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

Clinical and economic burden of acute otitis media caused by Streptococcus pneumoniae in European children, after widespread use of PCVs-A systematic literature review of published evidence

BACKGROUND

Acute otitis media (AOM) is a common childhood disease frequently caused by Streptococcus pneumoniae. Pneumococcal conjugate vaccines (PCV7, PCV10, PCV13) can reduce the risk of AOM but may also shift AOM etiology and serotype distribution. The aim of this study was to review estimates from published literature of the burden of AOM in Europe after widespread use of PCVs over the past 10 years, focusing on incidence, etiology, serotype distribution and antibiotic resistance of Streptococcus pneumoniae, and economic burden.

METHODS

This systematic review included published literature from 31 European countries, for children aged ≤5 years, published after 2011. Searches were conducted using PubMed, Embase, Google, and three disease conference websites. Risk of bias was assessed with ISPOR-AMCP-NPC, ECOBIAS or ROBIS, depending on the type of study.

RESULTS

In total, 107 relevant records were identified, which revealed wide variation in study methodology and reporting, thus limiting comparisons across outcomes. No homogenous trends were identified in incidence rates across countries, or in detection of S. pneumoniae as a cause of AOM over time. There were indications of a reduction in hospitalization rates (decreases between 24.5-38.8% points, depending on country, PCV type and time since PCV introduction) and antibiotic resistance (decreases between 14-24%, depending on country), following the widespread use of PCVs over time. The last two trends imply a potential decrease in economic burden, though this was not possible to confirm with the identified cost data. There was also evidence of an increase in serotype distributions towards non-vaccine serotypes in all of the countries where non-PCV serotype data were available, as well as limited data of increased antibiotic resistance within non-vaccine serotypes.

CONCLUSIONS

Though some factors point to a reduction in AOM burden in Europe, the burden still remains high, residual burden from uncovered serotypes is present and it is difficult to provide comprehensive, accurate and up-to-date estimates of said burden from the published literature. This could be improved by standardised methodology, reporting and wider use of surveillance systems.

ISOM 2023 research Panel 4 - Diagnostics and microbiology of otitis media

OBJECTIVES

To identify and review key research advances from the literature published between 2019 and 2023 on the diagnosis and microbiology of otitis media (OM) including acute otitis media (AOM), recurrent AOM (rAOM), otitis media with effusion (OME), chronic suppurative otitis media (CSOM) and AOM complications (mastoiditis).

DATA SOURCES

PubMed database of the National Library of Medicine.

REVIEW METHODS

All relevant original articles published in Medline in English between July 2019 and February 2023 were identified. Studies that were reviews, case studies, relating to OM complications (other than mastoiditis), and studies focusing on guideline adherence, and consensus statements were excluded. Members of the panel drafted the report based on these search results.

MAIN FINDINGS

For the diagnosis section, 2294 unique records screened, 55 were eligible for inclusion. For the microbiology section 705 unique records were screened and 137 articles were eligible for inclusion. The main themes that arose in OM diagnosis were the need to incorporate multiple modalities including video-otoscopy, tympanometry, telemedicine and artificial intelligence for accurate diagnoses in all diagnostic settings. Further to this, was the use of new, cheap, readily available tools which may improve access in rural and lowmiddle income (LMIC) settings. For OM aetiology, PCR remains the most sensitive method for detecting middle ear pathogens with microbiome analysis still largely restricted to research use. The global pandemic response reduced rates of OM in children, but post-pandemic shifts should be monitored.

IMPLICATION FOR PRACTICE AND FUTURE RESEARCH

Cheap, easy to use multi-technique assessments combined with artificial intelligence and/or telemedicine should be integrated into future practice to improve diagnosis and treatment pathways in OM diagnosis. Longitudinal studies investigating the in-vivo process of OM development, timings and in-depth interactions between the triad of bacteria, viruses and the host immune response are still required. Standardized methods of collection and analysis for microbiome studies to enable inter-study comparisons are required. There is a need to target underlying biofilms if going to effectively prevent rAOM and OME and possibly enhance ventilation tube retention.

