Comparative genomics of pathogenic Escherichia coli - Escherichia coli: Pathotypes and Principles of Pathogenesis - page 20

pathovars demonstrated that few pathovar-specific genes were identified. It was
hypothesized that the low level of conservation was in part due to the strain
selection bias that attempted to include as broad a collection of isolates as pos-
sible. These early studies highlighted the diversity in the species and pathovars.
In 2009, Touchon et al. published a paper that performed a pan-genome anal-
ysis on a larger number of sequenced genomes ( n = 20) ( Touchon et al., 2009 ).
The analysis demonstrated that the number of core genes in E. coli remained
around 2000. The analysis demonstrated the size variability in the E. coli chro-
mosome, from 4.6-5.3 Mb, and the variability in plasmid content between iso-
lates. Variation in the pan-genome conserved core between these two studies
could be attributed to using different bioinformatic methodologies, as well as
defining the term 'core pan-genome' differently. While these variations in the
absolute numbers are small, both studies highlight the fact that approximately
only half of the E. coli genome is highly conserved in all isolates examined.
At the time these studies were published this was an interesting finding that
impacted the definition of species.
To date approximately 60 E. coli/Shigella genomes have been completed
( Table 2.1 ) with representatives from each of the pathovars. Recent advances

TABLE 2.1 Complete E. coli/Shigella genomes

Genome
size (Mb)

Year
completed Species/strain name Pathovar

Escherichia coli CFT073 UPEC 5.23 2002

Escherichia coli 536 UPEC 4.94 2006

Escherichia coli UTI89 UPEC 5.18 2006

Escherichia coli IAI39 UPEC 5.13 2009

Escherichia coli UMN026 UPEC 5.36 2009

Escherichia coli NA114 UPEC 4.97 2011

Escherichia coli str. clone D UPEC 5.04 2011

Escherichia coli S88 ExPEC - Meningitis 5.17 2009

Escherichia coli IHE3034 ExPEC - Meningitis 5.11 2010

Escherichia coli O7:K1 str. CE10 ExPEC - Meningitis 5.38 2011

Escherichia coli HS Commensal 4.64 2008

Escherichia coli strain SE11 Commensal 5.16 2008

Escherichia coli ED1a Commensal 5.21 2009

Escherichia coli IAI1 Commensal 4.7 2009