The nasopharyngeal microbiome in infants with acute otitis media

Interspecies interactions within the nasopharyngeal microbiome are likely involved in the pathogenesis of acute otitis media (AOM). Capturing the breadth of microbial interactions requires a detailed description of the microbiome during health and AOM using sensitive culture-independent molecular techniques. In this study the nasopharyngeal microbiome was characterised in 163 infants less than 2 years of age with (n=153) or without (n=10) AOM. Multiplexed pyrosequencing of 16S rRNA gene amplicons was applied to nasopharyngeal swabs (NPS) collected during four winter seasons between 2004 and 2010. A total of 88,415 forward and 152,367 reverse reads (after quality filtering) were analysed. The nasopharyngeal microbiome in healthy and infants with AOM differed significantly from each other (community comparison p<0.005). Differences included higher richness and Shannon Diversity indices in the “healthy” as compared to the “AOM” microbiome (p=9E-9; p=0.002). Five bacterial families, including Streptococcaceae, Pasteurellaceae, Moraxellaceae, Staphylococcaceae and Corynebacteriacea predominated. Colonisation with non-pneumococcal Streptococcaceae was was more often identified in healthy (80%) versus AOM diseased infants (21.6%; p=0.0002). In infants with AOM, microbial community structure was significantly influenced by recent exposure to antibiotics (p<0.005) and vaccination with the heptavalent conjugated pneumococcal polysaccharide vaccine (PCV7) (p<0.05). Antibiotic exposure was associated with an increased abundance of Pasteurellaceae (p=0.05) and vaccination with PCV7 correlated with carrying a lower proportion of non-pneumococcal Streptococcaceae (p=0.05). Therefore, the nasopharyngeal microbiome of infants undergoes dramatic changes in association with AOM as compared to the healthy status. Modulating factors are recent antimicrobial exposure and vaccination with PCV7. Further dissection of the inter-species interactions within the nasopharyngeal microbiome during health and AOM may lead to new strategies for the prevention and treatment of AOM.