Phylogenetic Distribution of CRISPR-Cas Systems in Antibiotic-Resistant Pseudomonas aeruginosa

Abstract

Pseudomonas aeruginosa is an antibiotic-refractory pathogen with a large genome and extensive genotypic diversity. Historically, P. aeruginosa has been a major model system for understanding the molecular mechanisms underlying type I clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated protein (CRISPR-Cas)-based bacterial immune system function. However, little information on the phylogenetic distribution and potential role of these CRISPR-Cas systems in molding the P. aeruginosa accessory genome and antibiotic resistance elements is known. Computational approaches were used to identify and characterize CRISPR-Cas systems within 672 genomes, and in the process, we identified a previously unreported and putatively mobile type I-C P. aeruginosa CRISPR-Cas system. Furthermore, genomes harboring noninhibited type I-F and I-E CRISPR-Cas systems were on average ~300 kb smaller than those without a CRISPR-Cas system. In silico analysis demonstrated that the accessory genome (n = 22,036 genes) harbored the majority of identified CRISPR-Cas targets. We also assembled a global spacer library that aided the identification of difficult-to-characterize mobile genetic elements within next-generation sequencing (NGS) data and allowed CRISPR typing of a majority of P. aeruginosa strains. In summary, our analysis demonstrated that CRISPR-Cas systems play an important role in shaping the accessory genomes of globally distributed P. aeruginosa isolates.

CRISPR– cas Loci Profiling of Cronobacter Sakazakii Pathovars

“…The four out of eight ST8 isolates lacking the majority of the cas genes (except cas3) would suggest that the CRISPR arrays harbored on the genome are no longer active and hence cannot process or utilize their transcripts. This was previously identified in Pseudomonas aeruginosa where certain lineages harbored degenerative systems which contained the CRISPR array but lacked the cas genes [42]. Since no new spacer acquisition was observed in the Cronobacter isolates harboring all of the cas genes, this could suggest that active CRISPR-cas systems are not necessarily linked to new spacer acquisitions but to other functions.…”

“…CRISPR spacer array content has previously been strongly associated with sequence-based phylogeny and hence could be used as a rapid lineage-based detection method and as a discriminatory tool for epidemiological purposes [19,25,42].…”

Evolutionary Ecology of Prokaryotic Immune Mechanisms

“…For example, surface modification is generally more effective against phages than plasmids, although mucoid phenotypes were found to confer protection against a virulent plasmid (150). The RM and CRISPR-Cas systems can target both phages and plasmids (76,(151)(152)(153)(154), and pAgo appears to predominantly target plasmids (96), while Abi is typically induced by phages. Second, symbiont diversity is likely to also impact the evolution of stand-alone immune strategies, in particular along the innate-versus-adaptive-immunity axis and the specific-versus-nonspecific-immunity axis (Fig.…”

“…Anti-CRISPR proteins bind CRISPR-Cas components to interfere with either target DNA recognition or DNA destruction (237). AntiCRISPRs are encoded by an extremely diverse set of genes that are often located in a conserved locus on phage genomes (235,236) and other mobile genetic elements (153,236).…”

“…Several correlational studies indicate that the CRISPR-Cas system limits gene transfer. For example, genome sizes of strains of the opportunistic pathogen P. aeruginosa, which often causes lung infections in cystic fibrosis patients, are significantly smaller if they encode CRISPR-Cas systems than if they lack CRISPR-Cas systems (153). In accordance, CRISPRCas systems are absent from genomes of species that rely on gene transfer, such as Streptococcus pneumoniae, which causes pneumonia and requires natural transformation for capsule switching during infection (177).…”