Patient Population

In this single-center multi-decade longitudinal retrospective cohort study, we analyzed E. coli isolates from all patients attending the Calgary Adult CF Clinic, which provides care to all patients in Southern Alberta, Canada, with at least one E. coli-positive sputum culture between January 1983 and December 2016. Patients were routinely followed quarterly and serial sputum samples are collected and analyzed for the presence of pathogens (Lam et al., 2015). All morphologically distinct isolates identified on MacConkey agar were assayed and subsequently confirmed as E. coli (in real-time) using standard methodologies and subsequently stored at −80°C in our comprehensive biobank. Infection was defined as having E. coli recovered from at least one sputum sample; we use the terms infection and colonization/carriage interchangeably. Patients were classified as having persistent infection if they had ≥3 E. coli-positive sputum cultures with carriage beyond 6 months and transient infection if they had ≥1 E. coli-positive sputum culture but did not meet the criteria for persistent infection. Infection episodes were defined as distinct when the last E. coli positive sputum culture of the first episode was separated by multiple years (>1) from the first E. coli positive sputum culture of the second episode, with multiple E. coli-negative sputum cultures collected in between and a unique pulsotype recovered from the subsequent episode. The study is approved by the Conjoint Health Research Ethics Board of the University of Calgary (REB-15-0854 and REB 15-2744).