Exploring ambient mass spectrometry capacities for rapid detection and phenotyping of pseudomonas aeruginosa infection in cystic fibrosis patients

Abstract

Cystic fibrosis (CF) patients mostly succumb to respiratory failure, usually caused by Pseudomonas aeruginosa infection. Early, but not chronic, infection can be eradicated, mandating timely detection. However, current methods are insufficiently sensitive and unsuitable for children. This thesis explores the potential of novel ambient mass spectrometric (MS) tools for the phenotyping of P. aeruginosa and its detection in non-invasive samples. The hypotheses are that bacterial expression evolves as infection progresses and that the composition of host body fluids is impacted by P. aeruginosa acquisition. Rapid evaporative ionisation MS (REIMS) was applied to clinical isolate cultures including common CF pathogens. The detected metabolic profiles differentiated between species and led to the identification of virulence-associated metabolites in P. aeruginosa: quorum sensing molecules and rhamnolipids. Repeated analysis revealed differences between P. aeruginosa strains that allowed isolate classification. Although classification according to genetically-defined types was not achieved, REIMS potentially provides a finer resolution on quickly evolving virulence features. Exploration of intra-species disparity showed a higher metabolic diversity in chronic respiratory than in acute infections, attributed to lengthy and site-specific adaptation. The bacterial population was more disparate between than within CF patients. Variations in virulence factor levels between early and chronic isolates provided insight into P. aeruginosa‘s metabolism and adaptation, supporting the first hypothesis. These findings may support future clinical strategies. REIMS and desorption electrospray ionisation MS (DESI-MS) were evaluated as direct-from-sample diagnostic tools using sputum as a reference, and urine and skin secretions as easily accessible samples. REIMS could not detect P. aeruginosa in sputum and urine pellets, nor could DESI-MS on skin secretions. Nevertheless, the rich sputum metabolic profile and skin lipidome contained potentially highly relevant information about host physiology that may assist clinicians in the future. Although the second hypothesis was not verified, the data reported will generate future clinically relevant hypotheses.