Microbial community composition in explanted cystic fibrosis (CF) lungs

Introduction: Previous studies demonstrate a complex and diverse microbiota in sputum samples collected from CF patients. However, no studies have determined if the microbiota is different in distinct anatomical regions in the lung and whether such differences, if present, account for the regional variation in structural damage and lung disease characteristic of CF. Aim: To define the microbiota in the lungs of CF patients undergoing transplantation and determine (1) what is the spatial distribution of bacteria within the airways and does the microbiota in sputum differ from that in lower airway tissue; and (2) if the microbiome in end-stage CF lung disease is spatially heterogeneous and related to the lung microenvironment, localized structural damage and disease progression. Methods: Multiple airway tissue sample cores from distinct anatomical regions were extracted from frozen explanted CF lungs at the KU Leuven. Microbial DNA was extracted from the tissue cores and if a sputum plug was present in any core, it was removed and processed separately. Samples were processed using the Illumina MiSeq platform. Relative abundance of bacteria, richness (number of taxa detected) and the Shannon-Wiener Index (SW) of diversity were subsequently calculated for all samples. Principal coordinates analysis (PCoA) was performed to assess the effect specific taxa had within each sample. Results: Sixteen tissue samples (n= 2 patients) and 13 sputum samples (n= 6 patients) have been analysed with further sample processing ongoing. In general, sputum samples were dominated by a single organism (Pseudomonas, n=8; Achromobacter, n=3; Staphylococcus, n=1; Achromobacter/ Staphylococcus, n=1) with significantly more diversity observed in tissue samples. Richness was significantly greater in tissue (mean: 89.18; range: 22-132) compared to sputum samples (mean: 23.08; range: 8-44). Similarly, diversity (SW index) was significantly greater in tissue (mean: 1.38; range: 0.027-2.702) compared to sputum samples (mean: 0.117; range: 0.004-0.732). Moreover, for the two patients in which tissue samples were analysed, there was considerable variation in both richness and diversity between samples. PCoA for matched sputum and tissue samples from two patients revealed that the sputum samples were similar for both patients in that they were dominated by Pseudomonas spp. In contrast, there was clear separation between the community structures in tissue samples from different patients. Discussion: This study demonstrates that the microbiota in sputum differs from that in lower airway tissue and that diverse and spatially heterogeneous microbiota, not always dominated by “traditional CF pathogens,” may be present in some patients with end-stage CF lung disease. Future analysis will compare microbiome data with histology, high resolution computed tomography and micr°C T data to determine the relationship between microbiota composition, localised structural damage and disease progression.