Biology Reference
In-Depth Information
Shigella
is an obligate intracellular pathogen that causes intestinal dis-
ease, known as shigellosis, in humans (see Chapter 7) (
Kotloff et al., 1999
).
Shigella
are separated into four 'species' based on serotyping:
S. boydii
,
S. sonnei
,
S. dysenteriae
, and
S. flexneri
(
Hale, 1991
). Despite their name, only
one clade,
S. dysenteriae
, contains isolates that produce Shiga toxin. Clinical
symptoms cannot distinguish
Shigella
infection from some types of
E. coli
infection (
Johnson, 2000
). Furthermore, biochemical tests have been used to
differentiate
Shigella
from
E. coli
, but cannot always differentiate
Shigella
from
some enteroinvasive
E. coli
(EIEC) (
Johnson, 2000
).
Shigella
are characterized
by an invasive phenotype encoded by the large (∼200 kb) invasion plasmid,
pINV(28). pINV contains the genetic machinery for a T3SS, which consists of
approximately 50 proteins involved in the assembly and regulation of the T3SS
(
Parsot et al., 1995
).
Shigella
are also characterized by gene loss compared to
E. coli
(
Hershberg et al., 2007
), which is often associated with obligate
pathogens (
Moran, 2002
).
Molecular analyses has determined that
Shigella
is actually a phenotype of
E. coli
that has emerged on multiple independent occasions (
Ochman et al.,
1983
). A phylogeny based on a concatenated alignment of multiple conserved
genes (MLST) demonstrated that the
Shigella
phenotype has emerged at least
seven times from
E. coli
(
Pupo et al., 2000
). Therefore, the emergence of
Shigella
is associated with plasmid acquisition and convergent evolution,
including genome size reduction.
The first
Shigella
genome sequenced was
S. flexneri
301 in 2002 (
Jin et al.,
2002
). A comparison of this genome with K12 and O157:H7 EDL933 revealed
that the
S. flexneri
genome contains a repertoire of unique insertion elements
and pathogenicity islands. Despite these differences, all three genomes share
an essentially co-linear 3.9 Mb backbone. The related genome,
S. flexneri
2a
2457T, was published in 2003 (
Wei et al., 2003
). A comparison of this genome
with the genome of K12 and O157:H7 identified ∼2800 ORFs shared between
the three genomes. A comparison of
S. flexneri
2a 2457T with
S. flexneri
2a 301
demonstrated that the two genomes differ by 45 insertion sequence loci. This
large number of insertion sequences is characteristic of
Shigella
genomes.
In 2005, the genomes of
S. boydii
227,
S. sonnei
046, and
S. dysenteriae
197 were all sequenced to completion (
Table 2.1
); all of these isolates were col-
lected from epidemics in China in the 1950s (
Yang et al., 2005
). A comparative
analysis of multiple
Shigella
genomes demonstrated genomic rearrangements
in both the chromosome and in the invasion plasmid. Phylogenetic analyses
have previously demonstrated that
S. dysenteriae
197 is more closely related
to O157:H7 EHEC than to other
Shigella
species (
Touchon et al., 2009
;
Sahl
et al., 2011
). This finding has been re-confirmed when comparing additional
phylogenetically diverse isolates (
Figure 2.1
).
A phylogeny inferred from a large number of concatenated, recombination
filtered (
Bruen et al., 2006
), coding regions identified that
Shigella
falls into
two main clusters (
Ogura et al., 2009
). A feature frequency profile method also
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