We thank Dr Daniels for his comments on our paper and agree that “a cross-sectional study … provides no information as to the direction of transfer of bacteria between the upper and lower airways”. We therefore concluded in the abstract of our publication that “further longitudinal analyses and comparison with invasive methods are required”. Such a longitudinal study is on the way with the first results being published at the recent European Cystic Fibrosis Conference.1

However, we consider Dr Daniels' assumption that “in any patient with a ‘colonised’ lower airway, fomites from the lower airway will lodge within the nasopharynx” to be too simplistic. As shown in table 2 of our publication, numerous microbes preferentially resided in either the upper or the lower airways. In other words, the microbiota in these two compartments are distinct. The retrograde contamination of the nasal turbinates by expectorated bronchial secretions is not an ongoing regular process, as Dr Daniels makes us believe in his letter, but heavily depends on the capacity of the microbe to colonise and persist in the habitat. Pseudomonas aeruginosa, for example, is recovered with only low efficacy from nasal swabs because the organism resides in the distal parts of the nasal turbinate that is not reached by the swab. Correspondingly, expectorated sputum will typically not contaminate the niche in the upper airways where P aeruginosa is preferentially thriving.

In summary, Dr Daniels' commonsense argument does not give consideration to the complex microbial ecology of the upper airways.