	Humans	en_US
dc.subject.mesh	Escherichia coli	en_US
dc.subject.mesh	DNA, Bacterial	en_US
dc.subject.mesh	Virulence Factors	en_US
dc.subject.mesh	Computational Biology	en_US
dc.subject.mesh	Genomics	en_US
dc.subject.mesh	Conserved Sequence	en_US
dc.subject.mesh	Genes, Bacterial	en_US
dc.subject.mesh	Genome, Bacterial	en_US
dc.subject.mesh	Molecular Sequence Data	en_US
dc.subject.mesh	Adult	en_US
dc.title	The pangenome structure of Escherichia coli: Comparative genomic analysis of E. coli commensal and pathogenic isolates	en_US
dc.type	Journal Article
utslib.citation.volume	20	en_US
utslib.citation.volume	190	en_US
utslib.for	06 Biological Sciences	en_US
utslib.for	07 Agricultural and Veterinary Sciences	en_US
utslib.for	11 Medical and Health Sciences	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - ithree - Institute of Infection, Immunity and Innovation
utslib.copyright.status	closed_access
pubs.issue	20	en_US
pubs.publication-status	Published	en_US
pubs.volume	190	en_US

Abstract:

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. Copyright © 2008, American Society for Microbiology. All Rights Reserved.

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http://hdl.handle.net/10453/39749