Three clinically distinct chronic pediatric airway infections share a common core microbiota

Abstract

Rationale: DNA-based microbiological studies are moving beyond studying healthy human microbiota to investigate diverse infectious diseases, including chronic respiratory infections, such as those in the airways of people with cystic fibrosis (CF) and non-CF bronchiectasis. The species identified in the respiratory secretion microbiota from such patients can be classified into those that are common and abundant among similar subjects (core) versus those that are infrequent and rare (satellite). This categorization provides a vital foundation for investigating disease pathogenesis and improving therapy. However, whether the core microbiota of people with different respiratory diseases, which are traditionally associated with specific culturable pathogens, are unique or shared with other chronic infections of the lower airways is not well studied. Little is also known about how these chronic infection microbiota change from childhood to adulthood.

Objectives: We sought to compare the core microbiota in respiratory specimens from children and adults with different chronic lung infections.

Methods: We used bacterial 16S rRNA gene pyrosequencing, phylogenetic analysis, and ecological statistical tools to compare the core microbiota in respiratory samples from three cohorts of symptomatic children with clinically distinct airway diseases (protracted bacterial bronchitis, bronchiectasis, CF), and from four healthy children. We then compared the core pediatric respiratory microbiota with those in samples from adults with bronchiectasis and CF.

Measurements and main results: All three pediatric disease cohorts shared strikingly similar core respiratory microbiota that differed from adult CF and bronchiectasis microbiota. The most common species in pediatric disease cohort samples were also detected in those from healthy children. The adult CF and bronchiectasis microbiota also differed from each other, suggesting common early infection airway microbiota that diverge by adulthood. The shared core pediatric microbiota included both traditional pathogens and many species not routinely identified by standard culture.

Conclusions: Our results indicate that these clinically distinct chronic airway infections share common early core microbiota, which are likely shaped by natural aspiration and impaired clearance of the same airway microbes, but that disease-specific characteristics select for divergent microbiota by adulthood. Longitudinal and interventional studies will be required to define the relationships between microbiota, treatments, and disease progression.

Keywords: bronchiectasis; core microbiota; cystic fibrosis; protracted bacterial bronchitis.

Figure 1.

Box plot comparisons of bacterial diversity between the bronchiectasis (BE), protracted bacterial bronchitis (PBB), and cystic fibrosis (CF) cohorts. Given are three measures of diversity: species richness (S*), Simpson’s complement index (1-D), and Shannon-Wiener index (H’). The top and bottom boundaries of each box indicate the 75th and 25th quartile values, respectively, and lines within each box represent the 50th quartile (median) values. Ends of whiskers mark the lowest and highest diversity values in each instance. One-way ANOVA summary statistics are given in Table E2. The only significant difference found was for H’ between the CF and PBB cohorts (P = 0.027, Table E2).

Figure 2.

Dendrograms of bacterial community membership for all patients from the bronchiectasis (BE), protracted bacterial bronchitis (PBB), and cystic fibrosis (CF) cohorts. Black, gray, and white shaded boxes are given to show positions of BE, PBB, and CF samples, respectively. Patient species profiles were compared using the Sørensen index of similarity and unweighted pair-group method using arithmetic mean (UPGMA).

Figure 3.

Distribution and dispersal of bacterial species among bronchiectasis (BE), protracted bacterial bronchitis (PBB), and cystic fibrosis (CF) pediatric cohorts. (A) The number of samples for which each detected bacterial species (open circles) was observed, plotted against the abundance (log₁₀ scale) of that species among all samples within each cohort (BE, r² = 0.64, F_1,175 = 311.5, P < 0.0001; PBB, r² = 0.72, F_1,128 = 321.1, P < 0.0001; and CF, r² = 0.75, F_1,141 = 418.4, P < 0.0001). (B) A dispersal plot to identify which bacterial species are randomly distributed within each cohort, a measure used to assign core versus satellite status. Index of dispersion was calculated as the ratio of variance to mean of abundance for each species within each cohort and plotted for each sample. The line depicts the 2.5% confidence limit for the χ² distribution. Species that fall below this line are randomly distributed and were considered satellite species, whereas those that are above the line are nonrandomly distributed and were considered core species. The 97.5% confidence limit was not plotted, as no species fell below that line.

Figure 4.

Dendrograms of community membership similarity between the pediatric bronchiectasis (BE), protracted bacterial bronchitis (PBB), and cystic fibrosis (CF) bacterial metacommunities and compared with adult CF and BE metacommunities. Given are whole, core and satellite microbiota. Metacommunity profiles were compared using the Sørensen index of similarity and unweighted pair-group method using arithmetic mean (UPGMA). Similarities between the microbiota from different cohorts are read as the location of the horizontal line connecting those cohorts (the “node”) on the y axis; for example, the similarity between pediatric core microbiota was 90% or greater, whereas that between adult core microbiota was 40% or greater.

Figure 5.

Dendrograms of Raup and Crick probability-based similarity index (S_RC) between the pediatric bronchiectasis (BE), protracted bacterial bronchitis (PBB), and cystic fibrosis (CF) bacterial metacommunities and compared with adult CF and BE metacommunities. Given are the whole, core, and satellite microbiota. S_RC < 0.95 and S_RC > 0.05 denote similarity no greater than expected by chance. S_RC < 0.05 denotes significant dissimilarity, and S_RC > 0.95 significant similarity. The 0.05 and 0.95 thresholds are depicted with dashed lines in each instance. Dendrograms were constructed using unweighted pair-group method using arithmetic mean (UPGMA).