The monitoring of epidemic Pseudomonas aeruginosa is important for cystic fibrosis (CF) infection control. The prairie epidemic strain (PES) is common in western Canadian CF clinics. Using whole-genome sequencing, we identified a novel genomic island and developed a PCR assay for PES. Against a collection of 186 P. aeruginosa isolates, the assay had 98% sensitivity and 100% specificity.
Multiple epidemic strains of Pseudomonas aeruginosa have been described as infecting patients with cystic fibrosis (CF) (1-4). Many of these strains are associated with a poor prognosis, manifesting as increased rates of lung function decline, exacerbation frequency, and treatment burden; decreased quality of life; and hastened progression to end-stage lung diseases (5, 6). We recently described a novel epidemic P. aeruginosa strain, the prairie epidemic strain (PES) (multilocus sequence type 192) (7). PES was found in one-quarter of patients attending the Calgary Adult CF Clinic (CACFC) and from patients who were transferred from other Prairie-based clinics, suggesting broad endemicity in western Canada. Furthermore, its prevalence has been unchanged through 3 decades of patients who transitioned to the CACFC. PES is more likely to be antibiotic resistant than are unique strains of P. aeruginosa, and infection with PES has been associated with increased rates of lung function decline, pulmonary exacerbation frequency, and progression to death and/or transplantation (7,8).The importance of identifying epidemic P. aeruginosa strains in CF has long been recognized. Typing strategies that are commonly currently employed include pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and random amplified polymorphic DNA PCR (RAPD-PCR) (7, 9, 10). These modalities have, to varied degrees, the ability to distinguish bacterial strains from one another, identify known epidemic strains, and determine if novel strains are potentially shared. However, they are costly and laborious, precluding routine use in clinical laboratories. Accordingly, we sought to develop a simple PCR assay to distinguish PES from non-PES P. aeruginosa organisms for clinical and research purposes in areas where this strain is prevalent (western Canada). Similar assays have been developed for other epidemic P. aeruginosa strains, including Liverpool epidemic strain (LES), Midlands-1, Manchester, and Australia epidemic strain-1 (AUS-1), and they are used prospectively in infection control and research (1-4).We performed whole-genome sequencing on 8 nonsequential isolates of PFGE and MLST-confirmed PES from our prospectively maintained biobank. The isolates were sequenced on the Illumina HiSeq 2500 (150 bp, paired-end) and assembled using SPAdes 2.5.0 (11). These strains were sequenced as a part of a large sequencing study, and a more detailed description will be given in a forthcoming manuscript (M. G. Surette, unpublished data). We identified a novel 40-kb genomic island (GI) using IslandViewer (12) and GView (13) that was not present in other pub...
