The lung microbiome in children with HIV-bronchiectasis: a cross-sectional pilot study

Background: Data on the lung microbiome in HIV-infected children is limited. The current study sought to determine the lung microbiome in HIV-associated bronchiectasis and to assess its association with pulmonary exacerbations. Methods: A cross-sectional pilot study of 22 children (68% male; mean age 10.8 years) with HIV-associated bronchiectasis and a control group of 5 children with cystic fibrosis (CF). Thirty-one samples were collected, with 11 during exacerbations. Sputum samples were processed with 16S rRNA pyrosequencing. Results: The average number of operational taxonomy units (OTUs) was 298 +/- 67 vs. 434 +/- 90, for HIV-bronchiectasis and CF, respectively. The relative abundance of Proteobacteria was higher in HIV-bronchiectasis (72.3%), with only 22.2% Firmicutes. There was no correlation between lung functions (FEV1% and FEF25/75%) and bacterial community (r = 0.154; p = 0.470 and r = 0.178; p = 0.403), respectively. Bacterial assemblage of exacerbation and non-exacerbation samples in HIV-bronchiectasis was not significantly different (ANOSIM, RHIV-bronchiectasis = 0.08; p = 0.14 and RCF = 0.08, p = 0.50). Higher within-community heterogeneity and lower evenness was associated with CF (Shannon-Weiner (H') = 5.39 +/- 0.38 and Pielou's evenness (J) 0.79 +/- 0.10 vs. HIV-bronchiectasis (Shannon-Weiner (H') = 4.45 +/- 0.49 and Pielou's (J) 0.89 +/- 0.03. Conclusion: The microbiome in children with HIV-associated bronchiectasis seems to be less rich, diverse and heterogeneous with predominance of Proteobacteria when compared to cystic fibrosis.