Pseudomonas aeruginosa sequenced from early cystic fibrosis lung infection

Our study goal was to determine if Pseudomonas aeruginosa (Pa) strains were being shared between children with cystic fibrosis attending the Hospital for Sick Children, Toronto, Canada. We performed whole genome sequencing on 1029 Pseudomonas aeruginosa isolates in order to identify instances of cross infection. These isolates were divided into the main study cohort, and comparator cohorts. The main study cohort consisted of 70 children with early (new-onset) cystic fibrosis (CF) lung infections between 2011 and 2015; a mean of 4 isolates per infection were sequenced. The comparator cohorts were other clinical and environmental isolates collected at the same hospital from: 1) 24 children with chronic CF infection (longitudinal sampling in years 2009 to 2013) (2) isolates from 5 inpatient ward sink drains collected in 2018 (3) isolates from sterile site infections in 201 patients without CF (between 2001 to 2017) and (4) isolates causing asymptomatic gastrointestinal carriage in 22 patients in 2017.