Prevalence, conservation and functional analysis of Yersinia and Escherichia CRISPR regions in clinical Pseudomonas aeruginosa isolates

K. C. Cady, A. S. White, J. H. Hammond, M. D. Abendroth, R. S. G. Karthikeyan, P. Lalitha, M. E. Zegans, G. A. O'Toole
2011 Microbiology  
and the Aravind Eye Hospital in Madurai, India. We identified and located clustered regularly interspaced short palindromic repeats (CRISPR) in 45/122 clinical isolates and sequenced these CRISPR, finding that Yersinia subtype CRISPR regions (33 %) were more prevalent than the Escherichia CRISPR region subtype (6 %) in these P. aeruginosa clinical isolates. Further, we observed 132 unique spacers from these 45 CRISPR that are 100 % identical to prophages or sequenced temperate bacteriophage
more » ... ble of becoming prophages. Most intriguingly, all of these 132 viral spacers matched to temperate bacteriophage/prophages capable of inserting into the host chromosome, but not to extrachromosomally replicating lytic P. aeruginosa bacteriophage. We next assessed the ability of the more prevalent Yersinia subtype CRISPR regions to mediate resistance to bacteriophage infection or lysogeny by deleting the entire CRISPR region from sequenced strain UCBPP-PA14 and six clinical isolates. We found no change in CRISPR-mediated resistance to bacteriophage infection or lysogeny rate even for CRISPR with spacers 100 % identical to a region of the infecting bacteriophage. Lastly, to show these CRISPR and cas genes were expressed and functional, we demonstrated production of small CRISPR RNAs. This work provides both the first examination to our knowledge of CRISPR regions within clinical P. aeruginosa isolates and a collection of defined CRISPR-positive and -negative strains for further CRISPR and cas gene studies. Abbreviations: CRISPR, clustered regularly interspaced short palindromic repeats; crRNA, CRISPR RNA; DHMC, Dartmouth Hitchcock Medical Center; EOP, efficiency of plaquing; PAM, proto-spacerassociated motifs. A supplementary figure and five supplementary tables are available with the online version of this paper. Microbiology
doi:10.1099/mic.0.045732-0 pmid:28206903 fatcat:mzt73oa5xrgknhb4xnwwoofcvq