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

Abstract

BackgroundInterferences 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.MethodsWe 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.ResultsAmong 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.ConclusionOtopathogen 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.

Nasopharyngeal Lactobacillus is associated with a reduced risk of childhood wheezing illnesses following acute respiratory syncytial virus infection in infancy

“…In recent years, we and others have demonstrated that the upper airway bacterial microbiome plays an important role in the pathogenesis and pulmonary sequelae of viral ARIs. [9][10][11][12][13][14][15][16][17] For example, several studies in murine models have shown that priming of the nasal mucosa with certain taxa (such as Lactobacillus species) increases the resistance and beneficially modulates the immune response of mice against RSV, influenza, and pneumonia virus. 9,10 In a recent study of young children with RSV ARI, higher nasopharyngeal abundances of Haemophilus influenzae and Streptococcus were associated with a more proinflammatory immune response and a higher risk of hospitalization.…”

A method of processing nasopharyngeal swabs to enable multiple testing

“…Although obtaining a nasopharyngeal (NP) swab is minimally invasive, performance of multiple tests usually requires obtaining multiple specimens. Although some investigators have reported using nasal samples for multiple tests, (1)(2)(3)(4)(5) we are not aware of any studies that have used a single NP swab to evaluate viral, bacterial and host parameters.…”

Microbiome Characteristics of Induced Sputum compared to Bronchial Fluid and Upper Airway Samples

“…The Qiagen software identified all phyla whereas the alternative software could not assign 15% of bacterial DNA and this may be explained by the higher stringency set for the Qiagen software. There is not standard for stringency but these results suggest that although the higher stringency reduces the number of reads included in the analysis, the results are highly comparable to other methods and 17 and (in some situations) CF 18 . In the research setting, sampling from the upper airways has been validated as a surrogate for lower airway sampling 19,20 .…”