Porphyromonas, a potential predictive biomarker of Pseudomonas aeruginosa pulmonary infection in cystic fibrosis

Abstract

Introduction: Pseudomonas aeruginosa pulmonary infections are the primary cause of morbi-mortality in patients with cystic fibrosis (CF). In this cohort study, the objective was to identify candidate biomarkers of P. aeruginosa infection within the airway microbiota.

Methods: A 3-year prospective multicentre study (PYOMUCO study) was conducted in Western France and included patients initially P. aeruginosa free for at least 1 year. A 16S-targeted metagenomics approach was applied on iterative sputum samples of a first set of patients (n=33). The composition of airway microbiota was compared according to their P. aeruginosa status at the end of the follow-up (colonised vs non-colonised), and biomarkers associated with P. aeruginosa were screened. In a second step, the distribution of a candidate biomarker according to the two groups of patients was verified by qPCR on a second set of patients (n=52) coming from the same cohort and its load quantified throughout the follow-up.

Results: Porphyromonas (mainly P. catoniae) was found to be an enriched phylotype in patients uninfected by P. aeruginosa (p<0.001). This result was confirmed by quantitative PCR. Conversely, in patients who became P. aeruginosa-positive, P. catoniae significantly decreased before P. aeruginosa acquisition (p=0.014).

Discussion: Further studies on replication cohorts are needed to validate this potential predictive biomarker, which may be relevant for the follow-up in the early years of patients with CF. The identification of infection candidate biomarkers may offer new strategies for CF precision medicine.

Keywords: biomarkers; cystic fibrosis; microbiota; porphyromonas; pseudomonas aeruginosa.

Figure 1

Two-step approach of the study. Samples were issued from the PYOMUCO cohort study whose patients (n=96), initially (T0) all Pseudomonas aeruginosa (PA) free for at least 1 year, were separated into two groups (group 1 and group 2) according to their P. aeruginosa status at the end of the follow-up (Tf). Group 1 patients remained negative, whereas group 2 patients became positive. In a first step carried out in a first set of patients (n=33), bacterial biomarkers associated with P. aeruginosa were screened by 16S-targeted metagenomics; a candidate biomarker (Porphyromonas catoniae) was revealed. In a second step, distribution of the candidate biomarker according to the two groups of patients was verified by quantitative PCR (qPCR) on a second set of patients (n=52) coming from the same cohort. CF, cystic fibrosis.

Figure 2

Inverse correlation between Pseudomonas aeruginosa and Porphyromonas revealed by both 16S rRNA microbiota study and quantitative PCR study in the two groups of patients with cystic fibrosis: group 1 patients (G1) remained P. aeruginosa-negative from the initial visit (T0) to the last one (Tf); group 2 patients (G2), initially negative at T0, became P. aeruginosa-positive at Tf. (A) Results of random forest analysis showing the 15 taxa that contributed the most to each group based on the measure of mean decrease in accuracy. (B) Normalised abundance of P. aeruginosa in each group at the two time points. (C) Normalised abundance of Porphyromonas in each group at the two time points. (D) Absolute quantification of P. catoniae in each group (G1, G2) at the two time points (T0, Tf); a third time point was added (Tx) that corresponded to the visit which preceded the last one (Tf).