The Microbiome of Cystic Fibrosis Sputum and its Association with Incident Lower Airway Infections

Bowron, Lauren Ashley

The Microbiome of Cystic Fibrosis Sputum and its Association with Incident Lower Airway Infections

dc.contributor.advisor	Parkins, Michael
dc.contributor.author	Bowron, Lauren Ashley
dc.contributor.committeemember	Surette, Michael
dc.contributor.committeemember	Marie-Claire, Arrieta
dc.contributor.committeemember	Ebbert, Kirsten
dc.date	2024-11
dc.date.accessioned	2024-09-11T19:45:59Z
dc.date.available	2024-09-11T19:45:59Z
dc.date.issued	2024-09
dc.description.abstract	Cystic fibrosis (CF) is a genetic disease characterised by frequent respiratory infections that exacerbate symptoms, leading to a decline in lung function and increased morbidity and mortality. Pseudomonas aeruginosa is considered the primary pathogen in CF, contributing significantly to disease severity. Stenotrophomonas maltophilia is an emerging pathogen of interest, associated with increased pulmonary exacerbations and lung function decline. This thesis aimed to explore the CF sputum microbiome of persons with CF (pwCF) uninfected with these pathogens and to determine if the risk of future acquisition and persistence of these pathogens is linked to microbiome structure and composition. Individuals who experienced an incident infection with either P. aeruginosa or S. maltophilia were identified, and compared to uninfected controls matched for sex, age (+/-2 years), and birth cohort. Individuals were included if our longitudinal whole sputum biobank contained cryopreserved samples from one year prior to infection (pre), at the time of culture-based identification of infection (at), and one year following infection (post). Infection outcomes were classified as chronic/persistent (pathogen culture-positive in ≥50% of cultures in the subsequent year) or transient. The microbial community composition was assessed using V3-V4 16S ribosomal RNA (rRNA) gene sequencing. Relative abundance data were verified using both pathogen-specific qPCR and total 16S rRNA-targeted qPCR to assess bacterial bioburden. Strains were typed using pulse-field gel electrophoresis to differentiate strain types and distinguish incident infection episodes. Results from this work showed that the microbial community of pwCF that eventually developed P. aeruginosa, or S. maltophilia incident infections differed from those who remained uninfected at the times of sampling. Additionally, at the time of infection, the microbial community composition differed between individuals with persistent infections and those whose infections were cleared. These findings suggest that the sputum microbiome in pwCF is associated with future infection risk and persistence, indicating its potential as a biomarker for prognosis and personalised treatment.
dc.identifier.citation	Bowron, L. A. (2024). The microbiome of cystic fibrosis sputum and its association with incident lower airway infections (Master's thesis, University of Calgary, Calgary, Canada). Retrieved from https://prism.ucalgary.ca.
dc.identifier.uri	https://hdl.handle.net/1880/119687
dc.language.iso	en
dc.publisher.faculty	Graduate Studies
dc.publisher.institution	University of Calgary
dc.rights	University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission.
dc.subject	microbiome
dc.subject	cystic fibrosis
dc.subject	bronchiectasis
dc.subject	incident infections
dc.subject	pseudomonas aeruginosa
dc.subject	stenotrophomonas maltophilia
dc.subject.classification	Microbiology
dc.title	The Microbiome of Cystic Fibrosis Sputum and its Association with Incident Lower Airway Infections
dc.type	master thesis
thesis.degree.discipline	Medicine – Microbiology & Infectious Diseases
thesis.degree.grantor	University of Calgary
thesis.degree.name	Master of Science (MSc)
ucalgary.thesis.accesssetbystudent	I do not require a thesis withhold – my thesis will have open access and can be viewed and downloaded publicly as soon as possible.