Nasopharyngeal microbiota in infants and changes during viral upper respiratory tract infection and acute otitis media

Abstract

<div><p>Background</p><p>Interferences between pathogenic bacteria and specific commensals are known. We determined the interactions between nasopharyngeal microbial pathogens and commensals during viral upper respiratory tract infection (URI) and acute otitis media (AOM) in infants.</p><p>Methods</p><p>We analyzed 971 specimens collected monthly and during URI and AOM episodes from 139 infants. The 16S rRNA V4 gene regions were sequenced on the Illumina MiSeq platform.</p><p>Results</p><p>Among the high abundant genus-level nasopharyngeal microbiota were <i>Moraxella</i>, <i>Haemophilus</i>, and <i>Streptococcus</i> (3 otopathogen genera), <i>Corynebacterium</i>, <i>Dolosigranulum</i>, <i>Staphylococcus</i>, <i>Acinetobacter</i>, <i>Pseudomonas</i>, and <i>Bifidobacterium</i>. Bacterial diversity was lower in culture-positive samples for <i>Streptococcus pneumoniae</i>, and <i>Haemophilus influenzae</i>, compared to cultured-negative samples. URI frequencies were positively associated with increasing trend in otopathogen colonization. AOM frequencies were associated with decreasing trend in <i>Micrococcus</i> colonization. During URI and AOM, there were increases in abundance of otopathogen genera and decreases in <i>Pseudomonas</i>, <i>Myroides</i>, <i>Yersinia</i>, <i>and Sphingomonas</i>. Otopathogen abundance was increased during symptomatic viral infection, but not during asymptomatic infection. The risk for AOM complicating URI was reduced by increased abundance of <i>Staphylococcus and Sphingobium</i>.</p><p>Conclusion</p><p>Otopathogen genera played the key roles in URI and AOM occurrences. <i>Staphylococcus</i> counteracts otopathogens thus <i>Staphylococcal</i> colonization may be beneficial, rather than harmful. While <i>Sphingobium</i> may play a role in preventing AOM complicating URI, the commonly used probiotic <i>Bifidobacterium</i> did not play a significant role during URI or AOM. The role of less common commensals in counteracting the deleterious effects of otopathogens requires further studies.</p></div