Ibrahim, Ahmed Farah Mohamed
(2022)
Comparative genomics analysis of
escherichia coli: insight into its
pathogenicity.
Masters thesis, Universiti Sains Malaysia.
Abstract
Escherichia coli (E. coli) is a gram-negative bacilli bacterium from the
Enterobacteriaceae family that may colonise and survive as a commensal in the infant's
gastrointestinal tract (GIT) a few hours after birth, as well as in animals and the
environment. E. coli may cause infections in the intestine or extraintestinal organs in both
high and low-income nations including in serious invasive diseases such as bacteraemia
and sepsis. Furthermore, E. coli is the leading antibiotic resistance organisms such as E.
coli sequence type 131 (ST131), an example of a successful multidrug-resistant pandemic
clone. The aim of this study was to compare the 22 complete genome strains against 3
local draft genome strains of E. coli and gain insight into their pathogenicity.
Pathogenicity comparison between local strains and public strains was investigated based
on analysis of 25 strains genomic sequences that were retrieved from the NCBI database.
Islandviewer 4 was used to forecast genomic islands. OmicsBox 2.1.14 was employed as
a multi-locus sequence typing tool (MLST) to screen for sequence type. The
pathogenicity and non-pathogenicity relationship was analysed by constructing a
phylogenetic tree using neighbour joining method from MEGA software with 1000
bootstraps based on representative strains of 16S rRNA genes. Result from genome
comparison found that 11 of the 25 stains are pathogenic while others non-pathogenic.
Seven out of 11 of these pathogenic strains are extremely high pathogenic. Most strains
from the same locations in the phylogenetic analysis are found to be clustered together,
and two of the local strains (INF13/18/A and INF191/17/A) share a common ancestor
with the highly pathogenic strains that produce Shiga toxin (Al Ain and AR-0427), while the third local strain (INF32/16/A) shares a common ancestor with the non-pathogenic
laboratory strain K-12 substr. MG1655. Most pathogenic strains for the MLST study
came into the ST11 category, while non-pathogenic strains went into the ST10
classification. Our local strains seem to be associated with various sequence types;
INF13/18/A is associated with ST156, INF32/16/A with ST354, and INF191/17/A with
ST131, which all suggested as pathogen, Extraintestinal E. coli (ExPEC). As conclusion,
two of the local strains (INF13/18/A and INF191/17/A) have been identified to be highly
pathogenic while INF32/16/A is less pathogenic. In general, since they have less
pathogenicity and virulence genes, pathogenicity of local strains is less compared to other
22 strains.
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