Lung microbiome and disease progression in idiopathic pulmonary fibrosis: an analysis of the COMET study

Abstract

Background: The role of the lung microbiome in the pathogenesis of idiopathic pulmonary fibrosis is unknown. We investigated whether unique microbial signatures were associated with progression of idiopathic pulmonary fibrosis.

Methods: Patients (aged 35-80 years) with idiopathic pulmonary fibrosis within 4 years of diagnosis from the Correlating Outcomes with biochemical Markers to Estimate Time-progression (COMET) in idiopathic pulmonary fibrosis study were followed up for a maximum of 80 weeks. Progression-free survival was defined as time to death, acute exacerbation, lung transplant, or decrease in forced vital capacity (FVC) of 10% or greater or decrease in diffusion capacity of the lung (DLCO) of 15% or greater. DNA was isolated from 55 samples of bronchoscopic alveolar lavage. 454 pyrosequencing was used to assign operational taxonomic units (OTUs) to bacteria based on a 3% sequence divergence. Adjusted Cox models were used to identify OTUs that were significantly associated with progression-free survival at a p<0.10. These OTUs were then used in the analysis of the principal components. The association between principal components and microbes with high factor loadings and progression-free survival were assessed with Cox regression analyses. The COMET study is registered with ClinicalTrials.gov, number NCT01071707.

Findings: Mean FVC was 70.1% (SD 17.0) and DLCO 42.3% (14.0) of predicted. Disease progression was significantly associated with increased relative abundance of two OTUs-Streptococcus OTU 1345 (relative risk 1.11, 95% CI 1.04-1.18; p=0.0009) and Staphylococcus OTU 1348 (1.16, 1.03-1.31, p=0.012). Thresholds for relative abundance of each OTU associated with progression-free survival were more than 3.9% for Streptococcus OTU 1345 (10.19, 2.94-35.35; p=0.0002) and more than 1.8% for Staphylococcus OTU 1348 (5.06, 1.71-14.93; p=0.003).

Interpretation: These preliminary data suggest progression of idiopathic pulmonary fibrosis is associated with the presence of specific members within the Staphylococcus and Streptococcus genera. Additional research will be needed to identify the specific bacterial species and to ascertain whether this is a causal association.

Funding: National Institutes of Health.

Figure 1

Figure 1A. Survival curves generated from Cox regression model stratified by threshold of 3·9% relative abundance for Streptococcus OTU 1345 with average patient profile values substituted for other covariates. Solid line indicates relative abundance below 3·9%; Dashed line indicates relative abundance above 3·9%. Number at risk at 100 day intervals displayed below the figure. Comparison of survival between patients with Streptococcus OTU 1345 below 3·9% relative abundance and patients with Streptococcus OTU 1345 above 3·9% relative abundance, adjusted for the following mean values: age-64·3 years; probability of being male-67·2%; probability of smoking (current and past)-67·3%; FVC%-70·1; DLCO%-42·3; probability of desaturation<88%-52·7%; probability of history of reflux-56·4%; and probability of having Staphylococcus OTU 1348 above threshold relative abundance-29% Figure 1B. Survival curves generated from Cox regression model stratified by threshold of 1·8% for Staphylococcus OTU 1348 with average patient profile values substituted for other covariates. Solid line indicates relative abundance below 1·8%; Dashed line indicates relative abundance above 1·8%. Number at risk at 100 day intervals displayed below the figure. Comparison of survival between patients with Staphylococcus OTU 1345 below 1·8% relative abundance and patients with Staphylococcus OTU 1345 above 1·8% relative abundance, adjusted for the following mean values: age-64·3 years; probability of being male-67·2%; probability of smoking (current and past)-67·3%; FVC%-70·1; DLCO%-42·3; probability of desaturation<88%-52·7%; probability of history of reflux-56·4%; and probability of having Streptococcus OTU 1348 above threshold relative abundance-14·5%

Figure 1

Figure 1A. Survival curves generated from Cox regression model stratified by threshold of 3·9% relative abundance for Streptococcus OTU 1345 with average patient profile values substituted for other covariates. Solid line indicates relative abundance below 3·9%; Dashed line indicates relative abundance above 3·9%. Number at risk at 100 day intervals displayed below the figure. Comparison of survival between patients with Streptococcus OTU 1345 below 3·9% relative abundance and patients with Streptococcus OTU 1345 above 3·9% relative abundance, adjusted for the following mean values: age-64·3 years; probability of being male-67·2%; probability of smoking (current and past)-67·3%; FVC%-70·1; DLCO%-42·3; probability of desaturation<88%-52·7%; probability of history of reflux-56·4%; and probability of having Staphylococcus OTU 1348 above threshold relative abundance-29% Figure 1B. Survival curves generated from Cox regression model stratified by threshold of 1·8% for Staphylococcus OTU 1348 with average patient profile values substituted for other covariates. Solid line indicates relative abundance below 1·8%; Dashed line indicates relative abundance above 1·8%. Number at risk at 100 day intervals displayed below the figure. Comparison of survival between patients with Staphylococcus OTU 1345 below 1·8% relative abundance and patients with Staphylococcus OTU 1345 above 1·8% relative abundance, adjusted for the following mean values: age-64·3 years; probability of being male-67·2%; probability of smoking (current and past)-67·3%; FVC%-70·1; DLCO%-42·3; probability of desaturation<88%-52·7%; probability of history of reflux-56·4%; and probability of having Streptococcus OTU 1348 above threshold relative abundance-14·5%

Figure 2

% Relative abundance of OTU’s from two IPF lung explants taken from proximal and distal airway brushings after the lung was removed. IPF Lung 1 demonstrated 100% relative abundance of Streptococcus OTU 1350 in the proximal brushing. In the distal brushing, two Streptococcus OTU’s were identified, OTU 1350 at 23.89% and OTU 1345 at 0.81% relative abundance. Staphylococcus OTU 1348 was also identified in the distal brush at 1.86% relative abundance. In IPF Lung 2, neither Streptococcus nor Staphylococcus was identified in the proximal brush, but the distal brush demonstrated 15.29% relative abundance for Streptococcus OTU 1345.