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

Francesco Folino,Pasquale Capaccio,Paola Marchisio,Sara Torretta,Stefano Aliberti,Ilaria Coro,Lorenzo Drago,Luca Ruggiero

doi:10.3390/jcm9092845

Francesco Folino, Pasquale Capaccio + Show 6 more

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https://doi.org/10.3390/jcm9092845

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Abstract

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.

Highlights

The human microbiota consists of ecological communities of commensal, symbiotic and pathogenic microorganisms that colonize several body sites, as the gastrointestinal tract, respiratory system, oral cavity, skin and female reproductive system [1]
A diseased alteration in the composition of these bacterial communities, defined dysbiosis, can lead to many pathological conditions, including infections [5]. Most of these studies have been conducted with a marker gene analysis based on a broad-range PCR, using primers that target a segment of the 16SrRNA gene, a highly conserved region contained in bacterial genomes
There are some limitations that should be taken into account when interpreting data derived from these studies: it is not possible to determine whether taxa detected are alive or dead, active or inactive, there is limited functional information; it is susceptible to over amplification bias, especially with low biomass samples such as middle ear fluid; as a short segment of 16SrRNA gene is amplified and sequenced, taxonomic resolution is usually limited to family or genus level; there is great variability depending on technical aspects as region selection, amplicon size, sampling, storage, sequencing approach, and bioinformatic analysis

Summary

Introduction

The human microbiota consists of ecological communities of commensal, symbiotic and pathogenic microorganisms that colonize several body sites, as the gastrointestinal tract, respiratory system, oral cavity, skin and female reproductive system [1]. A diseased alteration in the composition of these bacterial communities, defined dysbiosis, can lead to many pathological conditions, including infections [5] Most of these studies have been conducted with a marker gene analysis based on a broad-range PCR, using primers that target a segment of the 16SrRNA gene, a highly conserved region contained in bacterial genomes. This method, combined with next-generation sequencing technologies, permits the simultaneous characterization of an entire community [6]. Acute otitis media (AOM) is the most common bacterial infection in childhood [8] and the leading cause of antibiotic prescription in pediatric patients [9]; otitis media with effusion (OME) is prevalent in the first years of life, as up to 80% of children suffer from one or more episodes by 10 years of age; it should be considered that the prevalence of OME varies across population and could be difficult to define accurately, as this condition is often asymptomatic [10]

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