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to colonize the host without causing disease. Colonization of pathogenic coun-
terparts, on the other hand, can result in clinically significant pathologies. For
example, the recommended regular dose of probiotic MutaFlorâ„¢, purported to
promote health, contains billions of live bacteria of E. coli strain Nissle-1917,
while the ingestion of only 100 bacteria of E. coli O157 strain or even fewer
of Shigella flexneri can produce fatal disease ( Todd et al., 2008 ; Allen et al.,
2010 ). Also, the spectrum of disease caused by E. coli varies significantly, from
diarrhea to meningitis, from asymptomatic bacteriuria to lethal urosepsis. This
spectrum is caused by several main pathotypes of E. coli - enterotoxigenic
(ETEC), enteropathogenic (EPEC), enterohemorrhagic (EHEC), enteroinva-
sive (EIEC/ Shigella ), enteroaggregative (EAEC) and extraintestinal-pathogenic
(ExPEC, among which uropathogenic, UPEC, is the most common), as detailed
elsewhere in this volume.
Despite being from the same species, different strains of E. coli are also
highly diverse genetically. In fact, a given strain of E. coli shares only a minor-
ity of its genes with every other strain of the species ( Rasko et al., 2008 ). This
diversity is especially obvious from the analysis of clonally unrelated strains,
i.e. those with different genotype profile based on the multi-locus sequence
typing (MLST). MLST profile (or sequence type, ST) is defined in E. coli by
comparing sequence identity of 400-500 bp long regions of seven housekeep-
ing genes that are spread across the bacterial chromosome ( Wirth et al., 2006 ).
Here, to assess the level of clonal diversity of E. coli , we selected 22 clonally
unrelated E. coli strains, ranging from commensal to different major pathotypes
( Figure 3.1 ),with fully assembled annotated genome sequences publically avail-
able at the time of preparation of this chapter. The strains' genome size ranged
from 4116 to 5379 genes. However, based on 95% nucleotide identity and length
preservation, a total of 16 148 genes were found in it least one of the 22 strains
examined, comprising a minimal estimate of the E. coli pangenome. Out of these
genes, 8573 genes were mosaic in nature, i.e. found in multiple (but not all!)
strains that, on average, comprised 49-67% of individual genomes. Only 1996
genes were found in every strain and could be defined as core genes, which con-
stituted from 37 to 49% of the genomes of individual strains. Finally, the rest of
the genes either were found only in a single strain so far or were highly diverse
orthologs (with less than 95% sequence identity) found in two or more strains.
The nucleotide-level difference found between the clonally unrelated E. coli
was even greater. Even if only the shared genes more than 95% identical in
sequence are considered, strain-to-strain polymorphisms affect over 100 000
nucleotides (2% of all gene sequences across the genome) on average. Out of
these, about 20 000 nucleotide changes resulted in allelic amino acid replace-
ments, with an average coded protein variant differing in 4-5 amino acids from
the variant coded by the same gene but in a different strain.
Furthermore, strains from different pathotypes tend not only to be from
different STs, but to belong to separate major phylogenetic clades that form
so-called ECOR groups of E. coli ( Figure 3.1 ) ( Ochman and Selander, 1984 ).
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