Assessing anaerobe detection in routine sputum analyses from cystic fibrosis patients

Pulmonary involvement in cystic fibrosis (CF) includes bronchiectasis and chronic airway infection, with nearly half of the airway bacteria being anaerobes. Some anaerobic species, such as Porphyromonas catoniae, have been identified as predictive biomarkers for Pseudomonas aeruginosa colonization, with P. catoniae decreasing as the disease progresses. Although 16S rRNA metagenomics offers a comprehensive view of airway anaerobes, it is not routinely performed in clinical microbiology laboratories. This study aimed to evaluate the ability of routine sputum culture to identify strict anaerobes in people with CF (pwCF) compared to 16S rRNA sequencing, and to assess the impact of sample transport conditions. Sputum from 48 pwCF was analyzed by anaerobic culture and 16S rRNA sequencing. Strict anaerobes were detected in 95.8% of patients by culture and 100% by 16S rRNA sequencing. Culture identified 23 strict anaerobic species (mean 2.6 per sample), while 16S rRNA sequencing revealed nearly 100 species (mean 43 per sample). Importantly, culture isolated key genera such as Veillonella and Prevotella, core members of the CF airway anaerobiome. Transport conditions (aerobic vs. anaerobic) did not affect anaerobe detection. 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.