Statistical Analyses
Summary descriptive statistics included means and standard deviations or median and range for continuous variables and frequencies and percentages for categorical data. Characteristics such as body mass index (BMI) that were repeated over the study period were averaged over their individual baseline and follow-up time. Differences between airway fungi groups were determined using ANOVAs or Chi-squared tests depending on the distribution. Given the potential impact of ABPA on clinical status, we also compared individuals with rare and frequent fungi by ABPA status, comparing characteristics and outcomes across the 4 groups. Multiple linear mixed effects regression models allowing for random slope and intercept per patient were used to assess percent predicted forced expiratory volume in one second (ppFEV1) over time by fungal exposure group using maximum likelihood estimation. ppFEV1 over follow-up time was standardized within patient by taking their average ppFEV1 during their baseline. The first model only included time and fungal exposure group, the second model adjusted for chronic P. aeruginosa and ABPA status, and the third and fourth models compared ppFEV1 by airway fungi and also adjusted for P. aeruginosastratified by ABPA status. Models were re-run adjusting for transition from one group to another in the follow up period to assess any change in association or inference. All three-way and two-way interactions between time with fungal status, ABPA, chronic or ever P. aeruginosa were assessed. Statistical significance was set at a Type I error rate of 0.05. All data cleaning, summaries, and testing were done using R (R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/).