Macquarie University
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Investigation of molecular adaptations in Pseudomonas aeruginosa cystic fibrosis isolates

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posted on 2022-03-28, 01:03 authored by Sheemal Shanista Kumar
Pseudomonas aeruginosa is the major pathogen contributing to morbidity and mortality among patients with cystic fibrosis (CF) lung infections. The opportunistic pathogen, P. aeruginosa is metabolically versatile and broadly found in the environment and on various hosts. The metabolic versatility can be attributed to its relatively large genome. In the CF lung P. aeruginosa is exposed to a variety of selective pressures including the host immune response, different microorganisms, environmental heterogeneity and antibiotics. This work explores the genetic and phenotypic differences among P. aeruginosa strains isolated from the sputum of CF patients with the model P. aeruginosa strain PAO1. Comparison of P. aeruginosa CF isolates PASS1-4 reveal differences in genetic and phenotypic adaption to the CF lung environment, including phenotypic variation in virulence related traits such as swimming motility, biofilm formation and mucin binding. Proteomic analyses revealed patterns in protein expression common to the CF isolates, but distinct from PAO1. Investigation of the catabolic capabilities of the CF isolates revealed that PASS4 showed a dramatically decreased capacity for utilisation of carbon sources, growing well only on adenosine and inosine out of the substrates tested. This strain was also shown to grow well on DNA suggesting it may be adapted to growth on DNA in the CF lung. Transcriptomic and proteomic analyses of PASS4 and PAO1 grown on DNA revealed increased expression of many virulence genes. Mutants of PASS4 were obtained that had an expanded carbon catabolic phenotype, and sequencing of these mutants showed they all contained a mutation in the purK gene involved in purine biosynthesis, suggesting that the inability of PASS4 to grow on a range of carbon sources because it is a purine auxotroph. The exploration of bacterial-fungal interaction revealed the highly virulent CF isolate PASS1 inhibited the growth of the fungal pathogen Scedosporium aurantiacum. PASS1 also has a significant effect on eukaryotic model organism zebrafish. Dual host-pathogen transcriptomics revealed an arsenal of virulence factors contributing to PASS1 infection, while the zebrafish host expressed an array of innate immunity mechanisms involved in inflammation, infection and tissue injury. Overall, this thesis provides insights into the various adaptations and mechanisms of P. aeruginosa involved in surviving in the CF host environment.


Table of Contents

1. Introduction -- 2. Genetically and phenotypically distinct Pseudomonas aeruginosa cystic fibrosis isolates share a core proteomic signature -- 3. A cystic fibrosis Pseudomonas aeruginosa isolate specialised to catabolise nucleic acids -- 4. Pseudomonas aeruginosa inhibits the growth of Scedosporium aurantiacum, an opportunistic fungal pathogen isolated from the lungs of cystic fibrosis patients -- 5. Dual transcriptomics of host-pathogen interaction of cystic fibrosis isolate Pseudomonas aeruginosa PASSI with Danio rerio -- 6. Proteomics of hosts and pathogens in cystic fibrosis -- 7. Discussion -- Appendices.


Thesis by publication.. Includes bibliographical references

Awarding Institution

Macquarie University

Degree Type

Thesis PhD


PhD, Macquarie University, Faculty of Science and Engineering, Department of Molecular Sciences

Department, Centre or School

Department of Molecular Sciences

Year of Award


Principal Supervisor

Ian T. Paulsen


Copyright Sheemal Shanista Kumar 2018. Copyright disclaimer:




1 online resource (xxv, 257 pages)

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