Microbiomes of the normal middle ear and ears with chronic otitis media

Cholesteatoma in the pediatric aerodigestive population

OBJECTIVES

To report the prevalence of cholesteatoma and related comorbidities in pediatric aerodigestive patients requiring tracheostomy or airway reconstruction procedures. To use study findings to inform clinical management of these complex patients.

METHODS

A repository of clinical data drawn from our institution's electronic medical records was queried to identify airway reconstruction (airway) and complex hospital control (control) patient cohorts. Retrospective chart review was then performed to investigate the occurrence of cholesteatoma and related pathologies in these patients, as well as clinical management.

RESULTS

The prevalence of cholesteatoma in airway and control patients was 6/374 (1.60 %) and 35/30,565 (0.11 %), respectively. The relative risk of cholesteatoma diagnosis in airway patients was 14.01 (95 % CI 6.06-32.14). Airway patients were more likely than control patients to have pressure equalization tube history (relative risk 3.25, 95 % CI 2.73-3.82). Age at cholesteatoma diagnosis and first surgical intervention was younger in airway compared to control patients (5.43 vs. 8.33, p = 0.0182, and 6.07 vs. 8.82, p = 0.0236). However, time from diagnosis to intervention and extent of surgery were similar between the groups.

CONCLUSION

This is the first study to investigate the prevalence of cholesteatoma in the pediatric aerodigestive population. The relative risk of cholesteatoma diagnosis was found to be 14 times higher in patients with tracheostomy or airway reconstruction history. Underlying eustachian tube and palatal dysfunction are likely contributing factors to the elevated risk. Additionally, cholesteatoma in this population was diagnosed and required surgical intervention at a younger age, which may suggest a more aggressive disease course. Providers should maintain a high degree of suspicion for cholesteatoma in this complex population.

Microbiome and Otic Quinolone Levels Following Tympanoplasty Assessed by Gelatin Sponge Analysis

OBJECTIVE

To determine if absorbable gelatin sponge (AGS) can be used to assess the posttympanoplasty microbiome and otic antibiotic exposure.

STUDY DESIGN

Prospective.

SETTING

Tertiary hospital.

METHODS

Patients undergoing tympanoplasty were prospectively enrolled. Intraoperatively, AGS was applied to the medial ear canal/tympanic membrane (TM) for 1 minute after canal incision, then saved for analysis. Ear canals were packed with AGS at the end of surgery. Otic ofloxacin was administered until the first postoperative visit, when AGS was collected. Microbial presence was assessed by culture. Ofloxacin levels were assessed by liquid-chromatography mass-spectrometry.

RESULTS

Fifty-three patients were included. AGS was collected in 92.9% of patients seen within 21 days compared to 70.8% of those seen at 22 to 35 days. At surgery, AGS yielded bacteria and fungi in 81% and 11%, respectively, including Staphylococcus species (55%) and Pseudomonas species (25%). Postoperatively, AGS yielded bacteria in 71% and fungi in 21% at the meatus, (staphylococci 57% and pseudomonas 25%). TM samples yielded bacteria in 69%, fungi in 6%, staphylococci in 53%, and pseudomonas in 19%. Ofloxacin concentration at the meatus was 248 μg/mL (95% confidence interval [CI]: 119-377) and at the TM was 126 μg/mL (95% CI: 58-194). Ofloxacin-resistant colonies were found in 75% of patients.

CONCLUSION

Analysis of AGS is a viable technique for noninvasively studying healing metrics posttympanoplasty, including the microbiome and otic antibiotic exposure. Despite exposure to a high concentration of quinolones, the tympanoplasty wound is far from sterile, which may impact healing outcomes.

[Chronic mesotympanic Otitis media - Part 1: Diagnosis and Medical Treatment]

Chronic mesotympanal otitis media (CMOM) is a well-developed clinical presentation that is established in diagnostics and therapy. On closer inspection, however, this principle cannot be confirmed in all its facets. Already the physiology and pathophysiology of the middle ear mucosa leave questions unanswered, starting with the distribution of the ciliated epithelium in the middle ear and mastoid to the function of gas exchange.In addition, there are new diagnostic and therapeutic approaches. In the future, optical coherence tomography could help to determine the status of the middle ear mucosa. In addition, there are new findings on the effectiveness of local and systemic antibiotics as well as antiseptics in chronic otorrhea. Other new developments include minimally invasive surgical procedures using endoscopic techniques. All this gives reason to provide an update on the topic of chronic mesotympanal otitis media, which should contribute in preparation for the specialist examination or refreshing.Basics of physiology and pathophysiology as well as new diagnostic approaches and medical treatment were covered in Part 1 of this paper. In Part 2, in addition to established methods, new developments in surgical therapy with minimally invasive surgical procedures are described in more detail.

Bacterial diversity of middle ear cholesteatoma by 16S rRNA gene sequencing in China

In this study, the bacterial diversity of acquired middle ear cholesteatoma (MEC) was evaluated to reveal its pathogenesis and provides a guide for the use of antibiotics. Twenty-nine cases of acquired MEC and eight cases of healthy middle ears undergoing cochlear implantation (CI) were evaluated. Full-length 16S rRNA gene sequencing was performed to profile the bacterial communities in lesions and healthy tissues of the middle ear. ACE (P = 0.043) and Chao1 (P = 0.039) indices showed significant differences in alpha diversity (P < 0.05). Analysis of PERMANOVA/Anosim using the Bray-Curtis distance matrix results suggested that the between-group differences were greater than the within-group differences (R = 0.238, P < 0.05, R² = 0.066, P < 0.05). Bacterial community analysis revealed that Alphaproteobacteria at the class level and Caulobacterales and Sphingomonadales at the order level were significantly different (P < 0.05). In the LefSe (Linear discriminant analysis effect size) analysis, Porphyromonas bennonis was elevated, and Bryum argenteum and unclassified Cyanobacteriales were reduced at the species level in MEC (P < 0.05). Fifteen metabolic pathways were found to be significantly different between the two groups by analysing the abundance of metabolic pathways in level 2 of the Kyoto Encyclopaedia of Genes and Genomes (KEGG). Seven and eight metabolic pathways were significantly elevated in the MEC and control groups, respectively (P < 0.05). The role of bacteria in the pathogenesis of acquired MEC was further refined through analysis of metabolic pathways. These findings indicate that the acquired MEC and healthy middle ear contain more diverse microbial communities than previously thought.

