Cystic fibrosis microbiology: Optimizing molecular diagnostic approaches

Aseeri, Abdullah 2024. Cystic fibrosis microbiology: Optimizing molecular diagnostic approaches. PhD Thesis, Cardiff University. Item availability restricted.

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Abstract

Cystic fibrosis (CF) lung infections are naturally polymicrobial, involving complex diverse microbial communities. This thesis addresses several aspects of CF pathogen detection, and microbial community diversity and composition, using advanced molecular techniques. A novel cystic fibrosis Ribosomal Intergenic Spacer Analysis (cfRISA) PCR method designed to identify CF pathogens was developed and optimised. This in-house designed cfRISA PCR method was evaluated and was shown to have better sensitivity and specificity in detecting CF pathogens compared to current PCR methods (chapter 3). Alternative DNA extraction methods (FastPrep and Maxwell) for microbial community profiling in CF sputum were compared. Analysis of these extraction methods showed no significant differences in terms of profiling microbiota diversity, although FastPrep showed a marginal advantage in capturing greater fungal diversity (chapter 4). Microbiota diversity and taxonomic composition in sputa from adults and children with CF were profiled through culture-independent 16S rRNA gene and ITS metabarcoding revealing significant microbial diversity within the sputum samples of people with CF (pwCF). This analysis emphasised the limitations of conventional culture-based diagnostics and the advantages of molecular techniques in capturing the CF lung diversity (chapter 5 and 6), as well as the potential of therapeutic agents to alter the CF lung microbiota. It also showed that therapeutics such as cystic fibrosis transmembrane conductance regulator (CFTR) modulators and the novel oligosaccharide, Oligo G, altered the microbiota present in the CF lung (chapter 6 and 7). The implications of these findings suggest that integrating molecular diagnostics into routine clinical practice could substantially improve the management of CF lung infection. It potentially can offer a more personalized approach to CF management based on microbial community profiles. Ultimately, this research contributes to a deeper understanding of the CF lung microbiota diversity and composition, and advocates a shift towards more advanced diagnostic molecular approaches and different respiratory samples to be used in clinical practice.

Item Type:	Thesis (PhD)
Date Type:	Completion
Status:	Unpublished
Schools:	Biosciences
Subjects:	Q Science > Q Science (General)
Uncontrolled Keywords:	cystic fibrosis; lung infection; microbiota analysis; molecular diagnostic
Date of First Compliant Deposit:	25 October 2024
Date of Acceptance:	25 October 2024
Last Modified:	25 Oct 2024 16:12
URI:	https://orca.cardiff.ac.uk/id/eprint/173357

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