Comparative genomics of pathogenic Escherichia coli - Escherichia coli: Pathotypes and Principles of Pathogenesis - page 30

based on a PCR screen analysis, BFP-positive and BFP-negative isolates would
be classified as tEPEC or aEPEC, respectively, despite potentially sharing a
closely related common ancestor. To incorporate phylogenetic information into
a clinical assay, comparative genomics were used to identify genomic markers
that distinguish between the different lineages of EPEC. A multiplex PCR reac-
tion was designed to detect classical virulence factors as well as phylogenetic
markers ( Hazen et al., 2012 ). This methodology will define a new paradigm in
which whole genome sequence data focuses better diagnostics to understand
both virulence profiles and phylogenetic history.
ENTEROTOXIGENIC E. COLI (ETEC)
Enterotoxigenic E. coli is a diverse pathovar ( Shaheen et al., 2003 ) character-
ized by the presence of a heat-labile (LT) and/or heat-stable (ST) enterotoxin
(see Chapter 6) ( So et al., 1976, 1978 ). ETEC is responsible for approximately
300 000 to 500 000 deaths annually, primarily in children in the developing
world ( WHO, 2006 ). In addition to the enterotoxins, ETEC possess plasmid-
encoded fimbrial appendages known as colonization factors (CFs) ( Gaastra and
Svennerholm, 1996 ); ETEC CFs are structurally diverse, with greater than 30
known structural CF proteins described ( Nada et al., 2011 ).
The first two ETEC genomes, E24377A and B7A, were sequenced in 2008
as part of an E. coli pan-genome analysis ( Rasko et al., 2008 ). Comparative
genome analysis of the completed genome of E. coli E24377A demonstrated
that the isolate contained six plasmids, several of which encoded known ETEC
virulence factors. The analysis also identified a limited number of features that
appeared to be unique to ETEC ( n = 9). Both of the ETEC genomes grouped
into the B1 phylogroup, however it is known that ETEC isolates occupy greater
phylogenetic space than just the B1 group.
The prototypical ETEC isolate is H10407 , which was sequenced in 2010
( Crossman et al., 2010 ). The authors concluded that H10407 , which falls within
E. coli phylogroup A, was a commensal isolate that acquired virulence plasmids
to become a human pathogen. Many of the virulence genes ( cexE , tibA , tia )
broadly associated with ETEC were identified in H10407 . However, compara-
tive studies have suggested that several of these virulence genes are not broadly
distributed across diverse ETEC isolates and thus will not make acceptable vac-
cine or therapeutic targets ( Turner et al., 2006 ). A recent transcriptomics analy-
sis demonstrated that the transcriptional response of ETEC isolates E24377A
and H10407 differed significantly in the presence of chemical signals, such as
glucose and bile salts ( Sahl and Rasko, 2012 ). This result demonstrates that
the use of a single prototypical isolate is insufficient at describing either the
genomic diversity or the pathogenesis of a pathovar.
As part of a large study, the multilocus sequence typing (MLST) profiles
were identified from 1019 ETEC isolates ( Steinsland et al., 2010 ). From this
analysis, five isolates from the most dominant sequence types were sequenced