Respiratory microbiota predicts clinical disease course of childhood acute otitis media

Background: Acute otitis media (AOM) is one of the commonest childhood infections, generally thought to be caused by ascension of bacteria from the nasopharynx (NP) to the middle ear. Using 16S rRNA-based sequencing, we evaluated the relationship between the NP and middle ear fluid (MEF) microbiota in children with acute tympanostomy-tube otorrhea (ATTO; as a proxy for AOM) and explored whether microbiota profiling predicts natural disease course.Methods: Microbiota profiles of paired NP and MEF samples of 94 children aged below five years with uncomplicated ATTO were determined.Results: Local diversity (p<0·001) and overall microbiota composition (p<0·001) of NP and MEF samples differed significantly, though paired NP and MEF samples were much more similar than unpaired samples (p<0·001). High qualitative agreement between the presence of individual bacteria in both niches was observed. Abundances of Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pyogenes, Turicella otitidis, Klebsiella pneumoniae, and Haemophilus spp. were strongly correlated between the two niches. Additionally, P. aeruginosa, S. aureus, T. otitidis and Streptococcus pneumoniae abundance in NP were predictive of the presence of a range of oral types of bacteria in MEF. Interestingly, there was no association between Moraxella catarrhalis in NP and MEF samples, which was highly present in NP but virtually absent in MEF. NP microbiota composition predicted duration of ATTO better than MEF microbiota.Conclusions: We observed substantial correlations between NP and MEF microbiota in children with ATTO. Our data indicate that NP microbiota profiling may support future clinical decision-making.