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Volume 157, Issue 2

Prevalence, conservation and functional analysis of and CRISPR regions in clinical isolates Free

Abstract

Here, we report the characterization of 122 clinical isolates from three distinct geographical locations: Dartmouth Hitchcock Medical Center in New Hampshire, USA, the Charles T. Campbell Eye Microbiology Lab at the University of Pittsburgh Medical Center, USA, 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 subtype CRISPR regions (33 %) were more prevalent than the CRISPR region subtype (6 %) in these clinical isolates. Further, we observed 132 unique spacers from these 45 CRISPR that are 100 % identical to prophages or sequenced temperate bacteriophage capable 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 bacteriophage. We next assessed the ability of the more prevalent 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 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 isolates and a collection of defined CRISPR-positive and -negative strains for further CRISPR and gene studies.

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Keyword(s): CRISPR, clustered regularly interspaced short palindromic repeats , crRNA, CRISPR RNA , DHMC, Dartmouth Hitchcock Medical Center , EOP, efficiency of plaquing and PAM, proto-spacer-associated motifs
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2011-02-01
2024-04-23
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Prevalence, conservation and functional analysis of Yersinia and Escherichia CRISPR regions in clinical Pseudomonas aeruginosa isolates
Microbiology 157, 430 (2011); https://doi.org/10.1099/mic.0.045732-0
/content/journal/micro/10.1099/mic.0.045732-0
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