Materials and Methods
Patient selection and clinical characteristics: People with CF seen at Children’s Hospital Colorado (CHCO) from 2004-2016 were identified by electronic medical records. Individuals were included in the study if they had a diagnosis of CF (sweat chloride ≥ 60mmol/L and/or two disease-causing CFTR gene mutations) as established by Cystic Fibrosis Foundation guidelines and at least 4 airway fungal cultures (sputum, BAL, and/or fungus positive oropharyngeal (OP) culture) over two consecutive years, and at least 2 years of clinical data available after baseline.15 Information included was patient demographics, CF diagnostic criteria, genotype, comorbidities including ABPA, asthma, and CF related diabetes (CFRD) present during the baseline or follow-up periods, lung function, growth parameters, microbiology culture results, and laboratory results for IgE and complete blood count with eosinophils. Microbiologic culture data prior to baseline period was captured starting in 2004. Lung function results available from children 6 years and older were recorded.CFTR modulators prescribed were recorded, however availability of approved modulators was limited during the study time. The study was approved by the Colorado Multiple IRB (#15-2376).
Cultures : Airway samples were collected as part of clinical care and processed at the CHCO clinical microbiology laboratory following standard CF culture procedures. Bacterial and fungal cultures are performed routinely on all sputum and BAL samples.16Oropharyngeal cultures are not routinely plated on fungal media in our institution’s microbiology lab, therefore result from oropharyngeal cultures were only included in the analysis if positive for fungi. Two or more positive cultures within one month of each other were considered a single positive culture. Fungal detection included any reported fungus species by our clinical lab, including the labels “yeast” and “fungus,” which in some instances were reported in this manner.
Defining infection status: Initially we compared patients with no fungal positive cultures, rare fungus (one positive), intermittent fungi (≥ 2 positive but < 50% positive), or chronic fungi (> 2 positive and at least 50% positive); however, given the limited group sample sizes we chose to dichotomize fungal exposure to agree with previously published literature and to provide greater power for group comparisons. Results from cultures over the two-year baseline period were used to categorize individuals as either havingrare fungus , defined as ≤ 1 positive fungal culture in the baseline period and no positive fungal cultures recorded prior to baseline, or frequent fungi , defined as having 2 or more positive fungal cultures in the baseline period. Definitions were based upon adaptations from previously published fungal and chronic bacterial infection studies in CF.7, 17 Given that we defined fungal exposure for individuals in the baseline period, individuals could transition groups during the follow-up period (e.g. those classified as rare could later meet critieria for frequent fungal infection). Participants were considered rare during follow-up if they had \(\leq\) 1 positive culture and considered frequent if they met criteria (\(\geq\) 2 positive cultures) in any year of follow-up. Chronic P. aeruginosa status during the baseline follow-up period was defined by Leed’s criteria of > 50% positive cultures for P. aeruginosa during at least one year. Individuals who met criteria for chronic P. aeruginosa within any year during the follow-up period were considered chronically infected.18 Ever P. aeruginosa status during the follow up period was defined as isolating P. aeruginosa at any point in time, regardless of frequency or year.