ReBAM. Identifying anaerobes in the everyday practice of CF sputum analysis
Background: Pulmonary involvement in Cystic fibrosis (CF) includes bronchiectasis and chronic airway infection. Almost half of the bacteria in the airways of patients with cystic fibrosis (pwCF) are anaerobes. Although their role and impact are still under discussion, certain species have been recognized as predictive biomarkers for Pseudomonas aeruginosa colonization, such as Porphyromonas catoniae, whose decrease is linked to the emergence of P. aeruginosa. Metagenomics provides an exhaustive description of anaerobes in the airways but is not routinely characterized in clinical microbiology laboratories. We evaluated the ability to identify anaerobes in everyday routine sputum culture analysis of pwCF. Methods: Sputum collected from 48 pwCF was analyzed for (i) viable and culturable anaerobic airway microbiota using anaerobic cultures and (ii) 16S rRNA16S metagenomics. The results obtained from the culture-based and metagenomics approaches were compared. Sputum culture results were also compared depending on whether the airway was in an aerobic or anaerobic atmosphere when it was transported to the laboratory. Results: We identified 46/48 (95.8%) pwCF carrying anaerobes using culture and 48/48 (100%) pwCF using metagenomics. Twenty-three species (~2.6 anaerobes/sample) and almost 100 species (~43 anaerobes/sample) were identified using culture and 16S rRNA metagenomic analysis, respectively. Notably, the culture enabled the identification of Veillonella and Prevotella, two core genera of the airway anaerobiome in people with cystic fibrosis (pwCF). Pre-analytical anaerobic control during sample transport to the lab had no impact on detecting key relevant anaerobes.  Conclusion: These new findings support changes in the processing of CF sputum in the everyday practice of clinical microbiology laboratories and promote the characterization of the culturable anaerobic airway microbiota.