Outer Ear and Nasopharynx as Sources of the Middle Ear Microbiome during Otitis Media with Effusion

Otitis media with effusion (OME) is characterized by accumulation of effusion in the middle ear cavity without symptoms of an acute infection. This common childhood disease is thought to be caused by a range of viruses or bacteria resident in the upper respiratory tract. In recent years however, fastidious ear canal bacteria were also detected at high relative abundances in OME middle ear effusion (MEE), raising the question if these bacteria contribute to the disease. So far, studies compared the MEE microbiota to either the upper respiratory tract or the ear canal, but never to both sites in the same patient.This research aimed to trace the origin of the middle ear microbiome during persistent OME (=3 months through 16S rRNA V4 amplicon sequencing of the upper respiratory tract (nares, nasopharynx, adenoids), middle ear and ear canal. Samples were collected from paediatric patients undergoing tympanostomy tube placement with or without concurrent adenoidectomy for treatment of chronic OME.Sequence pre-processing with the DADA2 pipeline in combination with classification against the EZBioCloud 16S RNA gene database allowed us to reach a subgenus-level resolution based on single nucleotide differences. Our data indicate that middle ear effusion samples harboured either ear canal bacteria (Alloiococcus, Turicella, Staphylococcus) which were almost absent in the upper respiratory tract, or typical upper respiratory tract bacteria (especially Haemophilus). Based on our results, we propose the hypothesis that the middle ear of children suffering from OME can be seeded by bacteria originating from the upper respiratory tract, via the Eustachian tube, as well as by bacteria originating from the ear canal, likely via tympanic membrane lesions.