I thank Mainz et al for their recent paper on concordance of upper airway with lower airway microbiology in cystic fibrosis (CF) using nasal lavage.1 However, their claim that their evidence supports a role for the upper airway in the “acquisition and persistence of opportunistic bacteria” in the lower airway does not stand up to scrutiny. Their work is of great interest and addresses an important and often neglected area of CF research: just how do bacteria gain access to the lower airways? They elegantly demonstrate the close association between the bacteria of the upper and lower airways. It is, however, a cross-sectional study and provides no information as to the direction of transfer of bacteria between the upper and lower airways. In subjects with a lower respiratory tract infection, as is quintessentially the case in CF, it is both general knowledge and scientifically well established that bacteria are expectorated in both sputum and fomites. Such knowledge is the basis of the cough swab or cough plate often used for lower airway microbiological surveillance in the paediatric CF population.2 It would therefore be natural to assume in any patient with a “colonised” lower airway that fomites from the lower airway will lodge within the nasopharynx. This would result in concordant upper and lower airway bacterial strains, as has been found in this study. However, the evidence provided here does not demonstrate that the upper airway is a source of bacterial seeding to the lower airway, merely that genetically identical strains are found in both compartments and the walls between these compartments are flimsy at best. In order to ascertain the direction of bacterial travel between these two compartments, it would be necessary to undertake a longitudinal study. If such a study were to demonstrate early bacterial travel from the upper to the lower airways, it would open up new avenues of potential therapies for this devastating disease.