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

<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

Relative abundance of microbiota in samples from subjects without and with AOM in the first year.

<p>Relative abundance of microbiota in samples from subjects without and with AOM in the first year.</p

Relative abundance of microbiota in healthy samples compared to sick visit (URI with or without AOM) samples.

<p>Relative abundance of microbiota in healthy samples compared to sick visit (URI with or without AOM) samples.</p

Characteristics of subjects and number of specimens.

<p>Characteristics of subjects and number of specimens.</p

Nasopharyngeal microbiota in infants and changes during viral upper respiratory tract infection and acute otitis media - Fig 2

<p><b>A-B. Shannon diversity index.</b> Fig 2A. Shannon Diversity Index by positive culture for otopathogens. Number in parentheses are number of samples with positive cultures. None = negative culture; S. pneu = <i>Streptococcus pneumoniae</i>; H. influ = <i>Haemophilus influenzae</i>; M. cat = <i>Moraxella catarrhalis</i>; > 1 path = positive culture for more than one of these pathogens. Fig 2B. Shannon Diversity Index by specific time point after antibiotic use. Samples were grouped based on the time of antibiotic use before sample collection: 7 days, 14 days, 1 month, 2 months, 3 months, and 6 months, comparison was made with samples collected after no history of antibiotic use.</p

Relative abundance of microbiota in virus-negative and virus-positive samples.

<p>Relative abundance of microbiota in virus-negative and virus-positive samples.</p

Shannon diversity index by type of samples.

<p>Healthy (grey circles) or sick visit (URI only or URI with AOM) samples (black circles).</p

Comparison of the most abundant genera in paired samples collected ≤ 7 days apart.

<p>The left set represents data from 14 pairs from subjects with URI that resolved without AOM complication. The right set represents data from 11 pairs from subjects with URI that were complicated with AOM (all within 3 days of the first URI samples).</p