A review of the auditory-gut-brain axis

Hearing loss places a substantial burden on medical resources across the world and impacts quality of life for those affected. Further, it can occur peripherally and/or centrally. With many possible causes of hearing loss, there is scope for investigating the underlying mechanisms involved. Various signaling pathways connecting gut microbes and the brain (the gut-brain axis) have been identified and well established in a variety of diseases and disorders. However, the role of these pathways in providing links to other parts of the body has not been explored in much depth. Therefore, the aim of this review is to explore potential underlying mechanisms that connect the auditory system to the gut-brain axis. Using select keywords in PubMed, and additional hand-searching in google scholar, relevant studies were identified. In this review we summarize the key players in the auditory-gut-brain axis under four subheadings: anatomical, extracellular, immune and dietary. Firstly, we identify important anatomical structures in the auditory-gut-brain axis, particularly highlighting a direct connection provided by the vagus nerve. Leading on from this we discuss several extracellular signaling pathways which might connect the ear, gut and brain. A link is established between inflammatory responses in the ear and gut microbiome-altering interventions, highlighting a contribution of the immune system. Finally, we discuss the contribution of diet to the auditory-gut-brain axis. Based on the reviewed literature, we propose numerous possible key players connecting the auditory system to the gut-brain axis. In the future, a more thorough investigation of these key players in animal models and human research may provide insight and assist in developing effective interventions for treating hearing loss.

Hearing rehabilitation and microbial shift after middle ear surgery with Vibrant Soundbridge in patients with chronic otitis media

INTRODUCTION

Patients with otitis media (OM) encounter significant functional hearing impairment with conductive, or a combined hearing loss and long-term sequelae involving impaired speech/language development in children, reduced academic achievement and irreversible disorders of middle and inner ear requiring a long time therapy and/or multiple surgeries. In its persistent chronic form, Otitis media (COM) can often only be treated by undergoing ear surgery for hearing restoration. The persistent inflammatory reaction plays a major role, often caused by multi-resistant pathogens in the ear. Herein, we present outcomes of patients implanted with currently the only FDA approved active Middle Ear Implant Vibrant Soundbridge (VSB), suffering from persistent COM.

METHODS

The study enrolled 42 patients, treated by performing middle ear (ME) surgery to different extents and implanted with the VSB to various structures in the ME. Included were 17 children and 25 adults that had recurrent and/or persisting OM and significant hearing loss. Preoperative and postoperative patients' audiometric data were evaluated and the benefit with VSB assessed using the Glasgow Benefit Inventory for adults and pediatric cohorts. The microbial spectrum of pathogens was assessed before and after surgery, exploring the colonization of the otopathogens, as well as the intestinal microbiome from individually burdened patients.

RESULTS

The mean functional gain is 29.7 dB HL (range from 10 to 56.2 dB HL) with a significant improvement in speech intelligibility in quiet. Following VSB implantation, no significant differences in coupling were observed at low complication rates. Postoperatively patients showed significantly increased benefit with VSB compared to the untreated situation, including less otorrhea, pain, medical visits, and medication intake, with no recurrent OM and significant bacterial shift in otopathogens. The analysis of the intestinal microbiome displayed a high abundance of bacterial strains that might be linked to chronic and persistent inflammation.

CONCLUSIONS

Functional ear surgery including rehabilitation with a VSB in patients suffering from COM present to be safe and effective. The successful acceptance accompanied by the improved audiological performance resulted in significant benefit with VSB, with a shift in the ear pathogens and altered microbiome and thus is a great opportunity to be treated.

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.

Identification of the Bacterial Pathogens in Children with Otitis Media: A Study in the Northwestern Portuguese District of Braga

Understanding the bacterial etiology of otitis media (OM) is important when designing and evaluating the best course of treatment. This study analyzed middle ear fluid (MEF) and nasopharynx (NP) samples collected from 49 children with OM undergoing myringotomy in the northwestern Portuguese district of Braga. A correlation between species in the NP and MEF was observed following pathogen detection by culture and quantitative polymerase chain reaction (qPCR) methods. Bacterial identification using culturing methods showed that Moraxella catarrhalis was the most representative in NP and MEF, followed by Streptococcus pneumoniae. However, qPCR of MEF showed a higher prevalence (61%) of Haemophilus influenzae. S. pneumoniae was not the most frequently identified species, but it still remains one of the leading causes of OM in this region despite 93.9% of the children being vaccinated with the pneumococcal conjugate vaccine. Furthermore, 46% of the samples analyzed by qPCR identified more than two bacterial species. M. catarrhalis and S. pneumoniae were the most frequent combination identified in NP and MEF samples by culturing methods. Additionally, a few NP and MEF samples simultaneously presented the three main otopathogens. These results point out that polymicrobial infections play an important role in OM. Further studies characterizing the serotypes of the strains isolated, their resistance profile, and their biofilm forming ability would help in the development of more targeted strategies against otitis media.

