Understanding acquisition and evolution of antifungal resistance in chronic respiratory disease

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Aspergillus fumigatus is a mould that can cause a wide spectrum of clinical syndromes. The effects of A. fumigatus depend largely on the interplay between the pathogen and host immune response ranging from asymptomatic colonisation to life-threatening infection. Invasive aspergillosis (IA), the most severe form of A. fumigatus infection, predominantly affects immunocompromised patients while immune hyperactivity that can lead to allergic bronchopulmonary aspergillosis (ABPA), characterised with progressive airway destruction and mucus impaction. Patients with pre-existing chronic respiratory disease (e.g. bronchiectasis including cystic fibrosis (CF)) are particularly susceptible to infection and allergy to A. fumigatus. In these individuals, A. fumigatus can result in lung cavity formation or infection of pre-existing cavities (mycetoma), ABPA development, or airway limited infection called tracheobronchitis. There is an increasing recognition of the causative and destructive role of A. fumigatus within chronic respiratory disease. Global estimates of chronic pulmonary aspergillosis are ~3 million cases. A high prevalence of Aspergillus-associated disease in non-CF bronchiectasis has recently been shown with ~300,000 bronchiectasis patients estimated in the UK. Aspergillus-associated lung disease (e.g. ABPA, bronchitis, colonisation) has been shown in up to ~20% of individuals with CF and has been shown to be associated with an increased hospitalisation rate. Chronic obstructive pulmonary disease remains a significant risk factor for development of invasive aspergillosis with high mortality.Triazoles are the most widely used antifungal agents in treatment of Aspergillus-related infection and allergy in chronic respiratory disease. Over the last decade, however, there has been increasing reports of A. fumigatus multiple tri-azole resistance (MTR) with subsequent treatment failure and increased mortality. Within individuals with chronic respiratory disease we have shown a prevalence of azole resistant A. fumigatus of ~15%. In the majority of these isolates, an environmentally driven mutation (TR34) is the cause of resistance; however the route of acquisition and evolution of MTR within individuals with chronic respiratory disease is as yet unclear. The rapid emergence and global spread of A. fumigatus MTR isolates, however, has raised the realistic possibility that in the future mould-active azoles may cease to be effective.Early detection of infection and resistance is key to outcome within chronic respiratory disease. Detection of A. fumigatus and MTR, however, is hampered by limitations in current fungal culture diagnostics which have poor sensitivity, and resistance detection, which is time-consuming, labour-intensive and costly. Through this project, we aim to validate a novel rapid assay (TR34-LAMP) to detect A. fumigatus and MTR isolates and advance our understanding of the evolution of MTR in chronic respiratory disease. The TR34-LAMP assay will be used to detect A. fumigatus and MTR directly in sputum from individuals with chronic respiratory disease whilst analysing prevalence of MTR in a large well-characterised cohort of bronchiectasis patients. This assay has the potential through a 'lab-on-a-chip' based format to enable accurate, low-cost, rapid, point-of-care detection of A. fumigatus MTR. To further understand the genomic evolution and acquisition of A. fumigatus MTR in chronic respiratory disease, a prospective whole genome sequencing approach will be used to analyse longitudinal A. fumigatus isolates from individuals with chronic respiratory disease starting antifungal therapy across 2 distinct clinical and geographical sites. Comprehensive environmental and cohort sampling will be performed to analyse acquisition and evolution of A. fumigatus MTR. This information will critically inform future infection control and antimicrobial stewardship strategies across chronic respiratory care.