Microbial Communities of the Upper Respiratory Tract and Otitis Media in Children

Abstract

Streptococcus pneumoniae asymptomatically colonizes the upper respiratory tract of children and is a frequent cause of otitis media. Patterns of microbial colonization likely influence S. pneumoniae colonization and otitis media susceptibility. This study compared microbial communities in children with and without otitis media. Nasal swabs and clinical and demographic data were collected in a cross-sectional study of Philadelphia, PA, children (6 to 78 months) (n = 108) during the 2008-2009 winter respiratory virus season. Swabs were cultured for S. pneumoniae. DNA was extracted from the swabs; 16S rRNA gene hypervariable regions (V1 and V2) were PCR amplified and sequenced by Roche/454 Life Sciences pyrosequencing. Microbial communities were described using the Shannon diversity and evenness indices. Principal component analysis (PCA) was used to group microbial community taxa into four factors representing correlated taxa. Of 108 children, 47 (44%) were colonized by S. pneumoniae, and 25 (23%) were diagnosed with otitis media. Microbial communities with S. pneumoniae were significantly less diverse and less even. Two PCA factors were associated with a decreased risk of pneumococcal colonization and otitis media, as follows: one factor included potentially protective flora (Corynebacterium and Dolosigranulum), and the other factor included Propionibacterium, Lactococcus, and Staphylococcus. The remaining two PCA factors were associated with an increased risk of otitis media. One factor included Haemophilus, and the final factor included Actinomyces, Rothia, Neisseria, and Veillonella. Generally, these taxa are not considered otitis media pathogens but may be important in the causal pathway. Increased understanding of upper respiratory tract microbial communities will contribute to the development of otitis media treatment and prevention strategies.

Staphylococcus aureusandStreptococcus pneumoniaeinteraction and response to pneumococcal vaccination: Myth or reality?

“…2,3 During the following years multiple epidemiological studies in different geographical regions observed similar findings of a negative association between carriage of S. pneumoniae and S. aureus in young children. [4][5][6][7][8] The carriage of both species was associated with age, with the peak S. pneumoniae carriage and lowest S. aureus carriage at 6 months to 3 years [4][5][6][7][8][9][10] and peak S. aureus colonization at age <6 months and 5-7 y 11 The negative association was significant even after adjusting for age, but this interference was not observed in older children and adults. 8,12 Interestingly, most studies 2,3,5,9 found that the inverse correlation between S. pneumoniae and S. aureus was significant only for carriage of vaccine-type S. pneumoniae strains, which were carried more commonly before the introduction of the pneumococcal vaccine.…”

“…45 In line with this, Laufer et al observed that S. pneumoniae colonization was more frequently detected when the microbiome had lower population diversity. 4 S. aureus has also been shown to affect and be affected by other species in the upper respiratory niche. Analysis of the nasal microbiome by Lina et al found a negative association between Corynebacterium species and S. aureus carriage, 28 and similarly, Yan et al found that various species of Corynebacterium were either positively (C. accolens) or negatively (C. pseudodiphtheriticum) associated with the presence of S. aureus.…”

“…42 Metagenomic analyses showed the presence of a highly diverse nasopharyngeal microbiome including up to 2042 observed operational taxonomic units and as many as 1,219,310 observed unique sequences. 4,43,44 Considering the vast diversity in the nasal microbiome with which the two pathogens interact, the relationship between the two pathogens should take into consideration the possible roles of other species in the nasal microbiome, possibly by inhibiting or promoting the growth of S. aureus or S. pneumoniae.…”

Multifaceted Interfaces of Bacterial Competition

“…The presence of Corynebacterium spp. in the nasal cavity is often inversely correlated with pathogenic Streptococcus pneumoniae (58). Like S. epidermidis, Corynebacterium accolens also utilizes a secreted enzyme, LipS1, to interfere with a competitor.…”

Early-Life Intranasal Colonization with Nontypeable Haemophilus influenzae Exacerbates Juvenile Airway Disease in Mice

“…The description of the infant respiratory microbiome is only just beginning (45,56,57), but a recent study found an association between early-life H. influenzae nasopharyngeal colonization and microbial population perturbations brought on by viral infection and antibiotic treatment (49). A long-term study performed in Denmark showed that children who exhibited signs of asthma and wheezing by age 7 years had an abnormal immune response to H. influenzae at age 6 months, as measured by cytokine levels and T-cell responses in stored peripheral blood mononuclear cells (PBMCs) obtained from the study participants.…”