Assessing the reliability of upper airway sampling for microbiological surveillance in cystic fibrosis

Sputum analysis is the standard method for microbiological surveillance in cystic fibrosis (CF). However, CFTR modulator therapy has markedly reduced sputum production, creating an urgent need to evaluate alternative sampling strategies. Upper airway sampling has been proposed as a potential surrogate, but its ability to reflect the lower airway microbiota remains unclear. This study evaluated whether upper airway microbiota profiling can reliably represent the lower airway in adults with CF. In this prospective observational study, we compared the airway microbiota of 70 adults with CF and 10 healthy volunteers using oropharyngeal rinse (OPR) and sputum samples. Microbiota profiling was performed using 16S rRNA gene sequencing, with alpha- and beta-diversity, taxonomic composition, and divergence from healthy controls assessed for both sample types. The OPR and sputum microbiota of adults with CF were compositionally distinct, whereas healthy volunteers exhibited highly similar communities between sample types. Firmicutes dominated within OPR samples, while Proteobacteria, particularly Pseudomonas, predominated in sputum. Only 3 of 52 awCF who had Pseudomonas detected in sputum showed detectable, low-level OPR signals. Both sample types became increasingly dysbiotic with worsening lung function, reflecting greater deviation from healthy community structure. Although dysbiosis correlated across sample types, the divergence between upper and lower airways did not relate to lung function. These findings indicate that OPR sampling does not reliably identify key lower-airway pathogens. However, the association between OPR and lung function suggests that upper-airway sampling may reflect the degree of lower-airway dysbiosis, warranting further investigation.