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

Abstract

Background: Early life acute respiratory infection (ARI) with respiratory syncytial virus (RSV) has been strongly associated with the development of childhood wheezing illnesses, but the pathways underlying this association are poorly understood.

Objective: To examine the role of the nasopharyngeal microbiome in the development of childhood wheezing illnesses following RSV ARI in infancy.

Methods: We conducted a nested cohort study of 118 previously healthy, term infants with confirmed RSV ARI by RT-PCR. We used next-generation sequencing of the V4 region of the 16S ribosomal RNA gene to characterize the nasopharyngeal microbiome during RSV ARI. Our main outcome of interest was 2-year subsequent wheeze.

Results: Of the 118 infants, 113 (95.8%) had 2-year outcome data. Of these, 46 (40.7%) had parental report of subsequent wheeze. There was no association between the overall taxonomic composition, diversity, and richness of the nasopharyngeal microbiome during RSV ARI with the development of subsequent wheeze. However, the nasopharyngeal detection and abundance of Lactobacillus was consistently higher in infants who did not develop this outcome. Lactobacillus also ranked first among the different genera in a model distinguishing infants with and without subsequent wheeze.

Conclusions: The nasopharyngeal detection and increased abundance of Lactobacillus during RSV ARI in infancy are associated with a reduced risk of childhood wheezing illnesses at age 2 years.

Keywords: 16S ribosomal RNA sequencing; Lactobacillus; Microbiome; Staphylococcus; asthma; infants; nasopharynx; respiratory syncytial virus; wheezing.

FIG. 1

Boxplots of nasopharyngeal diversity and richness in infants with RSV ARI at the OTU (A) or genus (B) level by 2-year subsequent wheeze. After rarefaction to the lowest library size, α diversity and richness estimates were calculated per each sample. This process was repeated 400 times and results were averaged. The Shannon and inverse Simpson indices were calculated to estimate abundance-based OTU or genus diversity, while the Chao1 estimator and observed taxa counts were calculated to estimate abundance-based OTU or genus richness. Both OTU and genus richness and diversity were lower in infants without 2-year subsequent wheeze, although this was not significant in any case.

FIG. 2

Boxplots of relative abundance of nasopharyngeal bacterial genera in infants with RSV ARI by 2-year subsequent wheeze. Within each sample, counts were normalized to simple proportions. The relative abundance of the 35 most abundant genera is shown; all other genera are not shown in this figure. The median (middle bar), third quartile (right-most bar), and first quartile (left-most bar) abundances are shown. Outliers are represented as dots.

FIG. 3

Probability of a nasopharyngeal bacterial genus being selected into a stability selection model distinguishing infants with RSV ARI with and without 2-year subsequent wheeze. The probability is plotted along the x-axis. The genera are indicated along the y-axis. The top 20 ranked genera are shown in this figure. Lactobacillus ranks highest among taxa selected into the model with a probability of being selected of 0.97.

FIG. 4

Box-Cox transformed nasopharyngeal relative abundance of Lactobacillus in infants with RSV ARI with (blue line) and without (red line) 2-year subsequent wheeze, plotted by RSS. Lines are local regression (LOESS) smoothed curves and gray areas are the 95% CIs. For the y-axis, values closer to 0 indicate a higher abundance. Not all individual data points are shown; a single data point is displayed for infants who had the same RSS and Lactobacillus abundance. In general, the relative abundance of Lactobacillus was lower among infants with subsequent wheeze over all values of the RSS.