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Title: Rapid species identification and antimicrobial susceptibility testing using Raman spectroscopy
Author: Kapel, Natalia
Awarding Body: Swansea University
Current Institution: Swansea University
Date of Award: 2013
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Infectious diseases remain a serious threat to human life and health as well as having important economical factor. One way of successful combating diseases is designing the most appropriate treatment plan following the correct diagnosis. Therefore, there is a need for a method combining reproducibility, precision and speed. The aim of this work was to evaluate the potential of micro-Raman spectroscopy for identifying bacteria at different taxonomic levels, strains revealing different antibiotic resistance profiles, and for phylogenetic investigation. The project was based on a selection of bacteria: Staphylococcus aureus (6571, Cowanl), Staphylococcus epidermidis (1457, 9142), Escherichia coli including wild- types (strain B, K12, Top 10), transformants expressing ampicillin and kanamycin resistance (Top10Amp, Top10Kan) and clinical isolates expressing extended-spectrum beta- lactamases (ESBL). Following a precise and detailed protocol, Raman spectra were recorded from bacterial colonies grown overnight on a Colombia Blood Agar. In order to remove background fluorescence, rolling-circle filter procedure was applied. The most critical peaks for differentiation between organisms as well as for characterising each microorganism were determined. The spectral data were analyzed using principal component and cluster analysis techniques. As expected, the degree of separation decreased in the order genus→species→strain. It was determined that DNA/RNA, proteins and amino-acids are responsible for the differentiation between strains on a lower level of similarity with more influence of the constituents of the bacterial envelope between more closely related organisms. Raman spectroscopy was capable of differentiating between susceptible and resistant strains as well as monitoring whether the organism has been grown under antibiotic pressure. Based on triplex PCR, clinical isolates of ESBL strains were assigned to one of the phylogenetic group characterising Esherichia genus and it was revealed that within CTX- M TEM-1 there were two distinct clusters of D and B2 groups. Overall we have demonstrated that the combination of micro-Raman spectroscopy, microbiology and bioinformatics has the potential for the successful discrimination of bacteria species and strains, for the determination of antibiotic resistance profiles and investigating phylogenetic grouping in a clinical environment.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available
Keywords: Raman spectroscopy