Upper Respiratory Tract Microbial Communities, Acute Otitis Media Pathogens, and Antibiotic Use in Healthy and Sick Children

<jats:title>ABSTRACT</jats:title> <jats:p> The composition of the upper respiratory tract microbial community may influence the risk for colonization by the acute otitis media (AOM) pathogens <jats:named-content content-type="genus-species">Streptococcus pneumoniae</jats:named-content> , <jats:named-content content-type="genus-species">Haemophilus influenzae</jats:named-content> , and <jats:named-content content-type="genus-species">Moraxella catarrhalis</jats:named-content> . We used culture-independent methods to describe upper respiratory tract microbial communities in healthy children and children with upper respiratory tract infection with and without concurrent AOM. Nasal swabs and data were collected in a cross-sectional study of 240 children between 6 months and 3 years of age. Swabs were cultured for <jats:named-content content-type="genus-species">S. pneumoniae</jats:named-content> , and real-time PCR was used to identify <jats:named-content content-type="genus-species">S. pneumoniae</jats:named-content> , <jats:named-content content-type="genus-species">H. influenzae</jats:named-content> , and <jats:named-content content-type="genus-species">M. catarrhalis</jats:named-content> . The V1-V2 16S rRNA gene regions were sequenced using 454 pyrosequencing. Microbial communities were described using a taxon-based approach. Colonization by <jats:named-content content-type="genus-species">S. pneumoniae</jats:named-content> , <jats:named-content content-type="genus-species">H. influenzae</jats:named-content> , and <jats:named-content content-type="genus-species">M. catarrhalis</jats:named-content> was associated with lower levels of diversity in upper respiratory tract flora. We identified commensal taxa that were negatively associated with colonization by each AOM bacterial pathogen and with AOM. The balance of these relationships differed according to the colonizing AOM pathogen and history of antibiotic use. Children with antibiotic use in the past 6 months and a greater abundance of taxa, including <jats:named-content content-type="genus-species">Lactococcus</jats:named-content> and <jats:named-content content-type="genus-species">Propionibacterium</jats:named-content> , were less likely to have AOM than healthy children (odds ratio [OR], 0.46; 95% confidence interval [CI], 0.25 to 0.85). Children with no antibiotic use in the past 6 months, a low abundance of <jats:named-content content-type="genus-species">Streptococcus</jats:named-content> and <jats:named-content content-type="genus-species">Haemophilus</jats:named-content> , and a high abundance of <jats:named-content content-type="genus-species">Corynebacterium</jats:named-content> and <jats:named-content content-type="genus-species">Dolosigranulum</jats:named-content> were less likely to have AOM (OR, 0.51; 95% CI, 0.31 to 0.83). An increased understanding of polymicrobial interactions will facilitate the development of effective AOM prevention strategies. </jats:p>