CRISPR-Cas Systems Impact Pseudomonas aeruginosa Genome Structure

Pseudomonas aeruginosa is both an antibiotic-resistant opportunistic pathogen and an important model of type I clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated protein (CRISPR-Cas) systems. Comparative genomics has identified several CRISPR-Cas subtypes, and it was previously unclear how these immune modules might influence the genome content of P. aeruginosa. To better understand the distribution of CRISPR-Cas subtypes and their impact on genome composition, we annotated 672 P. aeruginosa clinical isolates. We found that CRISPR-Cas systems modulate genome size and accessory elements. In addition, we identified a novel, putatively mobile type I-C CRISPR-Cas system. In the process, we also created a global spacer library that provides a new means of identifying accessory fragments, and facilitates CRISPR typing of many P. aeruginosa strains. Finally, we have made the assemblies of 282 newly-sequenced P. aeruginosa isolates public as an NCBI BioProject (ID: PRJNA297679).