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

Date Published: July 14, 2017

Publisher: Public Library of Science

Author(s): Tasnee Chonmaitree, Kristofer Jennings, Georgiy Golovko, Kamil Khanipov, Maria Pimenova, Janak A. Patel, David P. McCormick, Michael J. Loeffelholz, Yuriy Fofanov, Eliane N. Miyaji.


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.

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.

Among the high abundant genus-level nasopharyngeal microbiota were Moraxella, Haemophilus, and Streptococcus (3 otopathogen genera), Corynebacterium, Dolosigranulum, Staphylococcus, Acinetobacter, Pseudomonas, and Bifidobacterium. Bacterial diversity was lower in culture-positive samples for Streptococcus pneumoniae, and Haemophilus influenzae, compared to cultured-negative samples. URI frequencies were positively associated with increasing trend in otopathogen colonization. AOM frequencies were associated with decreasing trend in Micrococcus colonization. During URI and AOM, there were increases in abundance of otopathogen genera and decreases in Pseudomonas, Myroides, Yersinia, and Sphingomonas. 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 Staphylococcus and Sphingobium.

Otopathogen genera played the key roles in URI and AOM occurrences. Staphylococcus counteracts otopathogens thus Staphylococcal colonization may be beneficial, rather than harmful. While Sphingobium may play a role in preventing AOM complicating URI, the commonly used probiotic Bifidobacterium 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.

Partial Text

Otitis media is a common childhood disease; it is the leading cause of doctors’ visits by children, and the most frequent reason children consume antibiotics or undergo surgery [1–3]. Acute otitis media (AOM) occurs as a complication of viral upper respiratory tract infection (URI) [4]. AOM is a polymicrobial disease; its pathogenesis involves complex interactions between bacteria, viruses, and the host inflammatory response [5, 6].

We studied nasopharyngeal microbiota in nearly one thousand samples, collected longitudinally during health and disease (URI and AOM) from one month of age through the first year. Our results suggested that bacterial otopathogen genera (Haemophilus, Streptococcus, and Moraxella) played the key role in the disease process. The increasing trend in colonization of these otopathogen genera was also correlated positively with frequencies of URI, and their presence was associated with URI symptom expression during viral infection. Interestingly, Staphylococcus, but not the commonly used probiotic bacterium Bifidobacterium, played an important role in counteracting the deleterious effect of otopathogens.




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