Cholesteatoma has an altered microbiota with a higher abundance of Staphylococcus species

Objective

To compare the microbiota between cholesteatoma and chronic suppurative otitis media (COM) and to identify potential pathogens that explain the relevant phenotypes of cholesteatoma.

Study Design

Prospective cohort study.

Methods

Surgical specimens collected from 20 cholesteatomas and nine COMs were treated to dissolve biofilms and subjected to 16S ribosomal RNA (rRNA) gene sequencing and amplicon sequence variant-level analysis for microbiota profiling and quantitative comparison. Correlations between the relative abundance of potential pathogens and the volume of the primary resected cholesteatomas were examined.

Results

Differences in bacterial composition (beta diversity) were observed between cholesteatomas and COM (p = .002), with a higher abundance of Staphylococcus in cholesteatomas than in COM (p = .005). Common genera in the external auditory canal (EAC) flora, such as Staphylococcus, Corynebacterium, and Cutibacterium, were predominant in both cholesteatoma and COM; Staphylococcus aureus and Pseudomonas aeruginosa were increased in both diseases compared with the EAC flora. Furthermore, coagulase-negative staphylococci (CoNS) were more abundant in cholesteatomas than in COM (p = 0.002). Linear discriminant analysis coupled with effect size measurements (LEfSe) identified four CoNS as potential biomarkers for cholesteatoma. The relative abundance of S. aureus, a potential pathogen, was positively correlated with cholesteatoma volume (r = .60, p = .02).

Conclusion

The microbiota of cholesteatoma and COM originated from EAC flora, but the bacterial composition was largely altered. Our results suggested that S. aureus infection is involved in cholesteatoma progression.

Level of Evidence

3b.

High-Throughput Sequencing Investigation of Bacterial Diversity in Chronic Suppurative Otitis Media and Middle Ear Cholesteatoma

Background

Chronic otitis media is a common middle ear disease in otolaryngology. Bacterial infection is considered as the cause of the disease, but relying on conventional bacterial cultures can be problematic for identifying specific pathogens. Current research suggests that bacteria in microbial communities can only be identified by rDNA sequencing of bacteria.

Methods

This cross-sectional study utilized broad-range PCR amplification of 16S rRNA genes with clone analysis to compare bacterial diversity in lesions from 6 patients with chronic suppurative otitis media (CSOM) and 10 patients with cholesteatoma of middle ear lesions. Bacteria were analyzed at the levels of phylum, order, family, genus, and species.

Results

The age and sex difference between the patients with chronic suppurative otitis media and the patients with middle ear cholesteatoma were comparable (P > 0.05). Bacterial species abundance and species diversity were greater in cholesteatoma of the middle ear lesions than in CSOM lesions. The total number of detected operational taxonomic units (OTU) was 838, comprising 788 OTU detected in cholesteatoma pathological tissues, 230 in CSOM pathological tissues, and 180 OTU common to both groups. Proteus is a major part of CSOM (99.46%, P = 0.000321). The phyla detected in the Cholesteatoma samples were Proteus (Proteobacteria) (35.77%), thikum (Firmicutes) (44.21%, P = 0.001071), and Actinomycetes (Actinobacteria) (16.66%, P = 0.032464). At all bacterial taxonomic levels, the epithelial tissue of middle ear cholesteatoma was complex in terms of bacterial diversity, covering many Gram-positive and Gram-negative bacteria, likely related to bacterial microbiome formation. In contrast, the bacteriology of the CSOM lesions was relatively simple at all taxonomic levels, with all sequences characterized as belonging to Gram-negative bacteria.

Conclusion

Our results suggest that persistent middle ear cholesteatoma infection may be a microbial flora disorder related to conditional pathogenic bacteria rather than a single bacterial infectious disease. The pathogen is relatively single in the diseased tissue of chronic suppurative otitis media, which is the main reason for its effective antiinfection treatment.

Microbiota Associated With Cholesteatoma Tissue in Chronic Suppurative Otitis Media

Otitis media (OM), defined as infection or inflammation of the middle ear (ME), remains a major public health problem worldwide. Cholesteatoma is a non-cancerous, cyst-like lesion in the ME that may be acquired due to chronic OM and cause disabling complications. Surgery is required for treatment, with high rates of recurrence. Current antibiotic treatments have been largely targeted to previous culturable bacteria, which may lead to antibiotic resistance or treatment failures. For this study, our goal was to determine the microbiota of cholesteatoma tissue in comparison with other ME tissues in patients with long-standing chronic OM. ME samples including cholesteatoma, granulation tissue, ME mucosa and discharge were collected from patients undergoing tympanomastoidectomy surgery for chronic OM. Bacteria were profiled by 16S rRNA gene sequencing in 103 ME samples from 53 patients. Respiratory viruses were also screened in 115 specimens from 45 patients. Differences in bacterial profiles (beta-diversity) and the relative abundances of individual taxa were observed between cholesteatoma and ME sample-types. Additionally, patient age was associated with differences in overall microbiota composition while numerous individual taxa were differentially abundant across age quartiles. No viruses were identified in screened ME samples. Biodiversity was moderately lower in cholesteatoma and ME discharge compared to ME mucosal tissues. We also present overall bacterial profiles of ME tissues by sample-type, age, cholesteatoma diagnosis and quinolone use, including prevalent bacterial taxa. Our findings will be useful for fine-tuning treatment protocols for cholesteatoma and chronic OM in settings with limited health care resources.

Defining the microbiome of the head and neck: A contemporary review

OBJECTIVE

The purpose of this paper is to define the microbiome of the head and neck by characterizing and distinguishing the commensal bacteria from pathogenic species.

