In silico genomic analyses reveal three distinct lineages of Escherichia coli O157:H7, one of which is associated with hyper-virulence
Date
2009-06-29
Authors
Laing, Chad R.
Buchanan, Cody
Taboada, Eduardo N.
Zhang, Yongxiang
Karmali, Mohamed A.
Thomas, James E.
Gannon, Victor P.J.
Journal Title
Journal ISSN
Volume Title
Publisher
BioMed Central
Abstract
Background: Many approaches have been used to study the evolution, population structure and
genetic diversity of Escherichia coli O157:H7; however, observations made with different genotyping
systems are not easily relatable to each other. Three genetic lineages of E. coli O157:H7 designated
I, II and I/II have been identified using octamer-based genome scanning and microarray comparative
genomic hybridization (mCGH). Each lineage contains significant phenotypic differences, with
lineage I strains being the most commonly associated with human infections. Similarly, a clade of
hyper-virulent O157:H7 strains implicated in the 2006 spinach and lettuce outbreaks has been
defined using single-nucleotide polymorphism (SNP) typing. In this study an in silico comparison of
six different genotyping approaches was performed on 19 E. coli genome sequences from 17
O157:H7 strains and single O145:NM and K12 MG1655 strains to provide an overall picture of
diversity of the E. coli O157:H7 population, and to compare genotyping methods for O157:H7
strains.
Results: In silico determination of lineage, Shiga-toxin bacteriophage integration site, comparative
genomic fingerprint, mCGH profile, novel region distribution profile, SNP type and multi-locus
variable number tandem repeat analysis type was performed and a supernetwork based on the
combination of these methods was produced. This supernetwork showed three distinct clusters of
strains that were O157:H7 lineage-specific, with the SNP-based hyper-virulent clade 8 synonymous
with O157:H7 lineage I/II. Lineage I/II/clade 8 strains clustered closest on the supernetwork to E.
coli K12 and E. coli O55:H7, O145:NM and sorbitol-fermenting O157 strains.
Conclusion: The results of this study highlight the similarities in relationships derived from multilocus
genome sampling methods and suggest a "common genotyping language" may be devised for
population genetics and epidemiological studies. Future genotyping methods should provide data
that can be stored centrally and accessed locally in an easily transferable, informative and extensible
format based on comparative genomic analyses.
Description
BioMed Central
Keywords
Citation
Laing et al. In silico genomic analyses reveal three distinct lineages of Escherichia coli O157:H7, one of which is associated with hyper-virulence. BMC Genomics 2009 10:287