The role of bacteria in the pathogenesis and progression of idiopathic pulmonary fibrosis

Abstract

Rationale: Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease of unknown cause that leads to respiratory failure and death within 5 years of diagnosis. Overt respiratory infection and immunosuppression carry a high morbidity and mortality, and polymorphisms in genes related to epithelial integrity and host defense predispose to IPF.

Objectives: To investigate the role of bacteria in the pathogenesis and progression of IPF.

Methods: We prospectively enrolled patients diagnosed with IPF according to international criteria together with healthy smokers, nonsmokers, and subjects with moderate chronic obstructive pulmonary disease as control subjects. Subjects underwent bronchoalveolar lavage (BAL), from which genomic DNA was isolated. The V3-V5 region of the bacterial 16S rRNA gene was amplified, allowing quantification of bacterial load and identification of communities by 16S rRNA quantitative polymerase chain reaction and pyrosequencing.

Measurements and main results: Sixty-five patients with IPF had double the burden of bacteria in BAL fluid compared with 44 control subjects. Baseline bacterial burden predicted the rate of decline in lung volume and risk of death and associated independently with the rs35705950 polymorphism of the MUC5B mucin gene, a proven host susceptibility factor for IPF. Sequencing yielded 912,883 high-quality reads from all subjects. We identified Haemophilus, Streptococcus, Neisseria, and Veillonella spp. to be more abundant in cases than control subjects. Regression analyses indicated that these specific operational taxonomic units as well as bacterial burden associated independently with IPF.

Conclusions: IPF is characterized by an increased bacterial burden in BAL that predicts decline in lung function and death. Trials of antimicrobial therapy are needed to determine if microbial burden is pathogenic in the disease.

Keywords: Muc5b; bacteria; idiopathic pulmonary fibrosis; microbiome.

Figure 1.

Bacterial burden in patients with idiopathic pulmonary fibrosis (IPF) compared with control subjects. Patients with IPF (red) (n = 64) had a significantly higher bacterial burden than subjects with chronic obstructive pulmonary disease (COPD) (green) (n = 17) and the healthy control subjects (blue) (n = 27) (P = 0.006 and P = 0.0007, respectively). The box signifies the 25th and 75th percentiles, and the median is represented by a short line within the box. BAL = bronchoalveolar lavage.

Figure 2.

Kaplan–Meier curves for time until death. Subjects with idiopathic pulmonary fibrosis (IPF) in the tertile with the highest bacterial load (16S copy number/ml of bronchoalveolar lavage) are shown in red, and were at increased risk of mortality compared with subjects with IPF in the tertile with the lowest bacterial burden, shown in blue (hazard ratio, 4.59; 95% confidence interval, 1.05–20).

Figure 3.

A phylogenetic tree and heatmap of bacterial 16S rRNA sequences grouped by disease status: idiopathic pulmonary fibrosis (IPF), chronic obstructive pulmonary disease (COPD), and healthy control subjects. This depicts operational taxonomic units (OTUs) with identifiers organized phylogenetically by tree with abundance indicated by the color (darker blue or red more abundant). The OTUs of interest are highlighted in red.

Figure 4.

Differences in bacterial operational taxonomic unit (OTU) frequencies between idiopathic pulmonary fibrosis (IPF) and control subjects. Box plots showing significant differences (P < 0.01) in OTUs between control subjects (blue) and patients with IPF (red). Triangles represent subjects with chronic obstructive pulmonary disease (COPD), circles healthy control subjects, and squares subjects with IPF. The box signifies the 25th and 75th percentiles, and the median is represented by a short line within the box.