CRISPRs: Molecular Signatures Used for Pathogen Subtyping

Abstract

ABSTRACTRapid and accurate strain identification is paramount in the battle against microbial outbreaks, and several subtyping approaches have been developed. One such method usesclusteredregularinterspacedshortpalindromicrepeats (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, includingMycobacterium tuberculosis,Salmonella enterica, and the plant pathogenErwinia 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 typeMycobacteriumspecies, as well as in-depth consideration of newer, higher-throughput CRISPR-based protocols.