title: CRISPRs: molecular signatures used for pathogen subtyping.
abstract: Rapid and accurate strain identification is paramount in the battle against microbial outbreaks, and several subtyping approaches have been developed. One such method uses clustered regular interspaced short palindromic repeats (CRISPRs), DNA repeat elements that are present in approximately half of all bacteria. Though their signature function is as an adaptive immune system against invading DNA such as bacteriophages and plasmids, CRISPRs also provide an excellent framework for pathogen tracking and evolutionary studies. Analysis of the spacer DNA sequences that reside between the repeats has been tremendously useful for bacterial subtyping during molecular epidemiological investigations. Subtyping, or strain identification, using CRISPRs has been employed in diverse Gram-positive and Gram-negative bacteria, including Mycobacterium tuberculosis, Salmonella enterica, and the plant pathogen Erwinia amylovora. This review discusses the several ways in which CRISPR sequences are exploited for subtyping. This includes the well-established spoligotyping methodologies that have been used for 2 decades to type Mycobacterium species, as well as in-depth consideration of newer, higher-throughput CRISPR-based protocols.
authors.affiliation: Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA.
authors.forename: Nikki
authors.initials: N
authors.lastname: Shariat
authors.forename: Edward G
authors.initials: EG
authors.lastname: Dudley
mesh_terms: D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D044084:Erwinia amylovora / Q000235:genetics / Q000472:pathogenicity; D017720:Molecular Epidemiology; D058889:Molecular Typing / Q000379:methods*; D009161:Mycobacterium / Q000235:genetics / Q000472:pathogenicity; D060888:Real-Time Polymerase Chain Reaction; D019779:Salmonella enterica / Q000235:genetics / Q000472:pathogenicity