Porphyromonas, a neglected potential key genus of the lung microbiota: description in patients with cystic fibrosis (CF)

Abstract

Recent data showed the importance of anaerobes in chronic pulmonary diseases. To date, their impact on lung homeostasis is not clearly established and metagenomics studies provide a limited description of those key bacteria. We investigated the genus Porphyromonas , whose role as a potential predictive biomarker of P. aeruginosa infection was previously described (Keravec 2019). ANA-MUCO is a prospective, monocentric and non-interventional study. In 2018, 101 CF patients from the CF center of Roscoff, France were included. Sputum samples were collected via a device specially designed for the study in order to protect strict anaerobes. Complete identification of anaerobes, including Porphyromonas species, were performed by culturomics and qPCR. Antimicrobial susceptibility testing was conducted for Porphyromonas . Antagonistic effect of Porphyromonas against P. aeruginosa was screened in co-culture. 93.3 % of samples were positive in culture to at least one species of anaerobes (median: 7 species). Among them, 13 isolates were identified as Porphyromonas including: 8 P. pasteri (PP), 2 P. catoniae (PC), 2 P. uenonis (PU) and 1 P. gingivalis (PG). All Porphyromonas were multisensible, except PC resistant to vancomycin, and PU resistant to clindamycin. No anti-pseudomonal effect was observed for PP and PC (main lung species). PU and PG activity test are currently conducted. The ANA-MUCO study was the largest descriptive study of pulmonary anaerobes conducted on a French CF cohort. Even fastidious, bacteria belonging to the genus Porphyromonas were successfully isolated in culture providing the possibility of an accurate description of each species. These results highlighted the importance to complete metagenomics with culturomics, as the anaerobes impact on lung health may vary totally from one species to another (Guilloux 2020). This may explain the contradictory Results of metagenomics studies. As no direct antimicrobial activity against P. aeruginosa has been detected, the hypothesis of an indirect effect via priming of innate immunity will be investigated.