Abstract
Background: Pulmonary non-tuberculous mycobacterial (NTM) disease is a challenging and increasingly prevalent infection. The factors which govern the development of clinical NTM disease and its subsequent clinical course are poorly understood.

Aims: The aims of this thesis have been i) to investigate the host response to NTM infection using whole blood gene expression profiling, ii) to characterise the lung microbiome associated with pulmonary NTM disease using sequencing of the bacterial 16S rRNA gene and iii) to develop a culture-free method of characterising the mycobacterial communities present in the lung.

Methods, Results & Conclusions: Gene expression analysis found that in NTM disease there was reduced expression the gene encoding interferon-γ, a key cytokine in the response to mycobacterial infection, as well as a number of genes associated with T-cell receptor signalling. In NTM disease survival was associated with genes involved in T- and B-cell function and mortality with genes related to the innate immune response and inflammation.

Characterisation of the microbiome in both NTM disease and controls revealed an abundance of Proteobacteria. Compared with controls, dominance by Pseudomonas was less common in NTM disease, whereas Stenotrophomonas and Achromobacter dominance was more common. Several genera including Stenotrophomonas, Achromobacter, Burkholderia and Staphylococcus were more abundant in NTM disease.

Sequencing of the hsp65 gene was used to characterise mycobacterial communities in the lung. Mycobacteria were found in all samples regardless of their isolation in culture or the presence of clinical NTM disease. Multiple species of mycobacteria were present in almost all samples, in contrast to culture which did not detect more than one species in any sample. Communities were often dominated by one species, with a lower diversity seen in subjects with clinical disease. Within subjects with NTM disease, lower diversity was seen in those who died and those with low IFNG expression.