Comparative genomic indexing reveals the phylogenomics of Escherichia coli pathogens

Abstract

The Escherichia coli O26 serogroup includes important food-borne pathogens associated with human and animal diarrheal disease. Current typing methods have revealed great genetic heterogeneity within the O26 group; the data are often inconsistent and focus only on verotoxin (VT)-positive O26 isolates. To improve current understanding of diversity within this serogroup, the genomic relatedness of VT-positive and -negative O26 strains was assessed by comparative genomic indexing. Our results clearly demonstrate that irrespective of virulence characteristics and pathotype designation, the O26 strains show greater genomic similarity to each other than to any other strain included in this study. Our data suggest that enteropathogenic and VT-expressing E. coli O26 strains represent the same clonal lineage and that VT-expressing E. coli O26 strains have gained additional virulence characteristics. Using this approach, we established the core genes which are central to the E. coli species and identified regions of variation from the E. coli K-12 chromosomal backbone.

FIG. 1.

Validation of CGI approach by identification of known deletions. The ln(normalized intensity ratio) at 635 nm versus 532 nm from microarray hybridization is shown for each CDS of three E. coli K-12 control strains against MG1655. The strains were (a) MG1655, (b) GC4468, and (c) KL773.

FIG. 2.

Genomic index of 26 pathogenic E. coli strains. An average linkage hierarchical clustering of the E. coli strains was compiled in GeneSpring version 5.0 from CGI data with the Pearson coefficient correlation. CDS present (ln[red/green] = 1) are shown in blue, absent CDS (ln [red/green] ≥ 2) are shown in red, and CDS with ln(red/green) between 1.5 and 2.0 are shown in yellow. Strains of the O26 serotype are labeled in red; other strains in the EPEC cluster are labeled in green, O157 strains are labeled in blue, and O86 strains are labeled in orange. The scale for distance score (ds) is also shown.