Comparative Analysis of the Orphan Crispr2 Locus in 242 Enterococcus Faecalis Strains

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dc.contributor.authorHullahalli, Karthiken_US
dc.contributor.authorRodrigues, Marinelleen_US
dc.contributor.authorSchmidt, Brendan D.en_US
dc.contributor.authorLi, Xiangen_US
dc.contributor.authorBhardwaj, Poojaen_US
dc.contributor.authorPalmer, Kelli L.en_US
dc.contributor.utdAuthorHullahalli, Karthiken_US
dc.contributor.utdAuthorRodrigues, Marinelleen_US
dc.contributor.utdAuthorSchmidt, Brendan D.en_US
dc.contributor.utdAuthorLi, Xiangen_US
dc.contributor.utdAuthorBhardwaj, Poojaen_US
dc.contributor.utdAuthorPalmer, Kelli L.en_US
dc.date.accessioned2016-03-28T20:14:42Z
dc.date.available2016-03-28T20:14:42Z
dc.date.created2015-09-23en_US
dc.date.issued2015-09-23en_US
dc.description.abstractClustered, Regularly Interspaced Short Palindromic Repeats and their associated Cas proteins (CRISPR-Cas) provide prokaryotes with a mechanism for defense against mobile genetic elements (MGEs). A CRISPR locus is a molecular memory of MGE encounters. It contains an array of short sequences, called spacers, that generally have sequence identity to MGEs. Three different CRISPR loci have been identified among strains of the opportunistic pathogen Enterococcus faecalis. CRISPR1 and CRISPR3 are associated with the cas genes necessary for blocking MGEs, but these loci are present in only a subset of E. faecalis strains. The orphan CRISPR2 lacks cas genes and is ubiquitous in E. faecalis, although its spacer content varies from strain to strain. Because CRISPR2 is a variable locus occurring in all E. faecalis, comparative analysis of CRISPR2 sequences may provide information about the clonality of E. faecalis strains. We examined CRISPR2 sequences from 228 E. faecalis genomes in relationship to subspecies phylogenetic lineages (sequence types; STs) determined by multilocus sequence typing (MLST), and to a genome phylogeny generated for a representative 71 genomes. We found that specific CRISPR2 sequences are associated with specific STs and with specific branches on the genome tree. To explore possible applications of CRISPR2 analysis, we evaluated 14 E. faecalis bloodstream isolates using CRISPR2 analysis and MLST. CRISPR2 analysis identified two groups of clonal strains among the 14 isolates, an assessment that was confirmed by MLST. CRISPR2 analysis was also used to accurately predict the ST of a subset of isolates. We conclude that CRISPR2 analysis, while not a replacement for MLST, is an inexpensive method to assess clonality among E. faecalis isolates, and can be used in conjunction with MLST to identify recombination events occurring between STs.;en_US
dc.description.sponsorship"This work was supported by National Institutes of Health grant K22AI099088."en_US
dc.identifier.bibliographicCitationHullahalli, Karthik, Marinelle Rodrigues, Brendan D. Schmidt, Xiang Li, et al. 2015. "Comparative Analysis of the Orphan CRISPR2 Locus in 242 Enterococcus faecalis Strains." PLOS One 10(9): e0138890, doi: 10.1371/journal.pone.0138890.en_US
dc.identifier.issn1932-6203en_US
dc.identifier.issue9en_US
dc.identifier.urihttp://hdl.handle.net/10735.1/4818
dc.identifier.volume10en_US
dc.publisherPublic Library of Scienceen_US
dc.relation.urihttp://dx.doi.org/10.1371/journal.pone.0138890
dc.rightsCC BY 4.0 (Attribution)en_US
dc.rights©2015 The Authorsen_US
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en_US
dc.sourcePLOS One
dc.subjectEnterococcus faecalisen_US
dc.subjectClustered Regularly Interspaced Short Palindromic Repeats (CRISPR)en_US
dc.subjectGenetic Locien_US
dc.subjectSequence Analysisen_US
dc.subjectPhylogenyen_US
dc.titleComparative Analysis of the Orphan Crispr2 Locus in 242 Enterococcus Faecalis Strainsen_US
dc.type.genreArticleen_US

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Palmer, Kelli L.
NSM Staff-Student Research