Experimental lung infection - Impact of infection route. The sketch highlights the differential experimental set-up for intranasal and intratracheal infection in mice. Compared to an intranasal infection route the intratracheal instillation bypasses the initial host immune response conducted by the respiratory epithelium of the upper airways and deposits more bacteria into the distal airways. The basic defect in CF impairs the mucociliary clearance . Ciliated respiratory epithelium is abundant in the upper and conducting airways, decreasing with the increasing branching of the airways. Correspondingly mucociliary clearance plays a prominent role for the elimination of the pathogen from these compartments, but not from the alveolar space. Please note the differential abundance of respiratory epithelium in the upper airways (right photograph) and the lower conducting airways of mice (left photograph).