Understanding acquisition and evolution of antifungal resistance in chronic respiratory disease

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.

Aspergillus species are ubiquitous, saprophytic fungi with airborne conidia that grow on organic matter. Aspergillus fumigatus is the principal causative agent of human aspergillosis, which can range from allergy to invasive aspergillosis, a life-threatening infection in immunocompromised hosts. In chronic respiratory disease, there is a significant global burden of Aspergillus related disease with high mortality and morbidity with oral triazole antifungal drugs the front-line therapy. We have shown a rapid global emergence of multiple triazole resistance (MTR) in A. fumigatus over the past decade with ~15% prevalence in chronic respiratory disease patient isolates. The major target for MTR mutations is the Cyp51A-gene which is the target for triazole antifungals. The acquisition of MTR in this increasing population of patients is however as yet unclear with MTR selection environments including patient azole therapy and organic matter containing agricultural triazole fungicide residues. Detection is further hampered by poor sensitivity of Aspergillus culture methodology and PCR commercial testing of sputum in culture-negative patients. This project aims to validate and use a novel TR34-loop-mediated isothermal amplification assay to map prevalence of MTR in chronic respiratory disease and through population genomic methods link spatial, environmental and biological covariates into a description of patterns of genome wide diversity in A. fumigatus in which resistance evolves. The TR34-LAMP assay will be validated in clinical A. fumigatus MTR and wild-type isolates, prospective sputum from 2 clinical sites and a sample biobank of sputum DNA from a European cohort of non-cystic fibrosis bronchiectasis patients. A landscape whole genome sequencing approach of prospective chronic respiratory patients on azole therapy alongside comprehensive environmental and nosocomial sampling will be used to enable a phylogenomic analysis of A. fumigatus MTR acquisition and evolution.

This project aims to validate a novel LAMP-TR34/46 assay to map prevalence of triazole resistance in chronic respiratory disease and through population genomic methods link spatial, environmental and biological covariates into a description of patterns of genome-wide diversity in A. fumigatus upon which resistance to triazoles evolves. The data generated from this project will directly impact public health policy by informing healthcare of the scale and evolution of multi-triazole resistant (MTR) A. fumigatus infection in chronic respiratory disease to achieve optimal antimicrobial stewardship and infection control alongside informing agricultural strategy of the implications of azole use.

Chronic respiratory disease patient numbers infected by aspergillosis are large. The European Centre for Disease Prevention and Control estimates that there are 2,100,000 patients in Europe with allergic bronchopulmonary aspergillosis (ABPA), 240,000 with chronic pulmonary aspergillosis (CPA) and 63,000 with invasive aspergillosis (IA) in whom underlying chronic obstructive pulmonary disease (COPD) is a significant risk factor. Notably, patients developing CPA and IA have severe morbidity comprising a significant expenditure to healthcare systems that is on par with antibiotic usage. The wider public health impact of MTR A. fumigatus across heterogeneous chronic respiratory patient groups is unknown, however all studies to date have shown that azole resistance is associated with treatment failure. This research will lead to innovation in point of care MTR A. fumigatus diagnostics to enable low-cost, rapid detection method in a lab-on-chip platform. Given the global burden of aspergillosis in resource-poor settings, this will have a significant public health impact. Data from this project will additionally enable a better understanding of the scale and acquisition/evolution of MTR A. fumigatus in chronic respiratory disease. This will directly impact antimicrobial and infection control policy to prevent treatment failure and be of significant interest to policy makers and government agencies at an international level as it will further highlight the currently under-appreciated scale of MTR A. fumigatus infection in chronic respiratory disease. By highlighting the impact of agricultural azole use, this project will again directly inform significant policy-relevant activity at a governmental (DEFRA) and international level to review levels of biosecurity aimed at preventing emerging fungal diseases

This project will lead to novel insights into the interface between fungal genetics and respiratory innate immunity and will drive expertise in this important area in the next 10 years directly benefiting clinical and academic researchers. This project will develop a network hub of academic and clinical pulmonary fungal disease research centres to enable translational outputs from the research in the areas of diagnostics and therapeutics with the potential to improve the quality of life for patients with pulmonary diseases within the next 10-20 years and further interventional multi-centre trials. As the research validates novel diagnostic technology, we would anticipate opportunities for commercial exploitation which will be discussed with the MRC and the Enterprise Office at Imperial College. Likewise, as this project encompasses systematic whole genome sequencing of numerous clinical and environmental A. fumigatus isolates, it is likely that mutations will be identified which may be targets for novel therapeutics. These will be identified over the duration of the project and taken forward for further academic studies. Hence, data from this project will also benefit interested private sector diagnostic and pharmaceutical companies that will increase the economic competitiveness of the UK.