Characterisation of airway microbiome in two severe asthma cohorts using Nanopore sequencing of induced sputum and nasal lavage

Asthma is the commonest chronic lung disease globally. Persistent bacterial airways infection may drive immune pathology in severe asthma, particularly in 'type-2 low', neutrophilic asthma. Previous microbiome studies in severe asthma have lacked sequencing depth for species-level taxonomic identification of bacteria. In this study we apply a previously validated method of metagenomic sequencing using Nanopore on induced sputum samples and nasal lavage taken from two large severe asthma cohorts during stable disease. In health and mild asthma high sputum microbial diversity was preserved. By contrast in 23% of severe asthmatics the microbiome was dominated by a single respiratory pathogen, namely H. influenzae, M. catarrhalis, S. pneumoniae or P. aeruginosa. The microbiome of the upper and lower airways is distinct in severe asthma.