Association of sputum microbiota profiles with severity of community-acquired pneumonia in children

Abstract

BackgroundCompetitive interactions among bacteria in the respiratory tract microbiota influence which species can colonize and potentially contribute to pathogenesis of community-acquired pneumonia (CAP). However, understanding of the role of respiratory tract microbiota in the clinical course of pediatric CAP is limited.MethodsWe sought to compare microbiota profiles in induced sputum and nasopharyngeal/oropharyngeal (NP/OP) samples from children and to identify microbiota profiles associated with CAP severity. We used 16S ribosomal RNA sequencing and several measures of microbiota profiles, including principal component analysis (PCA), to describe the respiratory microbiota in 383 children, 6 months to <18 years, hospitalized with CAP. We examined associations between induced sputum and NP/OP microbiota profiles and CAP severity (hospital length of stay and intensive care unit admission) using logistic regression.ResultsRelative abundance of bacterial taxa differed in induced sputum and NP/OP samples. In children 6 months to < 5 years, the sputum PCA factor with high relative abundance of Actinomyces, Veillonella, Rothia, and Lactobacillales was associated with decreased odds of length of stay ≥ 4 days [adjusted odds ratio (aOR) 0.69; 95 % confidence interval (CI) 0.48–0.99]. The sputum factor with high relative abundance of Haemophilus and Pasteurellaceae was associated with increased odds of intensive care unit admission [aOR 1.52; 95 % CI 1.02–2.26]. In children 5 to < 18 years, the sputum factor with high relative abundance of Porphyromonadaceae, Bacteriodales, Lactobacillales, and Prevotella was associated with increased odds of length of stay ≥ 4 days [aOR 1.52; 95 % CI 1.02–2.26]. Taxa in NP/OP samples were not associated with CAP severity.ConclusionCertain taxa in the respiratory microbiota, which were detected in induced sputum samples, are associated with the clinical course of CAP.Electronic supplementary materialThe online version of this article (doi:10.1186/s12879-016-1670-4) contains supplementary material, which is available to authorized users.

Characterization of the nasopharyngeal viral microbiome from children with community‐acquired pneumonia but negative for Luminex xTAG respiratory viral panel assay detection

“…Mycoplasma, these bacteria frequently colonize the nasopharynx in healthy children and are also common pathogens in the respiratory tract. 18,19,21 However, due to enrichment for viruses, the bacterial sequences found in this study are likely biased and not representative for these patients. These results provide a crude characterization of the bacterial content in these samples along with contigs of other origin.…”

“…Infection of these pathogens may be the main reason for CAP in these children, especially for Streptococcus. 18,19 Veillonella and…”

Respiratory microbiota and lower respiratory tract disease

“…46 This result was partly consistent with a pediatric study assessing the association between upper and lower respiratory tract microbiota and pneumonia severity. 66 Presence of Lactobacillales was associated with longer hospital stay in children older than five years of age, but with a less severe pneumonia in under-five children underscoring the importance of age-related host-microbe interactions and immune system dynamics. Two studies did not support the association between low microbiota diversity and disease.…”

“…Prevotella dominant oropharyngeal microbiota was more frequent in healthy adults than in adults with pneumonia, but more frequent in older children with severe pneumonia than in non-severe pneumonia cases. 46,66 Veillonella and Dolosigranulum were frequently sequenced in healthy individuals or patients with less severe pneumonia in upper respiratory tract samples, the latter particularly in young children. 46,66,67,73 Interestingly, despite Moraxella being associated with pneumonia, Moraxella lacunata was significantly more frequent in pediatric viral vs. non-viral pneumonia, and more frequent in controls than in all-cause pneumonia, highlighting the necessary caution in establishing associations based on phylum or genera-level taxonomics.…”

The Nasopharyngeal Microbiota of Children With Respiratory Infections in Botswana

“…However, over the past decade, studies employing high-throughput sequencing methods have identified diverse microbial communities in both the upper and lower respiratory tracts. 3,4 More recent conceptual models of pneumonia pathogenesis postulate that overgrowth of a single bacterial species within the respiratory tract is a function of complex interactions between the microbiota, potential pneumonia pathogens, and the host immune system. 4 In particular, the nasopharyngeal microbiota provides a barrier to colonization and invasion by bacterial respiratory pathogens through competition for nutrients, production of inhibitory substances, and modulation of the local immune response.…”