STUDY DESIGN

Literature review.

METHODS

Pubmed and Google scholar databases were queried for relevant articles. Keywords such as "middle ear microbiome", "outer ear microbiome", "sinonasal microbiome", "tonsil microbiome", and "laryngeal microbiome" were utilized separately to identify articles pertaining to each topic of study. All applicable abstracts were chosen for initial review and relevant abstracts were then selected for review of the full texts. Articles that did not study the human microbiome, those not written primarily in English, those that were not readily available for full review, and case reports were excluded from the study.

RESULTS

Limited studies that investigate the microbial environments of isolated anatomic subsites in the head and neck exist, however the comprehensive microbiome of the head and neck has yet to be completely defined. Based on this review, various studies of the ears, larynx, tonsils and sinus microbiomes exist and yield valuable information, however they are limited in scope and anatomic subsite. In this literature review, these studies are compiled in order to create a comprehensive text inclusive of the known microbial elements of the major anatomic subsites of the head and neck, namely the tonsils, larynx, sinus, outer ear and middle ear.

CONCLUSIONS

The significance of the human microbiome in identifying and preventing disease has been established in various physiologic systems, however there is limited research on the microbiome of the head and neck. Understanding the microbiome of the head and neck can help differentiate disease-prone patients from normal patients and guide treatment regimens and antibiotic usage, to aid in resistance control and limit adverse effects of antibiotic overuse. Understanding the elements that lead to dysbiosis can help treat and even prevent common conditions as tonsillitis and rhinosinusitis. In this review, we provide a comprehensive review to serve as an initial background for future studies to define the head and neck microbiome distinguished by all relevant subsites.

[Microbiome of the external auditory canal and preoperative preparation of patients in otosurgery (literature review)]

OBJECTIVE

To analyze the effectiveness of methods of antiseptic and hygienic preoperative preparation of the operating field in otosurgery.

MATERIAL AND METHODS

A review and an expert assessment of the corresponding research objectives of scientific publications contained in the PubMed and Google Scholar databases have been carried out.

RESULTS

Various studies indicate a lower ototoxicity of 5-10% of the drug povidone-iodine compared to others. Drugs, such as Miramistin, Okomistin, Dioxidine, are actively used in otiatrics in Russia, but no data on their ototoxicity have been noted. The collected data point to the relevance and prospects of studying the microbiome of the external auditory canal, assessing its effect on the course of the postoperative period, depending on various methods of preparation (antiseptic, removal of earwax and hair depilation) of the surgical field for otosurgery.

Clinical anaerobic infections in an Indian tertiary care hospital: A two-year retrospective study

OBJECTIVE

To study the spectrum of anaerobic infections and the frequency of clinically relevant anaerobes in various infections in a tertiary care hospital in North India.

METHOD

In this two-year (2018-2019) retrospective study, a total of 22,177 samples were processed both anaerobically and aerobically. The samples included blood, pus, body fluids, necrotic tissues, abscess, peritoneal fluids, and other specimens of conditions predisposing to anaerobic infections. The recovered bacterial isolates were identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS).

RESULT

Of the 22,177 samples processed anaerobically, 1094 showed significant anaerobic growth yielding 1464 anaerobes. Bacteroides fragilis (12.7%) and Peptoniphilus harei (12.2%) were the most predominant anaerobes, whereas Escherichia coli (32.6%) and Staphylococcus aureus (13.2%) were the most frequently recovered facultative anaerobes in polymicrobial growth. Both aerobic and anaerobic data were available for 673/1094 samples, of which 68% represented a polymicrobial etiology and 32% as monomicrobial. Of the cases where complete clinical information was available (504/1094), the majority of the anaerobes were recovered from the skin and soft tissue infections (36.3%) and intra-abdominal infections (17.1%). The clinical specimen most frequently growing anaerobes was abscess (29.1%), followed by diabetic foot ulcers (14.1%).

CONCLUSION

The study documents the frequency of clinically significant anaerobic bacteria in various infections, and their associations with aerobes in polymicrobial growth. The present study may aid us in devising better therapeutic strategies against both aerobes and anaerobes in anaerobic infections, which is often empirical. Besides, the data can update clinicians with the changing patterns of anaerobic infections, which remains a neglected concern.

Characteristics of the bacterial microbiota in the upper respiratory tract of children

PURPOSE

The respiratory tract microbiota are deemed as the gatekeeper to health. Consequently, microbiota dysbiosis can lead to the development of diseases. To identify the exact origins of the localized pathogenic bacteria, we investigated bacterial composition in the upper airway tract.

METHODS

Separate mucosal swabs were collected from nostril or oropharynx of each participant. Meanwhile, the lymphoid tissues including adenoids and tonsils were collected during operation. DNAs were exacted from all the samples for the following 16S rRNA analysis.

RESULTS

At the phylum level, the basic bacterial structures in the adenoids, tonsils, oropharynx, and nostrils were generally similar: five main phyla Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria form the majority of the microbiota. However, across these four sites, the microbiota composition differed. More specifically, the bacterial composition in the nostrils was unique. There, Firmicutes and Actinobacteria were the most abundant phyla, while Bacteroides and Fusobacteria were the least abundant. At the genus level, Staphylococcus, Dolosigranulum, Corynebacterium, and Moraxella were the most plentiful, while Fusobacteria was the least ample. Across all sites, Streptococcus displayed similar abundances. Fusobacteria exhibited higher abundances in the lymphoid tissues and oropharynx. Haemophilus and Neisseria were more plentiful in the tonsils and oropharynx. Notably, Klebsiella, which is normally localized to the gut, was abundant in the adenoids and tonsils.

CONCLUSION

Our data indicate that promising pathogenic bacteria originate from all sites in the upper airway. The upper tract lymphoid tissues, normally considered as immune organs, may also serve as reservoirs for pathogenic bacteria.

