Characterising the allergic fungal rhinosinusitis microenvironment using full length 16S rRNA gene amplicon sequencing and fungal ITS sequencing

Introduction: Allergic fungal rhinosinusitis (AFRS) is a severe phenotype of chronic rhinosinusitis (CRS) characterised by nasal polyposis (NP), eosinophilic mucin and localised, exaggerated type 2 inflammation. While fungal antigenic stimulation of unregulated Th2 mediated inflammation is the core pathophysiological mechanism, the direct and synergistic role of bacteria in disease modification has been a pervasive hypothesis. We set out to define the microenvironment of AFRS to elucidate virulent organisms that may be implicated in the pathophysiology of AFRS.Methodology: We undertook a cross-sectional study of AFRS patients and CRSwNP patients in which fungus had not been identified. Demographics, disease severity, culture and microbiome sequences were analysed. Multimodality microbiome sequencing included next generation sequencing(NGS) on the Illumina Miseq (16S rRNA and ITS) and full length 16S rRNA sequencing on the Oxford Nanopore GridION.