Viral Inactivation Impacts Microbiome Estimates in a Tissue-Specific Manner

The global emergence of novel pathogenic viruses presents an important challenge for research, as high biosafety levels are required to process samples. While inactivation of infectious agents facilitates the use of less stringent safety conditions, its effect on other biological entities of interest present in the sample is generally unknown. Here, we analyzed the effect of five inactivation methods (heat, ethanol, formaldehyde, psoralen, and TRIzol) on microbiome composition and diversity in samples collected from four different body sites (gut, nasal, oral, and skin) and compared them against untreated samples from the same tissues. We performed 16S rRNA gene sequencing and estimated abundance and diversity of bacterial taxa present in all samples. Nasal and skin samples were the most affected by inactivation, with ethanol and TRIzol inducing the largest changes in composition, and heat, formaldehyde, TRIzol, and psoralen inducing the largest changes in diversity. Oral and stool microbiomes were more robust to inactivation, with no significant changes in diversity and only moderate changes in composition. Firmicutes was the taxonomic group least affected by inactivation, while Bacteroidetes had a notable enrichment in nasal samples and moderate enrichment in fecal and oral samples. Actinobacteria were more notably depleted in fecal and skin samples, and Proteobacteria exhibited a more variable behavior depending on sample type and inactivation method. Overall, our results demonstrate that inactivation methods can alter the microbiome in a tissue-specific manner and that careful consideration should be given to the choice of method based on the sample type under study. IMPORTANCE Understanding how viral infections impact and are modulated by the microbiome is an important problem in basic research but is also of high clinical relevance under the current pandemic. To facilitate the study of interactions between microbial communities and pathogenic viruses under safe conditions, the infectious agent is generally inactivated prior to processing samples. The effect of this inactivation process in the microbiome is, however, unknown. Further, it is unclear whether biases introduced by inactivation methods are dependent on the sample type under study. Estimating the magnitude and nature of the changes induced by different methods in samples collected from various body sites thus provides important information for current and future studies that require inactivation of pathogenic agents.

Dysregulation of immune response in otitis media

Objective

Otitis media (OM) is a common reason for children to be prescribed antibiotics and undergo surgery but a thorough understanding of disease mechanisms is lacking. We evaluate the evidence of a dysregulated immune response in the pathogenesis of OM.

Methods

A comprehensive systematic review of the literature using search terms [otitis media OR glue ear OR AOM OR OME] OR [middle ear AND (infection OR inflammation)] which were run through Medline and Embase via Ovid, including both human and animal studies. In total, 82 955 studies underwent automated filtering followed by manual screening. One hundred studies were included in the review.

Results

Most studies were based on in vitro or animal work. Abnormalities in pathogen detection pathways, such as Toll-like receptors, have confirmed roles in OM. The aetiology of OM, its chronic subgroups (chronic OM, persistent OM with effusion) and recurrent acute OM is complex; however, inflammatory signalling mechanisms are frequently implicated. Host epithelium likely plays a crucial role, but the characterisation of human middle ear tissue lags behind that of other anatomical subsites.

Conclusions

Translational research for OM presently falls far behind its clinical importance. This has likely hindered the development of new diagnostic and treatment modalities. Further work is urgently required; particularly to disentangle the respective immune pathologies in the clinically observed phenotypes and thereby work towards more personalised treatments.

Nasopharyngeal carriage rates and serotype distribution of Streptococcus pneumoniae among school children with acute otitis media in Central Java, Indonesia

Streptococcus pneumoniae is a common bacterial pathogen that causes acute otitis media (AOM) in children. In this study, we investigated nasopharyngeal carriage rates and serotype distributions of S. pneumoniae among school children with AOM in Banyumas Regency, Central Java, Indonesia, from 2018 to 2019. Nasopharyngeal swab specimens and demographic data were collected from 122 children between the ages of 6 and 12. The specimens were cultured for the identification of S. pneumoniae, and serotyping was performed using a sequential multiplex PCR assay. We found that the S. pneumoniae carriage rate was 73 % (89/122) among children with AOM. Serotypes 23A (11 %) and 6A/6B (10 %) were the most common serotypes among the 91 cultured S. pneumoniae strains, followed by 3 (8 %), 14 (7 %), 6C/6D (7 %), 11A/11D (6 %), 15B/15C (4 %) and 35 B (4 %). Moreover, 41 % of the strains could be covered by the 13-valent pneumococcal conjugate vaccine, PCV13. In conclusion, high nasopharyngeal carriage rates of S. pneumoniae were found in school children with AOM, with almost half of the strains being the vaccine-type. This finding provides a baseline for nasopharyngeal carriage of S. pneumoniae in school children with AOM and supports the implementation of pneumococcal conjugate vaccines in Indonesia.

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.