Respiratory viruses in the healthy middle ear and middle ear with otitis media with effusion

To investigate the presence of respiratory viruses in the middle ear cavity of the individuals with a healthy middle ear and the children with otitis media with effusion (OME). A total of 72 middle ear samples were collected from 25 children with OME (Group 1) and 47 individuals with no middle ear disease (Group 2). Multiplex real-time polymerase chain reaction was used to investigate the presence of 20 different respiratory viruses. Virus results were compared with bacteriomes of the same populations. At least one respiratory virus was detected in 56% of the patients in Group 1 and 12.8% of the individuals in Group 2. The viral co-infection rate for Group 1 and 2 was 8% and 2.1%, respectively. In Group 1, adenovirus was the most frequently detected virus with a rate of 24%, either alone (16%) or concurrent with other viruses (8%), followed by influenza B (12%), rhinovirus, and bocavirus (8%) each. Parainfluenza 4, coronavirus OC43, and RSV A/B were detected in 4% of the sample each. In Group 2, rhinovirus was detected in two samples (4.3%) followed by adenovirus, coronavirus OC43, coronavirus E299, and coronavirus NL63 with a rate of 2.1% each. The detection rate of respiratory viruses was significantly higher in children aged 6 to 11 years. There was no positive association between virus and bacteria found in the middle ear cavity. The current study has provided comprehensive data indicating the presence of diverse respiratory viruses in the healthy middle ear cavity. Our results also suggest that respiratory viruses might have a contribution to OME pathogenesis.

Microbiological investigation of samples collected from healthy middle ears during cochlear implant surgery

This study aimed to investigate the bacteriome in microscopically healthy middle ear mucosa using Next-generation sequencing (NGS) technology. A total of 60 middle ear washing fluids of pediatric and adult were obtained from 47 patients (35 children and 12 adults). Both children and adults with normal middle ears harbored diverse bacteriome. Seventeen different genera with a mean relative abundance of more than 1% were detected in all samples. Both in adult and children, the most abundant genus was Propionibacterium followed by Streptococcus, Staphylococcus, and Ralstonia. The species Propionibacterium acnes and Corynebacterium tuberculostearicum were significantly more abundant in the adult group. Although there were differences in the prevalence and relative abundance of some bacteria observed from adult and child groups, no specific genus or species was detected only in children or adults.

Outcomes After Tympanic Membrane Perforation During Primary Stapes Surgery for Otosclerosis

OBJECTIVE/HYPOTHESIS

Stapes surgery is occasionally complicated by an intraoperative tympanic membrane perforation (ITMP), traditionally indicating abortion of the procedure due to concerns for postoperative infection and sensorineural hearing loss (SNHL). This work examines outcomes and complications in completed primary stapes surgeries with and without ITMP.

STUDY DESIGN

Retrospective review.

METHODS

All patients diagnosed with otosclerosis between February 2008 and September 2017 at a tertiary otology referral center were reviewed retrospectively. Primary outcome measures were post-operative air-bone gap (ABG), air conduction and bone conduction pure tone averages, and post-operative complications.

RESULTS

Review revealed 652 primary stapes operations meeting inclusion criteria, of which ITMP occurred in 10. There were no significant differences in pre-operative hearing metrics or demographic characteristics between ears with and without ITMP. There were also no significant differences in post-operative ABG (6.4 vs. 8.0 dB HL, P = .43) or change in ABG after surgery (-21.6 vs. -18.2 dB, P = .34) between these two groups. Patients with ITMP were more likely to complain of post-operative dysgeusia (30.0% vs. 5.3%, P = .015) but were no more likely to develop reparative granuloma, otitis media, or SNHL (P > .05).

CONCLUSIONS

The first review of ITMP and hearing outcomes after stapes surgery is presented. Our findings suggest that it is likely safe and appropriate to proceed with primary stapes surgery and concurrent tympanoplasty in the presence of a small ITMP with minimal risk of infection, SNHL, or worsened hearing outcomes.

LEVEL OF EVIDENCE

4 Laryngoscope, 131:E2026-E2030, 2021.

Bitter Taste Receptors and Chronic Otitis Media

OBJECTIVE

To evaluate the presence of bitter taste receptors (T2Rs) in the middle ear and to examine their relationship with chronic ear infections.

STUDY DESIGN

Cross-sectional study.

SETTING

Tertiary care hospital.

METHODS

This study enrolled 84 patients being evaluated for otologic surgery: 40 for chronic otitis media (COM) and 44 for other surgical procedures (controls). We collected a small piece of mucosa from 14 patients for mRNA analysis and from 23 patients for immunohistochemistry. A total of 55 patients underwent a double-blind taste test to gauge sensitivity to phenylthiocarbamide, denatonium, quinine, sucrose, and sodium chloride; 47 patients gave a salivary sample for single-nucleotide polymorphism analysis of rs1376251 (TAS2R50) and rs1726866 (TAS2R38).

RESULTS

Bitter taste receptors were found in all samples, but the repertoire varied among patients. T2R50 was the most consistently identified receptor by mRNA analysis. Its rs1376251 allele was related to susceptibility to COM but not the expression pattern of T2R50. Ratings of bitterness intensity of phenylthiocarbamide, a ligand for T2R38, differed significantly between the COM and control groups.

CONCLUSION

T2Rs were found within the middle ear of every patient sampled; the rs1376251 allele of TAS2R50 appears to be related to chronic ear infections. These receptors are an intriguing target for future research and possible drug targeting.

Oral seeding and niche-adaptation of middle ear biofilms in health

The entrenched dogma of a sterile middle ear mucosa in health is incongruent with its periodic aeration and seeding with saliva aerosols. To test this, we sequenced 16S rRNA-V4 amplicons from otic secretions collected at the nasopharyngeal orifice of the tympanic tube and, as controls, oropharyngeal and buccal samples. The otic samples harbored a rich diversity of oral keystone genera and similar functional traits but were enriched in anaerobic genera in the Bacteroidetes (Prevotella and Alloprevotella), Fusobacteria (Fusobacterium and Leptotrichia) and Firmicutes (Veillonella) phyla. Facultative anaerobes in the Streptococcus genus were also abundant in the otic and oral samples but corresponded to distinct, and sometimes novel, cultivars, consistent with the ecological diversification of the oral migrants once in the middle ear microenvironment. Neutral community models also predicted a large contribution of oral dispersal to the otic communities and the positive selection of taxa better adapted to growth and reproduction under limited aeration. These results challenge the traditional view of a sterile middle ear in health and highlight hitherto unknown roles for oral dispersal and episodic ventilation in seeding and diversifying otic biofilms.

