Increased Moraxella and Streptococcus species abundance after severe bronchiolitis is associated with recurrent wheezing

Abstract

Background: The role of the airway microbiome in the development of recurrent wheezing and asthma remains uncertain, particularly in the high-risk group of infants hospitalized for bronchiolitis.

Objective: We sought to examine the relation of the nasal microbiota at bronchiolitis-related hospitalization and 3 later points to the risk of recurrent wheezing by age 3 years.

Methods: In 17 US centers researchers collected clinical data and nasal swabs from infants hospitalized for bronchiolitis. Trained parents collected nasal swabs 3 weeks after hospitalization and, when healthy, during the summer and 1 year after hospitalization. We applied 16S rRNA gene sequencing to all nasal swabs. We used joint modeling to examine the relation of longitudinal nasal microbiota abundances to the risk of recurrent wheezing.

Results: Among 842 infants hospitalized for bronchiolitis, there was 88% follow-up at 3 years, and 31% had recurrent wheezing. The median age at enrollment was 3.2 months (interquartile range, 1.7-5.8 months). In joint modeling analyses adjusting for 16 covariates, including viral cause, a 10% increase in relative abundance of Moraxella or Streptococcus species 3 weeks after day 1 of hospitalization was associated with an increased risk of recurrent wheezing (hazard ratio [HR] of 1.38 and 95% high-density interval [HDI] of 1.11-1.85 and HR of 1.76 and 95% HDI of 1.13-3.19, respectively). Increased Streptococcus species abundance the summer after hospitalization was also associated with a greater risk of recurrent wheezing (HR, 1.76; 95% HDI, 1.15-3.27).

Conclusions: Enrichment of Moraxella or Streptococcus species after bronchiolitis hospitalization was associated with recurrent wheezing by age 3 years, possibly providing new avenues to ameliorate the long-term respiratory outcomes of infants with severe bronchiolitis.

Keywords: Bronchiolitis; Haemophilus species; Moraxella species; Streptococcus species; longitudinal studies; microbiome; recurrent wheezing; respiratory syncytial virus; rhinovirus.

Fig 1

Cross-sectional comparison of Moraxella and Streptococcus species relative abundance and percentage of recurrent wheezing (RecWhz) outcomes. Microbiota samples were classified into those at greater than mean abundance (orange circles) and less than mean abundance (purple circles) by comparing the relative abundance of a genus at one of 4 time points (ie, index, clearance, summer, and seasonal) with the mean of this genus across all time points. The percentage of recurrent wheezing by age 3 years was computed at every time point for each group. The association between the abundance group (ie, greater than or less than the mean) and recurrent wheezing outcome at each time point was analyzed by using χ² tests. Abundance group membership was not consistent across time points; a taxon might be protective at one time point and a risk factor for recurrent wheezing at a different time point. Samples collected after the onset of recurrent wheeze were excluded. A, Increased abundance of Moraxella species (mean = 0.08) at the clearance time point is significantly associated with a greater percentage of recurrent wheezing (P = .04). B, Increased abundance of Streptococcus species (mean = 0.04) at the clearance (P = .01) and summer (P = .03) time points is significantly associated with a greater percentage of recurrent wheezing.

Fig 2

Associations between longitudinal Moraxella and Streptococcus species relative abundances and hazard of recurrent wheezing by age 3 years. The HRs for the relative abundance and abundance by time point interaction for Moraxella (left) and Streptococcus (right) species were calculated by using a Bayesian implementation of the joint model for longitudinal and time-to-event data. Bars and points indicate 95% HDIs and medians, respectively, for posterior distributions of log HRs. The shaded area represents the region of practical equivalence (ROPE) around zero, which was defined as [−0.05, 0.05]. Variables with HDIs that do not overlap the ROPE were considered statistically significant. The time-to-event models adjusted for clinical variables recorded at the index time point, with maternal asthma and RSV infection being significant in both models. RV, Rhinovirus.

Fig 3

Kaplan-Meier curves stratified by Moraxella and Streptococcus species risk groups for the onset of recurrent wheezing by age 3 years. Using the mean cutoffs for Moraxella (mean = 0.08) and Streptococcus (mean = 0.04) species at the relevant time points, infants were classified into 3 risk groups identified by the joint model: A, increased Moraxella species abundance at the clearance time point (n = 102); B, increased Streptococcus species abundance at the clearance time point (n = 48); and C, increased Streptococcus species abundance at the summer time point (n = 58). Kaplan-Meier curves were generated for each of the 3 risk groups for the outcome of recurrent wheezing by age 3 years. Curves were stratified by membership in the risk group. The table shows the number of subjects still at risk for recurrent wheeze based on event occurrences and study dropout. Infants can be included in more than 1 risk group. Log-rank test results indicated that differences in hazard functions of stratified curves were significant for all risk groups.

