Identification studies of Escherichia coli using FTIR profiles and strain typing by principal component analysis / Aiman Alwi

Escherichia coli (E. coli) is the most abundant facultative anaerobic bacteria present in the gastrointestinal tract and is normally harmless until gastrointestinal barriers are violated. Non-pathogenic E. coli strains can become pathogenic and cause diseases such as diarrhoea, dysentery, sepsis, an...

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Main Author:	Alwi, Aiman
Format:	Thesis
Language:	English
Published:	2022
Subjects:	QR Microbiology Near infrared spectroscopy
Online Access:	https://ir.uitm.edu.my/id/eprint/66904/1/66904.pdf
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spelling	my-uitm-ir.669042022-09-19T03:58:04Z Identification studies of Escherichia coli using FTIR profiles and strain typing by principal component analysis / Aiman Alwi 2022 Alwi, Aiman QR Microbiology Near infrared spectroscopy Escherichia coli (E. coli) is the most abundant facultative anaerobic bacteria present in the gastrointestinal tract and is normally harmless until gastrointestinal barriers are violated. Non-pathogenic E. coli strains can become pathogenic and cause diseases such as diarrhoea, dysentery, sepsis, and hemolytic-uremic syndrome (HUS). Conventional microbiology practice in determining the exact species of microorganisms include microscopic examination, colony morphology on selective and/or differential media, biochemical tests and serological typing. More precise identification requires application of methods based on molecular biology, which include pulse field gel electrophoresis (PFGE) or Polymerase Chain Reaction (PCR) are laborious, time and cost consuming and require technical expertise. Spectroscopy techniques has been successfully explored for the study of biological materials. Infra-red (IR) spectroscopy has become an accepted tool for the characterization of biomolecules and there is good potential of using IR for differentiating and identifying bacteria but specific tools to identify E. coli by using spectroscopy and chemometrics has not been addressed so far. Therefore this research aims to evaluate the potential of Fourier transform mid infrared (FT-MIR) and near infrared (FT-NIR) coupled with Principle Component Analysis (PCA) as chemometrics approach in differentiating pathogenic and non-pathogenic strains of E. coli. A selection of 11 species of bacteria from the family Enterobacteriaceae, including 4 strains of pathogenic E. coli and 3 strains of non-pathogenic E. coli, together with one strain of Bacillus subtilis as negative control was subjected to FT-MIR and FT-NIR spectroscopy using whole cells. The FT-MIR spectra analysis indicates that the region from 700 to 1810 cm‾¹ and 2660 to 3665 cm‾¹ were the best region to separate the different strains of E. coli due to high concentration of finger-print property of cell components. PCA analysis indicate that a maximum of 97.5% variance can be explained by the first two variable components. The FT-NIR spectra analysis showed the region from 7,200 to 4,000 cm‾¹ to be the best for strain separation and the first two variable components can account for 99.6% of all variations. Thus, FTIR spectroscopy has good potential as a tool in supporting the rapid diagnosis of pathogenic E. coli strain. 2022 Thesis https://ir.uitm.edu.my/id/eprint/66904/ https://ir.uitm.edu.my/id/eprint/66904/1/66904.pdf text en public masters Universiti Teknologi MARA (UiTM) Faculty of Applied Sciences Foong Abdullah, Mohd Faiz Jaafar, Mohd Juli
institution	Universiti Teknologi MARA
collection	UiTM Institutional Repository
language	English
advisor	Foong Abdullah, Mohd Faiz Jaafar, Mohd Juli
topic	QR Microbiology Near infrared spectroscopy
spellingShingle	QR Microbiology Near infrared spectroscopy Alwi, Aiman Identification studies of Escherichia coli using FTIR profiles and strain typing by principal component analysis / Aiman Alwi
description	Escherichia coli (E. coli) is the most abundant facultative anaerobic bacteria present in the gastrointestinal tract and is normally harmless until gastrointestinal barriers are violated. Non-pathogenic E. coli strains can become pathogenic and cause diseases such as diarrhoea, dysentery, sepsis, and hemolytic-uremic syndrome (HUS). Conventional microbiology practice in determining the exact species of microorganisms include microscopic examination, colony morphology on selective and/or differential media, biochemical tests and serological typing. More precise identification requires application of methods based on molecular biology, which include pulse field gel electrophoresis (PFGE) or Polymerase Chain Reaction (PCR) are laborious, time and cost consuming and require technical expertise. Spectroscopy techniques has been successfully explored for the study of biological materials. Infra-red (IR) spectroscopy has become an accepted tool for the characterization of biomolecules and there is good potential of using IR for differentiating and identifying bacteria but specific tools to identify E. coli by using spectroscopy and chemometrics has not been addressed so far. Therefore this research aims to evaluate the potential of Fourier transform mid infrared (FT-MIR) and near infrared (FT-NIR) coupled with Principle Component Analysis (PCA) as chemometrics approach in differentiating pathogenic and non-pathogenic strains of E. coli. A selection of 11 species of bacteria from the family Enterobacteriaceae, including 4 strains of pathogenic E. coli and 3 strains of non-pathogenic E. coli, together with one strain of Bacillus subtilis as negative control was subjected to FT-MIR and FT-NIR spectroscopy using whole cells. The FT-MIR spectra analysis indicates that the region from 700 to 1810 cm‾¹ and 2660 to 3665 cm‾¹ were the best region to separate the different strains of E. coli due to high concentration of finger-print property of cell components. PCA analysis indicate that a maximum of 97.5% variance can be explained by the first two variable components. The FT-NIR spectra analysis showed the region from 7,200 to 4,000 cm‾¹ to be the best for strain separation and the first two variable components can account for 99.6% of all variations. Thus, FTIR spectroscopy has good potential as a tool in supporting the rapid diagnosis of pathogenic E. coli strain.
format	Thesis
qualification_level	Master's degree
author	Alwi, Aiman
author_facet	Alwi, Aiman
author_sort	Alwi, Aiman
title	Identification studies of Escherichia coli using FTIR profiles and strain typing by principal component analysis / Aiman Alwi
title_short	Identification studies of Escherichia coli using FTIR profiles and strain typing by principal component analysis / Aiman Alwi
title_full	Identification studies of Escherichia coli using FTIR profiles and strain typing by principal component analysis / Aiman Alwi
title_fullStr	Identification studies of Escherichia coli using FTIR profiles and strain typing by principal component analysis / Aiman Alwi
title_full_unstemmed	Identification studies of Escherichia coli using FTIR profiles and strain typing by principal component analysis / Aiman Alwi
title_sort	identification studies of escherichia coli using ftir profiles and strain typing by principal component analysis / aiman alwi
granting_institution	Universiti Teknologi MARA (UiTM)
granting_department	Faculty of Applied Sciences
publishDate	2022
url	https://ir.uitm.edu.my/id/eprint/66904/1/66904.pdf
_version_	1783735643912798208

Identification studies of Escherichia coli using FTIR profiles and strain typing by principal component analysis / Aiman Alwi

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