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The middle ear mucosa harbors a rich bacterial community in health.

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Oral migration is the primary mechanism for seeding otic biofilms.

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Periodic aeration of the middle ear enriches for anaerobic taxa and promotes the ecological diversification of oral migrants.

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Our study challenges the entrenched dogma of a sterile middle ear in health.

Cerumen microbial community shifts between healthy and otitis affected dogs

Otitis externa is a common multifactorial disease in dogs, characterized by broad and complex modifications of the ear microbiota. The goal of our study was to describe the ear cerumen microbiota of healthy dogs, within the same animal and between different animals, and to compare the cerumen microbiota of otitis affected dogs with that of healthy animals. The present study included 26 healthy dogs, 16 animals affected by bilateral otitis externa and 4 animals affected by monolateral otitis externa. For each animal cerumen samples from the right and left ear were separately collected with sterile swabs, and processed for DNA extraction and PCR amplification of the 16S rRNA gene. Amplicon libraries were sequenced using an Ion Torrent Personal Genome Machine (PGM), and taxonomical assignment and clustering were performed using QIIME 2 software. Our results indicate that the bacterial community of the cerumen in healthy dogs was characterized by extensive variability, with the most abundant phyla represented by Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes and Fusobacteria. The analysis of both alpha and beta diversity between pairs of left and right ear samples from the same dog within the group of affected animals displayed higher differences than between paired samples across healthy dogs. Moreover we observed reduced bacterial richness in the affected group as compared with controls and increased variability in population structure within otitis affected animals, often associated with the proliferation of a single bacterial taxon over the others. Moreover, Staphylococcus and Pseudomonas resulted to be the bacterial genera responsible for most distances between the two groups, in association with differences in the bacterial community structure. The cerumen microbiota in healthy dogs exhibits a complex bacterial population which undergoes significant modifications in otitis affected animals.

Upper Respiratory Tract Microbiome and Otitis Media Intertalk: Lessons from the Literature

Otitis media (OM) is one of the most common diseases occurring during childhood. Microbiological investigations concerning this topic have been primarily focused on the four classical otopathogens (Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis and Streptococcus pyogenes) mainly because most of the studies have been conducted with culture-dependent methods. In recent years, the introduction of culture-independent techniques has allowed high-throughput investigation of entire bacterial communities, leading to a better comprehension of the role of resident flora in health and disease. The upper respiratory tract (URT) is a region of major interest in otitis media pathogenesis, as it could serve as a source of pathogens for the middle ear (ME). Studies conducted with culture-independent methods in the URT and ME have provided novel insights on the pathogenesis of middle ear diseases through the identification of both possible new causative agents and of potential protective bacteria, showing that imbalances in bacterial communities could influence the natural history of otitis media in children. The aim of this review is to examine available evidence in microbiome research and otitis media in the pediatric age, with a focus on its different phenotypes: acute otitis media, otitis media with effusion and chronic suppurative otitis media.

The microbiomes of adenoid and middle ear in children with otitis media with effusion and hypertrophy from a tertiary hospital in China

INTRODUCTION

Otitis media with effusion (OME) is one of the most common pediatric diseases worldwide. Several studies have analyzed the diversity of the microbiomes found in the middle ear effusions (MEEs) of populations from developed countries. However, no microbiological studies of MEEs from Chinese children with OME have been reported. This study investigated the middle ear and adenoid microbiological profiles of children with OME, and compared the microbial flora of the adenoid between children with and without otitis media.

METHODS

MEEs and adenoid swabs were acquired from 15 children undergoing ventilation tube insertion and adenoidectomy. Adenoid swabs from 15 patients with no ear disease were used as controls. Samples were analyzed by 16S rRNA sequencing. Operational taxonomic units (OTUs) abundance information were normalized. Alpha diversity analyses were used to assess the richness and diversity of the microbial community for each sample. Beta diversity analyses were used to determine the inter-group variability between microbiome structure.

RESULTS

Based on the mean relative abundance, the MEEs were dominated by Haemophilus (14.75%), Staphylococcus (9.37%) and Halomonas (7.85%), and the bacterial compositions of the adenoids in the OME groups were dominated by Haemophilus (21.87%), Streptococcus (19.65%), and Neisseria (5.8%). The bacterial compositions in the adenoids of the controls were dominated by Haemophilus (15.96%), Streptococcus (13.33%), and Moraxella (12.28%). Alpha diversity analyses showed that there were no significant differences in microbiome richness or diversity between the middle ear effusions (TM) and adenoids (TA) of OME subjects. Adenoid samples from OME patients (TA) and control patients (CA) were also similar. Beta diversity analyses showed that the microbiomes of the adenoids in OME patients were also similar to that of controls. However, the microbiome structure of middle ear effusions was dissimilar to those of the adenoids in OME patients according to beta diversity analyses.

CONCLUSIONS

Our results confirmed the microbial diversity of MEEs among Chinese children. However, the dissimilar microbiome composition between samples taken from the surface of the adenoids and from the middle ear effusions challenges the conventional theory that the adenoid serves as a microbial reservoir in children with otitis media with effusion.

