Microbial Communities of the Upper Respiratory Tract and Otitis Media in Children

<jats:title>ABSTRACT</jats:title> <jats:p> <jats:named-content content-type="genus-species">Streptococcus pneumoniae</jats:named-content> asymptomatically colonizes the upper respiratory tract of children and is a frequent cause of otitis media. Patterns of microbial colonization likely influence <jats:named-content content-type="genus-species">S. pneumoniae</jats:named-content> colonization and otitis media susceptibility. This study compared microbial communities in children with and without otitis media. Nasal swabs and clinical and demographic data were collected in a cross-sectional study of Philadelphia, PA, children (6 to 78 months) ( <jats:italic>n</jats:italic> = 108) during the 2008-2009 winter respiratory virus season. Swabs were cultured for <jats:named-content content-type="genus-species">S. pneumoniae</jats:named-content> . DNA was extracted from the swabs; 16S rRNA gene hypervariable regions (V1 and V2) were PCR amplified and sequenced by Roche/454 Life Sciences pyrosequencing. Microbial communities were described using the Shannon diversity and evenness indices. Principal component analysis (PCA) was used to group microbial community taxa into four factors representing correlated taxa. Of 108 children, 47 (44%) were colonized by <jats:named-content content-type="genus-species">S. pneumoniae</jats:named-content> , and 25 (23%) were diagnosed with otitis media. Microbial communities with <jats:named-content content-type="genus-species">S. pneumoniae</jats:named-content> were significantly less diverse and less even. Two PCA factors were associated with a decreased risk of pneumococcal colonization and otitis media, as follows: one factor included potentially protective flora ( <jats:italic>Corynebacterium</jats:italic> and <jats:italic>Dolosigranulum</jats:italic> ), and the other factor included <jats:italic>Propionibacterium</jats:italic> , <jats:italic>Lactococcus</jats:italic> , and <jats:italic>Staphylococcus</jats:italic> . The remaining two PCA factors were associated with an increased risk of otitis media. One factor included <jats:italic>Haemophilus</jats:italic> , and the final factor included <jats:italic>Actinomyces</jats:italic> , <jats:italic>Rothia</jats:italic> , <jats:italic>Neisseria</jats:italic> , and <jats:italic>Veillonella</jats:italic> . Generally, these taxa are not considered otitis media pathogens but may be important in the causal pathway. Increased understanding of upper respiratory tract microbial communities will contribute to the development of otitis media treatment and prevention strategies. </jats:p> <jats:p> <jats:bold>IMPORTANCE</jats:bold> Otitis media (middle ear infection) is the most common reason for pediatric sick visits in the United States. <jats:named-content content-type="genus-species">Streptococcus pneumoniae</jats:named-content> is a leading otitis media pathogen. <jats:named-content content-type="genus-species">S. pneumoniae</jats:named-content> must colonize the upper respiratory tract and compete with a complex community of nonpathogenic bacteria before infecting the middle ear. We compared microbial communities in the upper respiratory tract of children who had otitis media and those who did not. Members of the normal flora, i.e., <jats:italic>Corynebacterium</jats:italic> and <jats:italic>Dolosigranulum</jats:italic> , were protective for <jats:named-content content-type="genus-species">S. pneumoniae</jats:named-content> colonization and otitis media. As expected, the genera <jats:italic>Haemophilus</jats:italic> was associated with otitis media. Surprisingly, <jats:italic>Actinomyces</jats:italic> , <jats:italic>Rothia</jats:italic> , <jats:italic>Neisseria</jats:italic> , and <jats:italic>Veillonella</jats:italic> were associated with an increased risk of otitis media. These bacteria are not otitis media pathogens but may be associated with antibiotic use or involved in the causal pathway to disease. Increased understanding of upper respiratory tract microbial communities will lead to new ways to prevent middle ear infections, including probiotics. </jats:p>