Nasopharyngeal microbiota in healthy children and pneumonia patients

Abstract

Our study is the first to compare the nasopharyngeal microbiota of pediatric pneumonia patients and control children by 454 pyrosequencing. A distinct microbiota was associated with different pneumonia etiologies. Viral pneumonia was associated with a high abundance of the operational taxonomic unit (OTU) corresponding to Moraxella lacunata. Patients with nonviral pneumonia showed high abundances of OTUs of three typical bacterial pathogens, Streptococcus pneumoniae complex, Haemophilus influenzae complex, and Moraxella catarrhalis. Patients classified as having no definitive etiology harbored microbiota particularly enriched in the H. influenzae complex. We did not observe a commensal taxon specifically associated with health. The microbiota of the healthy nasopharynx was more diverse and contained a wider range of less abundant taxa.

FIG 1

The composition of nasopharyngeal microbiota of control children (left) and children with nonviral (center) or viral (right) pneumonia. Nonviral-pneumonia patients were further subdivided according to S. pneumoniae diagnosis (patients with both PCR positivity and CRP levels of >40 mg/dl were grouped apart from patients with only one or none of these features). The 12 most abundant operational taxonomic units (OTUs) are shown. Sequences belonging to OTUs which contain <0.5% of total number of sequences were pooled and are labeled “Remaining OTUs.” The samples where respiratory viruses were detected are labeled accordingly, i.e., AdV (adenovirus), RV-EV (rhinovirus or enterovirus), HRSV (human respiratory syncytial virus), and HMPV (human metapneumovirus). “NEG” along the x axis indicates negativity for virus detection. ND, not determined; NA, not available.

FIG 2

Multivariate analysis including 12 most common OTUs. PCA-biplot representation of microbiota of control children and children with bacterial (nonviral) and viral pneumonia. Arrows represent projections of the taxa that are responsible for the differences between groups. Large points represent the group means, and ellipses represent 95% confidence limits.

FIG 3

Mean relative abundance of 12 most common OTUs in samples from pneumonia patients (P) and controls (C). Pneumonia patients are further differentiated as having nonviral pneumonia (P-NV) or viral pneumonia (P-V). OTUs containing <0.5% of the total number of sequences were pooled and are labeled “Remaining OTUs.”