Bacterial biofilm in adenoids of children with chronic otitis media. Part II: a case-control study of nasopharyngeal microbiota, virulence, and resistance of biofilms in adenoids

Background: We previously described that adenoid tissue in children with chronic otitis media (COM) contained more mucosal biofilms than adenoid tissue removed for hypertrophy.Aims/objectives: The aim of the second part was to characterize nasopharyngeal microbiota and explore virulence of the most common middle ear pathogens.Material and methods: Bacteriological analysis was performed following a culture-based approach on the samples recovered from 30 patients of COM group (15 biofilm-positive and 15 biofilm-negative) and from 30 patients of a control group (15 biofilm-positive and 15 biofilm-negative). Virulence factors of Streptococcus pneumoniae, Streptococcus pyogenes, and Haemophilus influenzae were investigated.Results: The most frequent species were Firmicutes followed by Proteobacteria and Actinobacteria. The presence of biofilm was statistically associated with an increase of the number of bacterial species and Firmicutes phylum regardless of the condition (case/control). No virulence factors associated with invasive isolates were found for the most common middle ear pathogens.Conclusions and significance: This case-control study demonstrated that the presence of COM plus biofilm was associated with a given microbiota which contained more Firmicutes. Our study allows a better understanding of physiopathological mechanisms involved in chronic otitis media and paves the way for further investigations.

Panel 2- recent advance in otitis media bioinformatics

OBJECTIVES

To update the medical literature on recent large-scale studies employing bioinformatics data analysis tools in otitis media (OM) disease models with a principal focus on developments in the past 5 years.

DATA SOURCES

Pubmed indexed peer-reviewed articles.

REVIEW METHODS

Comprehensive review of the literature using the following search terms: 'genomics, inflammasome, microRNA, proteomics, transcriptome, bioinformatics' with the term 'otitis media', and 'middle ear'. Included articles published in the English language from January 1, 2015-April 1, 2019.

IMPLICATIONS FOR PRACTICE

Large scale bioinformatics tools over the past five years lend credence to the paradigm of innate immune response playing a critical role in host defense against bacteria contributing to Otitis Media (OM) progression from acute to chronic. In total, genomic, miRNAomic, and proteomic analyses all point to the need for a tightly regulated innate immune and inflammatory response in the middle ear. Currently, there is an urgent need for developing novel therapeutic strategies to control immunopathology and tissue damage, improve hearing and enhance host defense for both acute and chronic OM based on full understanding of the basic molecular pathogenesis of OM.

Panel 4: Recent advances in understanding the natural history of the otitis media microbiome and its response to environmental pressures

OBJECTIVE

To perform a comprehensive review of otitis media microbiome literature published between 1^st July 2015 and 30th June 2019.

DATA SOURCES

PubMed database, National Library of Medicine.

REVIEW METHODS

Key topics were assigned to each panel member for detailed review. Draft reviews were collated and circulated for discussion when the panel met at the 20th International Symposium on Recent Advances in Otitis Media in June 2019. The final draft was prepared with input from all panel members.

CONCLUSIONS

Much has been learned about the different types of bacteria (including commensals) present in the upper respiratory microbiome, but little is known about the virome and mycobiome. A small number of studies have investigated the middle ear microbiome; however, current data are often limited by small sample sizes and methodological heterogeneity between studies. Furthermore, limited reporting of sample collection methods mean that it is often difficult to determine whether bacteria detected in middle ear fluid specimens originated from the middle ear or the external auditory canal. Recent in vitro studies suggest that bacterial interactions in the nasal/nasopharyngeal microbiome may affect otitis media pathogenesis by modifying otopathogen behaviours. Impacts of environmental pressures (e.g. smoke, nutrition) and clinical interventions (e.g. vaccination, antibiotics) on the upper respiratory and middle ear microbiomes remain poorly understood as there are few data.

IMPLICATIONS FOR PRACTICE

Advances in understanding bacterial dynamics in the upper airway microbiome are driving development of microbiota-modifying therapies to prevent or treat disease (e.g. probiotics). Further advances in otitis media microbiomics will likely require technological improvements that overcome the current limitations of OMICs technologies when applied to low volume and low biomass specimens that potentially contain high numbers of host cells. Improved laboratory models are needed to elucidate mechanistic interactions among the upper respiratory and middle ear microbiomes. Minimum reporting standards are critically needed to improve inter-study comparisons and enable future meta-analyses.

Reviewing the Pathogenic Potential of the Otitis-Associated Bacteria Alloiococcus otitidis and Turicella otitidis

Alloiococcus otitidis and Turicella otitidis are common bacteria of the human ear. They have frequently been isolated from the middle ear of children with otitis media (OM), though their potential role in this disease remains unclear and confounded due to their presence as commensal inhabitants of the external auditory canal. In this review, we summarize the current literature on these organisms with an emphasis on their role in OM. Much of the literature focuses on the presence and abundance of these organisms, and little work has been done to explore their activity in the middle ear. We find there is currently insufficient evidence available to determine whether these organisms are pathogens, commensals or contribute indirectly to the pathogenesis of OM. However, building on the knowledge currently available, we suggest future approaches aimed at providing stronger evidence to determine whether A. otitidis and T. otitidis are involved in the pathogenesis of OM. Such evidence will increase our understanding of the microbial risk factors contributing to OM and may lead to novel treatment approaches for severe and recurrent disease.

Comparative Analysis of Microbiome in Nasopharynx and Middle Ear in Young Children With Acute Otitis Media

Acute otitis media (AOM) is the most common pediatric infection for which antibiotics are prescribed in the United States. The role of the respiratory tract microbiome in pathogenesis and immune modulation of AOM remains unexplored. We sought to compare the nasopharyngeal (NP) microbiome of children 1 to 3 weeks prior to onset of AOM vs. at onset of AOM, and the NP microbiome with the microbiome in middle ear (ME). Six children age 6 to 24 months old were studied. Nasal washes (NW) were collected at healthy visits 1 to 3 weeks prior to AOM and at onset of AOM. The middle ear fluids (MEF) were collected by tympanocentesis at onset of AOM. Samples were stored in Trizol reagents or phosphate-buffered saline (PBS) at -80°C until use. The microbiome was characterized by 16S rRNA gene sequencing. Taxonomic designations and relative abundance of bacteria were determined using the RDP classifier tool through QIIME. Cumulative sum scaling normalization was applied before determining bacterial diversity and abundance. Shannon diversity index was calculated in Microsoft excel. The relative abundance of each bacteria species was compared via Mann-Whitney U test. We found that the NW microbiome of children during healthy state or at baseline was more diverse than microbiome during AOM. At AOM, no significant difference in microbiome diversity was found between NW and MEF, although some bacteria species appear to differ in MEF than in NW. The microbiome of samples stored in PBS had significant greater diversity than samples stored in Trizol reagent.

