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

Qingfu Xu,Lei Xu,Steve Gill,Michael E Pichichero,Eduardo Gonzalez

doi:10.3389/fgene.2019.01176

Abstract

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.

Highlights

Acute otitis media (AOM) is one of the most common bacterial infections in children for which antibiotics are prescribed in the United States of America (Vergison et al, 2010; Monasta et al, 2012)
Samples were either directly stored in 1 ml phosphate-buffered saline (PBS) at −80°C, or centrifuged at 3,000 rpm for 10 min at 4°C, after which the pellets were stored in 1 ml of Trizol reagents (Sigma) at −80°C until use for microbiome analyses
We found that the NP microbiome had significantly greater diversity during health than at onset of AOM (Figure 1)

Summary

Introduction

Acute otitis media (AOM) is one of the most common bacterial infections in children for which antibiotics are prescribed in the United States of America (Vergison et al, 2010; Monasta et al, 2012). Middle ear (ME) microbiome has been reported in chronic otitis media (Santos-Cortez et al, 2016; Krueger et al, 2017; Boers et al, 2018; Johnston et al, 2019), and NP microbiome is associated with pathogenesis of upper respiratory traction infection and AOM (Lappan et al, 2018). None of these studies investigate changes in NP microbiota during onset of AOM. We sought to compare the microbiome in nasal wash (NW) of children 2 to 3 weeks prior to their onset of AOM (but otherwise healthy) versus those same children at onset of AOM, and compare their NW microbiome with ME microbiome during AOM

Methods

Results

Conclusion