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Original Investigation
February 2017

Identification of the Bacterial Reservoirs for the Middle Ear Using Phylogenic Analysis

Author Affiliations
  • 1Department of Otolaryngology–Head and Neck Surgery, Adelaide University, Adelaide, Australia
  • 2Department of Otolaryngology–Head and Neck Surgery, The Women’s and Children’s Hospital, Adelaide, Australia
  • 3now with Department of Otolaryngology–Head and Neck Surgery, Queen Elizabeth Hospital, Adelaide University, Adelaide, Australia
JAMA Otolaryngol Head Neck Surg. 2017;143(2):155-161. doi:10.1001/jamaoto.2016.3105
Key Points

Question  Does the external auditory canal (EAC) act as a bacterial reservoir for the middle ear in patients with otitis media with effusion?

Findings  In this phylogenetic analysis using 16S ribosomal RNA gene paired-end sequencing of samples from 18 children with otitis media with effusion, the EAC microbiota correlated with the microbiota of the middle ear. Furthermore, after correlating with previously published data, the adenoid pad and EAC were found to contribute to the middle ear microbiome.

Meaning  Clinicians may need to consider the role of EAC bacteria in the treatment and management of otitis media with effusion, particularly that of Alloiococcus otitidis.


Importance  The adenoid pad has long been considered a reservoir for bacteria in the pathogenesis of otitis media with effusion (OME). However, bacteria more reminiscent of external auditory canal (EAC) commensals are often demonstrated within middle ear aspirates.

Objective  To compare the microbiota of the EAC, the middle ear with OME, and the adenoid pad to further clarify the true source of middle ear bacteria.

Design, Setting, and Participants  Middle ear fluid (MEF) aspirates and EAC lavages were collected from 18 children with OME undergoing ventilation tube insertion from June 1, 2014, to August 31, 2015, at Women and Children’s Hospital, Adelaide, Australia. Adenoid pad and MEF samples were included from a previous study. Samples were analyzed using sequencing of the 16S ribosomal RNA gene. Previously collected microbiota data from the adenoid pad were collated for analysis.

Main Outcome Measures  Mean relative abundance of top bacterial genera for the MEF, EAC, and adenoid pad samples.

Results  Eighteen pediatric patients with chronic OME (6 female; 12 male; mean [SD] age, 48 [36] months) were recruited prospectively, with 34 paired MEF and EAC samples. The MEF microbiota (mean relative abundance [SD]) consisted of Alloiococcus otitidis (37.5% [40.0%]), Haemophilus (14.4% [29.1%]), Moraxella (10.0% [26.4%]), Staphylococcus (8.2% [21.9%]), and Streptococcus (3.8% [13.1%]). The mean relative abundance (SD) microbiota of the EAC demonstrated a sparsity of classic otopathogens, including Haemophilus (0.3% [0.8%]), Moraxella (0.3% [0.7%]), and Streptococcus (0.2% [0.6%]), but had a high abundance of Alloiococcus (58.0% [44.1%]), Staphylococcus (20.8% [34.0%]), and Pseudomonas (3.2% [17.1%]). In contrast, based on previously collected data, the microbiota of the adenoid pad showed a high abundance of the classic otopathogens with a sparsity of EAC genera for Alloiococcus (0.1% vs 28.9%, respectively; P < .001), Haemophilus (25.2% vs 18.2%, respectively; P = .002), Staphylococcus (0.2% vs 10.8%, respectively; P = .02), Streptococcus (12.7% vs 4.2%, respectively; P < .001), and Pseudomonas (0 vs 2.1% respectively; P < .001). The microbiota of the MEF collected during 2 consecutive years were similar (Alloiococcus, 22.7% vs 37.5%; Haemophilus, 22.5% vs 14.0%; Staphylococcus, 10.9% vs 10.7%; Moraxella, 5.0% vs 9.7%; Corynebacteria, 6.2% vs 3.1%; Streptococcus, 4.8% vs 3.7%; and Pseudomonas, 1.1% vs 3.0%; P ≥ .05).

Conclusions and Relevance  The EAC and the nasopharynx could serve as reservoirs for microbiota of the middle ear. Furthermore, the microbiota of the middle ear with effusion appear to be relatively stable over time and between populations with OME.