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

Abstract

Introduction 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.\xa0aeruginosa infection was previously described (Keravec 2019). Methods ANA-MUCO is a prospective, monocentric and non-interventional study. In 2018, 101\xa0CF 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.\xa0aeruginosa was screened in co-culture. Results 93.3\xa0% of samples were positive in culture to at least one species of anaerobes (median: 7\xa0species). Among them, 13\xa0isolates were identified as Porphyromonas including: 8\xa0P.\xa0pasteri (PP), 2\xa0P.\xa0catoniae (PC), 2\xa0P.\xa0uenonis (PU) and 1\xa0P.\xa0gingivalis (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. Conclusion 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.\xa0aeruginosa has been detected, the hypothesis of an indirect effect via priming of innate immunity will be investigated.