Increased prevalence of Pneumocystis jirovecii colonisation in acute pulmonary exacerbations of cystic fibrosis

•Prevalence of P. jirovecii in stable patients with cystic fibrosis is low at 2%.•Prevalence of P. jirovecii in exacerbating patients with cystic fibrosis is 9.2%.•Recent co-trimoxazole use is associated with lower detection of P. jirovecii.