Fig 4

Associations between longitudinal Moraxella and Streptococcus species relative abundances and hazard of recurrent wheezing by age 3 years accompanied by asthma at age 4 years. HRs for the relative abundance and abundance by time point interaction for Moraxella (left) and Streptococcus (right) species were calculated by using a Bayesian implementation of the joint model for longitudinal and time-to-event data. Bars and points indicate 95% HDIs and medians, respectively, for the posterior distributions of log HRs. The shaded area represents the region of practical equivalence (ROPE) around zero, which was defined as [−0.05, 0.05]. Variables with HDIs that do not overlap the ROPE were considered statistically significant. The time-to-event models adjusted for clinical variables were recorded at the index time point, with maternal asthma, RSV infection, and history of eczema being significant in both models. RV, Rhinovirus.

Fig 5

Longitudinal variation of relative abundances for Moraxella and Streptococcus species risk groups in the time after hospitalization. Loess curves were fit for the relative abundance of Moraxella (blue lines) and Streptococcus (red lines) species by using the time since day 1 of hospitalization for infants in the 3 risk groups identified by the joint model: A, increased Moraxella species abundance at the clearance time point (n = 102); B, increased Streptococcus species abundance at the clearance time point (n = 48); and C, increased Streptococcus species abundance at the summer time point (n = 58). Infants were classified into risk groups by using the mean cutoffs for Moraxella (mean = 0.08) and Streptococcus (mean = 0.04) species at the relevant time points and might have been included in more than 1 risk group. Shaded regions indicate 95% CIs. Curves show the transience of the increased abundance of the risk genera.

Fig E1

Relation of Haemophilus species relative abundance to recurrent wheezing (RecWhz) by age 3 years. A, Based on the mean abundance of Haemophilus species across all time points (mean = 0.04), microbiota samples were classified into greater than mean (orange circles) and less than mean (purple circles) groups. The percentage of recurrent wheezing was computed at every time point for each abundance group. Abundance group membership was not consistent across time points, and samples collected after onset of recurrent wheeze were excluded. B, HRs for relative abundance and abundance by time point interaction for Haemophilus species were calculated by using a Bayesian implementation of the joint model for longitudinal and time-to-event data. Bars and points indicate 95% HDIs and medians, respectively, for posterior distributions of log HRs. The shaded area represents the region of practical equivalence (ROPE) around zero, which was defined as [−0.05, 0.05]. Variables with HDIs that did not overlap the ROPE were considered statistically significant. The time-to-event model adjusted for clinical variables recorded at the index time point, with maternal asthma and RSV infection being significant in both models (data not shown).

Fig E2

Overlap of participants in the Moraxella and Streptococcus species risk groups. Using the mean cutoffs for Moraxella (mean = 0.08) and Streptococcus (mean = 0.04) species at the relevant time points, infants were classified into risk groups identified by using the joint model: A (blue), increased Moraxella species abundance at the clearance time point (n = 102); B (red), increased Streptococcus species abundance at the clearance time point (n = 48); and C (light red), increased Streptococcus species abundance at the summer time point (n = 58). The overlap between these 3 risk groups is depicted by using a Venn diagram. There is minimal overlap between the risk groups, with only 2 subjects belonging to all 3 risk groups and 6 subjects having increased Streptococcus species abundance at both the clearance and summer time points.

Fig E3

Longitudinal variation of relative abundances for highly abundant genera in the time after hospitalization categorized by the Moraxella and Streptococcus species risk groups. Loess curves were fit for relative abundances of 8 of the top 10 genera by using the time since day 1 of hospitalization for infants in each of the risk groups identified by the joint model: A, increased Moraxella species abundance at the clearance time point (n = 102); B, increased Streptococcus species abundance at the clearance time point (n = 48); and C, increased Streptococcus species abundance at the summer time point (n = 58). Infants were classified into risk groups using the mean cutoffs for Moraxella (mean = 0.08) and Streptococcus (mean = 0.04) species abundance at the relevant time points and might have been included in more than 1 risk group. The rug plot along the x-axis denotes the distribution of observation times for subjects in the specified risk group. Acinetobacter and Bacillus species abundances did not have noticeable variation over time and were excluded to improve readability.