Biology Reference
In-Depth Information
Chapter 1
The ecology of
Escherichia coli
David M. Gordon
The Australian National University, Canberra, ACT, Australia
THE GENUS
ESCHERICHIA
The genus
Esherichia
and the species
E. coli
have been recognized for over
a century. In 1985, Farmer and colleagues described the first new species in
the genus,
E. fergusonii
(
Farmer et al., 1985
). In 2003, Huys and colleagues
described the second new species,
E. albertii
(
Huys et al., 2003
).
Hyma et al.
(2005)
described the evolutionary relationship of
E. albertii
to
E. coli
, and its
identity to the diarrheal pathogen,
Shigella boydii
serotypes 7 and 13. All of the
other named species and serotypes of
Shigella
are actually members of
E. coli
(
Sims and Kim, 2011
). There are three other named species of
Escherichia
:
E. blattae
,
E. vulneris
, and
E. hermannii
, but strains of these species are only
distantly related to other
Escherichia
and are not valid members of the genus
(
Walk et al., 2009
).
The techniques of multi-locus sequence typing (MLST) and multi-locus
sequence analysis (MLSA) have revolutionized our understanding of the evolution,
ecology, epidemiology, and population genetics of bacteria (
Maiden et al., 1998
).
There are three MLST schemes used for
E. coli
and MLST data have been col-
lected for a great many isolates (
http://mlst.ucc.ie/mlst/dbs/Ecoli
,
www.pasteur.
number of studies that isolate and characterize
E. coli
from non-clinical sources
(
Gordon, 1997
;
Souza et al., 1999
;
Pupo et al., 2000,b
;
Gordon and Cowling, 2003
;
Power et al., 2005
;
Wirth et al., 2006
;
Walk et al., 2007
), and as a consequence our
understanding of the diversity of bacteria has increased enormously. These studies
have revealed substantially more genetic variation in the genus
Escherichia
, and five
'cryptic clades' of
Escherichia
were described (
Walk et al., 2009
). The term cryptic
clades was used because, based on standard phenotypic methods, strains belong-
ing to these novel
Escherichia
species are phenotypically indistinguishable from
E. coli
. Our current understanding of the relationships among the various
Escherichia
lineages is illustrated in
Figure 1.1
.
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