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Title: Comparative genomic approaches to understanding Achromobacter xylosoxidans
Author: Pongchaikul, Pisut
ISNI:       0000 0004 6058 1425
Awarding Body: University of Liverpool
Current Institution: University of Liverpool
Date of Award: 2015
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The investigation into the genome of the emerging pathogen reveals the genetic basis of the pathogen. In this study, Achromobacter xylosoxidans was used as an example for the genomic study of emerging pathogens. A. xylosoxidans is an emerging and opportunistic pathogen in patients with various underlying diseases, such as Cystic Fibrosis and cancers. In chapter 3, the objectives of the study were to compare and evaluate the approach for A. xylosoxidans identification. A wide range of methods, including phenotypic test, 16S rDNA gene sequencing, MALDI-TOF, RAPD and MLST, were utilised to demonstrate the species identification. MALDI-TOF was considered as the most appropriate method due to the least time consuming. The application of multiple approaches to identify A. xylosoxidans was suggested. In chapter 4, comprehensive genomic feature of A. xylosoxidans has not been elucidated. The objective of this study was to use comparative genomic tool to investigate genomic feature of A. xylosoxidans. The analysis revealed the opened pan-genome of the species. The core genome accounted for approximately 50% of the size of the genome. Furthermore, the analysis revealed recombination events in the core genome of the species. Interestingly, phylogenetic relationships demonstrated global distribution of the species without geographical structure. This study provided pan-genome structure of the species, allowing for studies of genetic exchange mechanism in the species. In chapter 5, the main objective of the chapter was to investigate the antibiotic resistance and genes associated with the resistance in the species. The whole genome sequence and bioinformatics were used to search for genes associated with antibiotic resistance phenotypes. Single-molecule real time (SMRT) sequencing was also used to investigate the integron. The analysis revealed conserved RND-type efflux transporters across the species. The complete genome sequence revealed class 1 integron carrying IMP-14 on the chromosome of multidrug resistant isolates. This study demonstrated the identification of antibiotic resistance genes using bioinformatics and SMRT sequencing. In chapter 6, the objective was to investigate the virulence of A. xylosoxidans in organism model. The great moth larva Galleria mellonella was used to test for the virulence of A. xylosoxidans. Bioinformatics analyses were conducted to predict genes associated with virulence determinants. The analysis resulted in hydrolase-containing protein and PscD type III secretion system predicted as virulence determinants based on G. mellonella infection model, paving the way for further studies. This study demonstrated the application of whole genome sequencing and bioinformatics to understand the biology of the emerging pathogen. The identification of the genome of the emerging pathogen is required for the facilitation of prevention and therapeutic in the future.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available
Keywords: QR Microbiology