Characterization of middle ear microbiome in otitis media with effusion in Hungarian children: Alloiococcus otitidis may potentially hamper the microbial diversity

Abstract

Introduction: Although otitis media with effusion (OME) is a common cause of hearing impairment in children, little is known about its microbiological background. We aimed to analyse the microbiome of the middle ear fluid (MEF) in OME to identify microbiological, demographic and environmental factors that may potentially influence the middle ear microbiome. In addition, we aimed to compare the results of conventional culture techniques and PCR-based methods. Methods: 39 samples from children with OME were investigated using conventional culture and 16S rRNA sequencing. Bioinformatic analyses were carried out to assess the microbial communities and their association with clinical data. Results: By conventional culture technique bacteria could be cultured in 33 % of the MEF samples; the most frequent bacterium was Haemophilus influenzae, followed by Staphylococcus species, Cutibacterium acne, and Streptococcus species. The 16S rRNA analysis showed that Alloiococcus was the most abundant bacterium, followed by Haemophilus, Streptococcus. and Sphingobium.A “High Alloiococcus group” with significantly lower and a “Low Alloiococcus group” with significantly higher alpha and beta diversity could be defined. Children born by Caesarean sections had lower beta and Shannon diversity than patients born by natural birth. Breastfeeding for at least six months showed a negative correlation with alpha diversity. Age, previous antibiotic treatment, parental smoking, duration of symptoms, existence of siblings, did not alter the significantly bacterial composition of MEF samples and there were no significant differences in regard to alpha or beta diversity. Conclusion: The conventional culture technique and 16S rRNA results were not congruent. Remarkably, Alloiococcus could not be cultured at all, even by 16S rRNA analysis the presence of Alloiococcus seems to be important. Based on our results, A. otitidis possibly impacts the diversity of middle ear microbiome in children with OME. However, further studies are required to determine the role of A. otidis in middle ear pathologies.

Keywords

• Alloiococcus otitidis
• Otitis media with effusion
• Microbiota
• Microbiome
• 16S rRNA analysis
• Middle ear