Differences in the Nasopharyngeal Microbiome During Acute Respiratory Tract Infection With Human Rhinovirus and Respiratory Syncytial Virus in Infancy

Abstract

Respiratory viruses alter the nasopharyngeal microbiome and may be associated with a distinct microbial signature. To test this hypothesis, we compared the nasopharyngeal microbiome of 135 previously healthy infants with acute respiratory infection due to human rhinovirus (HRV; n = 52) or respiratory syncytial virus (RSV; n = 83). The nasopharyngeal microbiome was assessed by sequencing the V4 region of the 16S ribosomal RNA. Respiratory viruses were identified by quantitative reverse-transcription polymerase chain reaction. We found significant differences in the overall taxonomic composition and abundance of certain bacterial genera between infants infected with HRV and those infected with RSV. Our results suggest that respiratory tract viral infections are associated with different nasopharyngeal microbial profiles.

Keywords: children; human rhinovirus; microbiome; nasopharynx; respiratory syncytial virus.

Figure 1.

Comparison of the abundance of nasopharyngeal bacterial genera between infants with acute respiratory tract infection due to human rhinovirus (HRV) or respiratory syncytial virus (RSV). Bacterial genera that are significantly different between groups after adjusting for multiple comparisons by using the DESeq2 package (see “Methods” section) are indicated by an asterisk. A, Mean proportional abundance and 95% bootstrap confidence intervals (CIs) of nasopharyngeal bacterial genera according to viral etiology. Within each sample, counts were normalized to simple proportions. Overlapping confidence intervals do not imply a lack of a significant difference in the DESeq2 analysis. The relative abundance of the 20 most abundant bacterial genera by simple proportions is shown. B, Log₂ fold change and log₂ fold change standard error of nasopharyngeal bacterial genera according to viral etiology as calculated with the DESeq2 analysis. The log₂ fold changes of the 20 most abundant bacterial genera by the DESeq2 adjusted base mean are shown. A log₂ fold change of >0 (pink bars) indicates that abundance was detected to be higher during RSV ARI as compared to HRV ARI, while a log₂ fold change of <0 (blue bars) indicates that abundance was detected to be higher during HRV ARI as compared to RSV ARI. Abbreviation: SE, standard error.