Examining the Evidence for an Adult Healthy Middle Ear Microbiome

Otitis media (OM) is a cluster of diseases of the middle ear that commonly result from bacterial infection. OM subtypes in which the tympanic membrane is intact (acute otitis media and otitis media with effusion) are presumed to result from pathogen translocation through the eustachian tube. Recent molecular-based studies have suggested that a diverse middle ear microbiome exists in the absence of disease. These have been largely unsupported by culture and feature species that commonly contaminate low-biomass sequencing data. Combining culture-based and molecular techniques, we undertook a detailed investigation of the evidence for bacterial colonization of the healthy middle ear. Middle ear (ME), nasopharynx (NP), and external ear canal (EC) swabs were collected from a total of 25 adult patients undergoing cochlear implant, stapedotomy, or translabyrinthine vestibular schwannoma resection. Diagnostic culture, microscopy, quantitative PCR, and 16S rRNA gene amplicon sequencing were used to assess sample bacterial content. EC and NP microbiota were consistent with previous reports. In contrast, bacterial levels in ME samples were not significantly above those in unused control swabs. Commonly detected taxa were among recognized sequencing contaminants (Methylobacterium, Pseudomonas, and Acinetobacter). Linear regression of dominant ME taxa confirmed a negative relationship between relative abundance and bacterial load, consistent with contamination. No bacteria were detected by microscopy or diagnostic culture in any middle ear sample. Our findings cast substantial doubt on previous reports identifying a healthy middle ear microbiome using 16S amplicon sequencing.IMPORTANCE Recent molecular-based studies have suggested that a diverse middle ear microbiome in adults and children can exist in the absence of disease. These studies have been largely unsupported by culture and feature species that commonly contaminate low-biomass sequencing data. While 16S rRNA gene amplicon sequencing has proven to be a highly informative technique in many clinical contexts, it is susceptible to spurious signal arising from sequencing reagent contaminants where sample biomass is low. Combining culture-based and molecular techniques, we undertook a detailed investigation of the evidence for bacterial colonization of the healthy middle ear. In finding no evidence of viable bacterial cells in middle ear samples, our study further underlines the importance of careful consideration of amplicon sequence data derived from very-low-biomass contexts and the value of analytical approaches that combine culture and molecular techniques.

Determination of Biofilm-Forming Capacity of Otopathogens Isolated from Discharging Ears in Children with Chronic Otitis Media

Chronic otitis media is a common disease of the developing world with persistent ear discharge, leading to major complications. This study describes the microorganisms isolated from the middle ear and nasopharynx of children with chronically discharging ears. Middle ear and nasopharyngeal swabs from 89 children were studied, and the microorganisms isolated were assessed for biofilm-forming ability. Methicillin-susceptible Staphylococcus aureus was common in the nasopharynx, while the middle ear showed predominantly pseudomonas and Methicillin-resistant S. aureus. Pseudomonas aeruginosa showed strong biofilm formation, whereas Escherichia coli, Proteus sp. and Providentia sp. were weak biofilm producers. S. aureus isolates were negative for biofilm formation.

A model of chronic, transmissible Otitis Media in mice

Infection and inflammation of the middle ears that characterizes acute and chronic otitis media (OM), is a major reason for doctor visits and antibiotic prescription, particularly among children. Nasopharyngeal pathogens that are commonly associated with OM in humans do not naturally colonize the middle ears of rodents, and experimental models in most cases involve directly injecting large numbers of human pathogens into the middle ear bullae of rodents, where they induce a short-lived acute inflammation but fail to persist. Here we report that Bordetella pseudohinzii, a respiratory pathogen of mice, naturally, efficiently and rapidly ascends the eustachian tubes to colonize the middle ears, causing acute and chronic histopathological changes with progressive decrease in hearing acuity that closely mimics otitis media in humans. Laboratory mice experimentally inoculated intranasally with very low numbers of bacteria consistently have their middle ears colonized and subsequently transmit the bacterium to cage mates. Taking advantage of the specifically engineered and well characterized immune deficiencies available in mice we conducted experiments to uncover different roles of T and B cells in controlling bacterial numbers in the middle ear during chronic OM. The iconic mouse model provides significant advantages for elucidating aspects of host-pathogen interactions in otitis media that are currently not possible using other animal models. This natural model of otitis media permits the study of transmission between hosts, efficient early colonization of the respiratory tract, ascension of the eustachian tube, as well as colonization, pathogenesis and persistence in the middle ear. It also allows the combination of the powerful tools of mouse molecular immunology and bacterial genetics to determine the mechanistic basis for these important processes.

Pathogen reservoir hypothesis investigated by analyses of the adenotonsillar and middle ear microbiota

INTRODUCTION

Adenotonsillar and middle ear diseases result in some of the most frequently performed operations in the pediatric population worldwide. The pathogen reservoir hypothesis (PRH) suggests that the adenoids act as a reservoir of bacteria which play a potential pathogenic role in otitis media. Evidence supporting this hypothesis is limited. This study sought to comprehensively determine and compare associations between the adenotonsillar and middle ear bacterial microbiota within individual patients via next-generation sequencing and microbial network analyses.

METHODS

Bacterial 16S rRNA gene-targeted amplicon sequencing was used to determine the bacterial composition of ten pediatric patients undergoing adenotonsillectomy and ventilation tube insertion for otitis media with effusion. At the time of surgery, swabs were taken from the adenoid surface, tonsil crypts and middle ear clefts (through the myringotomy incision).

