Airway microbiome and host inflammatory response in bronchiectasis

Non-cystic fibrosis bronchiectasis (hereby referred to as bronchiectasis) is a chronic respiratory disease characterized by irreversible dilation of bronchi in the context of chronic syndrome mainly represented by daily cough, sputum production and frequent pulmonary exacerbations. Bronchiectasis pathophysiology is recognised in the development of a vicious circle of infection, inflammation, mucous clearance and pulmonary damage. Although microbial community and inflammation have a very important role in respiratory diseases, few is known in bronchiectasis. The aim of this PhD project was to evaluate sputum microbiome and its interaction with the local host inflammatory response in adults with bronchiectasis during their stable state. Several studies were conducted to explore this research question. In the second chapter, we report the methodological selection of techniques for both microbiome and active neutrophil elastase (aNE) analysis in sputum. The third chapter is divided into three different sections. In the first, we identified two groups of adult bronchiectasis patients with different microbiome diversity levels. The low microbiome diversity group was found to be enriched in Pseudomonas, Staphylococcus and Streptococcus. Multivariate analysis identified FEV1%predict.<50, radiology and primary ciliary dyskinesia (PCD) to be independently associated with low microbiome diversity. The following section represents a preliminary study focused on bronchiectasis aetiologies, more specifically PCD and immunodeficiency. The study concerning PCD did not identify a clear association between aetiology, microbiome and inflammation comparing a group of matched PCD with idiopathic or post infective bronchiectasis, although, a trend could be observed.Subsequently, immunodeficiency was comparedto idiopathic bronchiectasis. These two groupsidentified, primary immunodeficiency and idiopathic differed in terms of alpha diversity and quantification of H. influenzae which was higher in the immunodeficiency group. Chapter fourfocuses on neutrophilic inflammation looking at the association of aNE in bronchiectasis with microbiome analysis. We found evidences of low microbiome diversity and P. aeruginosa identification in patients with high levels of aNE. The following study focused on active Cathepsin G (Cat-G) which is a putative biomarker for bronchiectasis. Cat-G was associated with disease severity, radiological severity, quality of life and chronic infection. It was also associated with low microbiome diversity and P. aeruginosa molecular detection. Finally, Cat-G and aNE resulted to be similar in predicting bronchiectasis severity (bronchiectasis severity index -BSI), severe exacerbation and chronic infection in bronchiectasis patients during stable state. Finally, in chapter five, we analyse microbiome and inflammation among adult bronchiectasis patients with chronic P. aeruginosa infection. Association network analysis identified differences in terms of number of interactions of Pseudomonas with other genera and interactions between cytokines and microbial effectors in patients with different exacerbations/year. We hope that this thesis may be a step forward in better understanding the role of both microbiome and inflammation in bronchiectasis that may lead to unravelling of endotypes and the identification of therapeutic targets. This will finally result in advances in a precise medicine approach for bronchiectasis patients.