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clade, variation in virulence (
Manning et al., 2008
) has been associated with
specific clades in the clonal complex. Whole genome sequence data have
been used to not only characterize the evolution of virulence of this important
pathogen, but will help in the surveillance of this pathogen.
In addition to O157:H7 EHEC isolates, genomes have also been sequenced
from other STEC/EHEC serotypes; these genomes include those of O111:H-
strain 11128, O26:H11 strain 11368, and O103:H2 strain 12009 (
Ogura et al.,
2009
). A phylogeny of 345 orthologous coding regions demonstrated that the
non-O157 EHEC isolates are not contained on a single phylogenetic branch
(
Ogura et al., 2009
). However, a phylogenetic tree based on the entire gene rep-
ertoire demonstrated that all EHEC genomes could be grouped together, most
likely due to the presence of common secreted effectors and LEE-associated
genes (
Ogura et al., 2009
).
Other LEE-negative STEC isolates have also been associated with severe
diarrheal symptoms and HUS (
Johnson et al., 2006
;
Newton et al., 2009
;
Rasko
et al., 2011
). Recently nine LEE-negative STEC isolates were sequenced and
comparative analysis demonstrates the extreme phylogenetic diversity of this
group (
Steyert et al., 2012
). This study of LEE-negative STEC has revealed
that these isolates are even less similar than the LEE-positive STEC, suggesting
a diverse evolutionary history. One would expect this finding considering the
typing schema is based on a mobile element that can insert into most
E. coli
genomes. Additional detailed comparative analysis demonstrated the diversity
of secreted effectors and
stx
insertion sites in the group. The major finding in
the study was that the Shiga-toxin phage and the genomic backbone are not
intimately linked, but some features of the phage define the location of insertion
(
Steyert et al., 2012
).
The genomic examination of STEC and EHEC isolates highlights the juxta-
position of the current typing schema; while the virulence factors are important
for the clinical treatment and identification of pathogens, these features do not
always concur with the phylogenetic relationships of the isolates. The advent
of the new sequencing technologies will allow rapid identification of whole
genome sequencing into the clinical paradigm and then it will be possible to
characterize isolates by their genomic content, and not phenotypic presentation;
problems of associating phenotype with gene content may be avoided.
ENTEROPATHOGENIC
E. COLI
(EPEC)
Enteropathogenic
E. coli
(EPEC) are traditionally classified by the presence of
the LEE and the absence of
stx
genes encoding Shiga toxins (
Kaper, 1996
). As
with EHEC, there are subclassifications within EPEC based on virulence factor
presence and absence. Isolates that contain the LEE region and the EPEC adher-
ence factor (EAF) plasmid (
Kaper et al., 2004
) encoding genes for a bundle
forming pilus (BFP) (
Giron et al., 1991
) are frequently termed typical EPEC
(tEPEC), while LEE-positive, BFP-negative isolates are classified as atypical
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