Nasopharyngeal microbiome analyses in otitis-prone and otitis-free children

OBJECTIVES

About 10-15% children develop frequent acute otitis media (AOM) confirmed by tympanocentesis. These children are designated sOP (stringently defined otitis-prone) because all AOM episodes have been microbiologically confirmed. The cause of otitis-proneness in sOP children is multi-factorial, including frequent otopathogen nasopharyngeal (NP) colonization and deficiency in innate and adaptive immune responses. A largely unexplored contributor to otitis proneness is NP microbiome composition. Since the microbiome modulates otopathogen NP colonization and immune responses, we hypothesized that the NP microbiome composition in sOP children might be dysregulated.

METHODS

We performed 16S rRNA sequencing to analyze microbiome composition in 157 NP samples from 28 sOP and 68 AOM-free children when they were 6 months or 12 months old and healthy. Bioinformatic approaches were employed to examine the composition difference between the two populations and its correlation with changes in levels of inflammatory cytokines.

RESULTS

A different global microbiome profile and reduced alpha diversity was observed in the NP microbiome of sOP children when 6 months old, compared with that from AOM-free children of the same age. This difference was resolved when groups were compared at 12 months old. We found 4 bacterial genera-Bacillus, Veillonella, Gemella, and Prevotella-correlated with higher levels of pro-inflammatory cytokines in the NP. Those 4 bacterial genera were in lower abundance in sOP compared to AOM-free children.

CONCLUSION

Dysbiosis occurs in the NP microbiome of sOP children at an early age even when they were healthy. This dysbiosis correlates with a lower inflammatory state in the NP of these children.

The P.E.A.N.U.T. Method: Update on an Integrative System Approach for the Treatment of Chronic Otitis Media with Effusion and Adenoid Hypertrophy in Children

BACKGROUND AND OBJECTIVES

Based on our previous single-center study on optimization of treatment of chronic otitis media with effusion (COME) and adenoid hypertrophy (AH) in children using a noninvasive system approach to lower the necessity of antibiotics, analgesic use, and surgical interventions, we proceeded to perform a multicenter investigation in an outpatient setting. The purpose of the previous prospective study in 2013-2015 was to compare outcomes in the treatment of COME and AH using the noninvasive multimodal integrative method (IM) versus conventional treatment practice (COM).

MATERIALS AND METHODS

In this paper, we retrospectively analyze the data of patients treated with the integrative method between 2017 and 2020 in a multicenter setting and compared the outcomes with data from 2013-2015 in order to evaluate generalizability. In both periods, all eligible and willing participants were included and treated with the IM protocol under real-life conditions. The treatment involved pneumatization exercises, education, an antiallergic diet, nasal hygiene, useful constitutional therapy, and thermal interventions (P.E.A.N.U.T.). A total of 48 versus 28 patients, aged 1-8, were assessed, presenting with COME and AH, with moderate to severe hearing impairment at entry.

RESULTS

The significant improvement found in both audiometric measures (intact hearing) and tympanometric measures (normal A-type curve) was similar in both datasets with respect to conventional treatment. The new data confirms that the P.E.A.N.U.T. method results in a significant reduction of antibiotics, analgesic use, and surgical interventions.

CONCLUSION

In this multicenter trial, we confirm the effectiveness of the noninvasive system approach for the treatment of COME in lowering the need for antibiotics and analgesic use and elective surgery. This could be especially important with respect to a generally observed increase in antibiotic resistance. The method is easy to perform in different clinical settings and is effective, safe, and well-tolerated.

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.

Panel 3: Genomics, precision medicine and targeted therapies

OBJECTIVE

To review the most recent advances in human and bacterial genomics as applied to pathogenesis and clinical management of otitis media.

DATA SOURCES

PubMed articles published since the last meeting in June 2015 up to June 2019.

REVIEW METHODS

A panel of experts in human and bacterial genomics of otitis media was formed. Each panel member reviewed the literature in their respective fields and wrote draft reviews. The reviews were shared with all panel members, and a merged draft was created. The panel met at the 20th International Symposium on Recent Advances in Otitis Media in June 2019, discussed the review and refined the content. A final draft was made, circulated, and approved by the panel members.

CONCLUSION

Trans-disciplinary approaches applying pan-omic technologies to identify human susceptibility to otitis media and to understand microbial population dynamics, patho-adaptation and virulence mechanisms are crucial to the development of novel, personalized therapeutics and prevention strategies for otitis media.

IMPLICATIONS FOR PRACTICE

In the future otitis media prevention strategies may be augmented by mucosal immunization, combination vaccines targeting multiple pathogens, and modulation of the middle ear microbiome. Both treatment and vaccination may be tailored to an individual's otitis media phenotype as defined by molecular profiles obtained by using rapidly developing techniques in microbial and host genomics.