EXPRESS: Metagenomic Oxford Nanopore sequencing of feline aural inflammatory polyps for pathogen discovery

ObjectivesFeline aural inflammatory polyps (FIAP) have been proposed to be induced by chronic viral or bacterial infections; however, the cause is still unknown. The aim of this study was to investigate potential etiologies of these polyps using metagenomic sequencing.MethodsPolyp tissue was collected from 13 cats following routine traction and avulsion procedures. Total nucleic acid was extracted and subjected to a host (feline) nucleic acid depletion protocol. Additionally, the Sequence-Independent Single-Primer Amplification (SISPA) method was used to enrich for low-abundance RNA viral genomes. Sequencing was conducted on the Oxford Nanopore MinION sequencing platform. Non-feline sequencing reads were taxonomically classified against custom bacterial/viral databases to calculate relative genus-level abundances.ResultsTaxonomic classification of sequencing reads identified various bacteria across samples and, in some samples, rare viruses. However, no common microbial sequences were associated with polyps to suggest a specific infectious etiology. Bacterial communities were dominated by Pseudomonadota, Actinomycetota, and Bacillota phyla, with Pseudomonadota and Actinomycetota being more frequently dominant. Lasallevirus was detected in few samples with unknown clinical relevance. Culture and sequencing showed partial concordance in identifying bacteria in some cases.Conclusions and relevanceNo common microbial-associated sequences found to be associated with polyp samples; therefore, no suspect causative agent was identified. 16S and ITS metagenomic sequencing on FIAP may help further elucidate if microbial population shifts have a role in polyp development and recurrence and/or persistence of inflammation leading to polyp development.