RESULTS

The most abundant sequences within the bacterial community at genus level across all anatomical sites were Fusobacterium, Haemophilus, Neisseria, and Porphyromonas. There was an observable difference in the relative abundance of bacterial communities, with a higher proportion of Haemophilus and Moraxella in the adenoid when compared with the middle ear. Furthermore, only one module (consisting of 4 bacterial OTUs) from one patient was identified through microbial network analyses to be significantly associated between middle ear and adenoid. In addition, microbial network analysis revealed that the adenoid and tonsil microbiota share greater similarity than do the adenoid and middle ear.

CONCLUSION

The results of this study suggest that the adenoid microenvironment does not correlate to the middle ear microenvironment. A future study at the species level, and over time, is required to further investigate whether the differing relationship between the microbiota of the adenoid and middle ear rejects the pathogen reservoir hypothesis.

Prospective observational case series evaluating middle ear fluid and tympanostomy tubes through pyrosequencing

OBJECTIVE

One of the most common sequelae of tympanostomy tube (TT) placement is post-tympanostomy tube otorrhea (PTTO). Granulation tissue formation has been reported in 5-13.8% of patients with TT placement. The purpose of this study is to determine the biodistribution of microorganisms on TTs and middle ear fluid obtained from patients with PTTO.

METHODS

This was a prospective observational study of subjects (6-months-16-years) who underwent standard of care treatment for chronic PTTO. Data was collected on diagnosis, existence of antibiotic resistance, duration of tube placement, and evidence of recurrent infection and/or PTTO. TTs and middle ear fluid were subjected to pyrosequencing; additionally, ear fluid samples were sent for culture-based laboratory diagnostics.

RESULTS

DNA-pyrosequencing analysis of bacteria from fluid and TTs of pediatric subjects with PTTO revealed a mixture of both aerobic and anaerobic populations. Retained tubes with minimal otorrhea revealed a predominance of Staphylococcus species, normal external auditory canal (EAC) microbiome, within middle ear fluid as well as on TTs. However, TTs with active mucopurulent otorrhea and granulation tissue unveiled prominence of Gram-negative facultative anaerobes such as Pseudomonas and Eikenella. Discrepancies in prominent bacteria were seen between standard culture-based techniques versus pyrosequencing.

CONCLUSION

Retained tympanostomy tubes are colonized primarily with normal flora of the EAC. However, mucopurulent otorrhea associated with granulation tissue formation revealed a prominence of Gram-negative facultative anaerobes. Standard culture-based diagnostics may identify bacteria, which are not predominant species of infection. Future studies are necessary to assess the association of Gram-negative facultative anaerobes with granulation tissue formation.

Metagenomics Analysis of Bacterial Population of Tympanosclerotic Plaques and Cholesteatomas

Objective Chronic otitis media can cause cholesteatomas or tympanosclerosis; however, the pathophysiology of such conditions is not completely known. The aim was to identify a bacterial genome that might be present in tympanosclerotic plaques and cholesteatomas using sequence analysis of the gene responsible for the transcription of 16 ribosomal RNA (rRNA). Study Design Metagenomics analysis of the samples. Setting Samples were collected and evaluated at tertiary care centers. Subjects and Methods Sixty-five tympanosclerotic plaques and 37 cholesteatomas were evaluated. The polymerase chain reaction (PCR) was performed using primers designed for the amplification of the gene responsible for the transcription of bacterial 16 rRNA. The PCR-positive samples were sequenced via Sanger method, and 46 selected samples were analyzed with next-generation sequencing (NGS). Results Sanger sequencing revealed the presence of bacterial genomes in a total of 18 of the 102 samples tested. Sequencing of these genomes indicated the presence of Alloiococcus otitis, Staphylococcus aureus, Achromobacter xylosoxidans, Escherichia coli, Staphylococcus sciuri, Staphylococcus caprae, Parvimonas spp., and Bacillus sp. in the tested samples. The NGS showed 1 or more different bacterial genomes in 44 (95.7%) of the 46 samples tested. Predominately, genome of Clostridiales (27 samples), Staphylococcaceae (24 samples), Peptoniphilaceae (12 samples), and Turicella otitidis (9 samples) were identified. Conclusion The middle ear is inhabited by a diverse microbial community than that previously known. With the use of molecular biology, it has become easier to identify the bacterial genomes and improve our understanding of the role of middle ear microbiota in the pathogenesis of chronic inflammatory ear diseases.

A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera

Background

Recurrent acute otitis media (rAOM, recurrent ear infection) is a common childhood disease caused by bacteria termed otopathogens, for which current treatments have limited effectiveness. Generic probiotic therapies have shown promise, but seem to lack specificity. We hypothesised that healthy children with no history of AOM carry protective commensal bacteria that could be translated into a specific probiotic therapy to break the cycle of re-infection. We characterised the nasopharyngeal microbiome of these children (controls) in comparison to children with rAOM (cases) to identify potentially protective bacteria. As some children with rAOM do not appear to carry any of the known otopathogens, we also hypothesised that characterisation of the middle ear microbiome could identify novel otopathogens, which may also guide the development of more effective therapies.

Results

Middle ear fluids, middle ear rinses and ear canal swabs from the cases and nasopharyngeal swabs from both groups underwent 16S rRNA gene sequencing. The nasopharyngeal microbiomes of cases and controls were distinct. We observed a significantly higher abundance of Corynebacterium and Dolosigranulum in the nasopharynx of controls. Alloiococcus, Staphylococcus and Turicella were abundant in the middle ear and ear canal of cases, but were uncommon in the nasopharynx of both groups. Gemella and Neisseria were characteristic of the case nasopharynx, but were not prevalent in the middle ear.

Conclusions

Corynebacterium and Dolosigranulum are characteristic of a healthy nasopharyngeal microbiome. Alloiococcus, Staphylococcus and Turicella are possible novel otopathogens, though their rarity in the nasopharynx and prevalence in the ear canal means that their role as normal aural flora cannot be ruled out. Gemella and Neisseria are unlikely to be novel otopathogens as they do not appear to colonise the middle ear in children with rAOM.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1154-3) contains supplementary material, which is available to authorized users.