THESIS
2014
xiii, 115 pages : illustrations (some color) ; 30 cm
Abstract
E. coli is an inhabitant of the gastrointestinal (GI) tracts of warm-blooded animals. It
is conventionally believed that E. coli lacks the ability to survive in the external
environment. In the previous study, a group of E. coli named UNISED was retrieved
from the marine intertidal sediment in Hong Kong, which was demonstrated
genetically distinct from the animal host associated E. coli. Similar to other findings
of the "environmental" E. coli, it is not clear that to what extent UNISED is divergent
from the animal host associated E. coli, and how different evolutionary forces
contributed to the formation of UNISED. Hence, we investigated the genetic and
phenotypic relation of isolates of UNISED and their animal host associated
counterparts, and explored the population genetics...[
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E. coli is an inhabitant of the gastrointestinal (GI) tracts of warm-blooded animals. It
is conventionally believed that E. coli lacks the ability to survive in the external
environment. In the previous study, a group of E. coli named UNISED was retrieved
from the marine intertidal sediment in Hong Kong, which was demonstrated
genetically distinct from the animal host associated E. coli. Similar to other findings
of the "environmental" E. coli, it is not clear that to what extent UNISED is divergent
from the animal host associated E. coli, and how different evolutionary forces
contributed to the formation of UNISED. Hence, we investigated the genetic and
phenotypic relation of isolates of UNISED and their animal host associated
counterparts, and explored the population genetics of E. coli from the two sources.
Our findings revealed the existence of the "Environment-specific" E. coli at both
genetic and phenotypic level, suggesting that E. coli of UNISED may adapt to the
marine sediment. It was found that mutation and purifying natural selection is
important to the formation of the "Environment-specific" E. coli population. However,
as current bacterial typing methods cannot totally fulfill our requirements on the
resolution and the coverage of genomic information of research on E. coli at strain
level, a novel shotgun proteomics-based method was developed for the bacterial strain
level characterization. Totally, 73 E. coli isolates pertaining to four species of
warm-blooded animals (i.e. human, cow, dog, and pig) were used as testing organisms
for this prove-of-principle research. The results of the Jackknife analysis indicated that
72 out of 73 isolates were assigned to the correct sources (ARCC=98.6%), while the
ARCC was only 80.8% using the traditional REP-PCR DNA fingerprinting. Moreover,
the partial least squares discriminant analysis (PLS-DA) was employed to extract the
potential host-specific spectra, which can be further developed as biomarkers. Our
findings suggested that this shotgun proteomics-based method is potential to work as an
effective tool for bacterial strain level characterization.
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