Microbial communities in the respiratory tract of patients with interstitial lung disease

Christian Garzoni, Silvio D Brugger, Weihong Qi, Sarah Wasmer, Alexia Cusini, Philippe Dumont, Meri Gorgievski-Hrisoho, Kathrin Mühlemann, Christophe von Garnier, Markus Hilty, Christian Garzoni, Silvio D Brugger, Weihong Qi, Sarah Wasmer, Alexia Cusini, Philippe Dumont, Meri Gorgievski-Hrisoho, Kathrin Mühlemann, Christophe von Garnier, Markus Hilty

Abstract

Background: Molecular methods based on phylogenetic differences in the 16S rRNA gene are able to characterise the microbiota of the respiratory tract in health and disease.

Objectives: Our goals were (1) to characterise bacterial communities in lower and upper airways of patients with interstitial lung disease (ILD) and (2) to compare the results with the microbiota of patients with Pneumocystis pneumonia (PCP) and normal controls.

Methods: We examined the upper and lower respiratory tract of 18 patients with ILD of whom 5, 6, and 7 had idiopathic interstitial pneumonia (IIP), non-IIP and sarcoidosis, respectively. In addition, six immune-compromised patients with PCP and nine healthy subjects were included as controls. Exclusion criteria were recent bacterial/viral respiratory tract infection, HIV-positivity and subjects receiving antibiotic therapy. Bronchoalveolar lavage fluid and oropharyngeal swabs were simultaneously collected, and microbiota was characterised by ultra-deep 16S rRNA gene sequencing.

Results: The microbiota in lower airways of the majority of patients (30; 90%) primarily consisted of Prevotellaceae, Streptococcaceae and Acidaminococcaceae. α and β diversity measurements revealed no significant differences in airway microbiota composition between the five different groups of patients. Comparison of bacterial populations in upper and lower respiratory tract showed significant topographical discontinuities for 7 (23%) individuals.

Conclusions: IIP, non-IIP and sarcoidosis are not associated with disordered airway microbiota and a pathogenic role of commensals in the disease process is therefore unlikely. Nevertheless, molecular analysis of the topographical microbiota continuity along the respiratory tract may provide additional information to assist management of individual patients.

Keywords: Bacterial Infection; Immunodeficiency; Respiratory Infection; Sarcoidosis.

Figures

Figure 1
Figure 1
α-Diversity indices of the lower airway microbiota. Indicated are the Richness (A) and Shannon-diversity (B) indices for subjects with idiopathic interstitial pneumonia (IIP), non-idiopathic interstitial pneumonia (non-IIP), sarcoidosis, Pneumocystis pneumonia (PCP) and normal controls. No significant differences were observed.
Figure 2
Figure 2
Comparison of bacterial communities in the lower airways by a non-metric multidimensional scaling ordination plot. Shown are the results for subjects with idiopathic interstitial pneumonia (IIP), non-idiopathic interstitial pneumonia (non-IIP), sarcoidosis, Pneumocystis pneumonia (PCP) and normal controls. Bray–Curtis distance matrices were used as input. Statistical differences between the five groups were non-significant (ie, small distances between central points). Five patients had different microbiota illustrated by the large distances to the central points (ID 64, 53, 73, 108 and 50). nMDS, non-metric multidimensional scaling.
Figure 3
Figure 3
Microbial community comparisons and relative abundances of the top 20 bacterial families in 33 bronchoalveolar lavage (BAL) and oropharyngeal samples. A tree illustrating similarities of the microbial communities of the BAL samples are shown on the left. Abundances of bacterial families for each subject (ID) are indicated by a greyscale value. The five groups consisting of idiopathic interstitial pneumonia (IIP), non-idiopathic interstitial pneumonia (non-IIP), sarcoidosis, Pneumocystis pneumonia (PCP) and normal controls, as well as if immunocompromised (IC) for each study subject are indicated. The quantities of bacterial species derived from conventional culture are provided in colony forming units (CFU). The concentrations of the amplification products (c) are indicated in ng/μL.
Figure 4
Figure 4
Comparison of the microbiota between upper and lower airways by procrustes analysis. Pairwise distance matrices were calculated between lower and upper microbial respiratory tract communities from which non-metric dimension plots were subsequently derived. Patients with procrustes residual exceeding the upper quantile (upper dashed line) were considered as containing different microbial communities (ID 64, 50, 73, 38, 53, 17 and 108). Study subjects are presented according to the clinical diagnosis: sarcoidosis, idiopathic interstitial pneumonia (IIP), non-idiopathic interstitial pneumonia (non-IIP), Pneumocystis pneumonia (PCP) and normal controls. ILD, interstitial lung disease.

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