Clustered regularly interspaced short palindromic repeats (CRISPRs) for the genotyping of bacterial pathogens

Methods Mol Biol. 2009:551:105-16. doi: 10.1007/978-1-60327-999-4_9.


Clustered regularly interspaced short palindromic repeats (CRISPRs) are DNA sequences composed of a succession of repeats (23- to 47-bp long) separated by unique sequences called spacers. Polymorphism can be observed in different strains of a species and may be used for genotyping. We describe protocols and bioinformatics tools that allow the identification of CRISPRs from sequenced genomes, their comparison, and their component determination (the direct repeats and the spacers). A schematic representation of the spacer organization can be produced, allowing an easy comparison between strains.

MeSH terms

  • Bacteria / classification
  • Bacteria / genetics*
  • Bacteria / isolation & purification
  • Bacteria / pathogenicity*
  • Base Sequence
  • DNA, Bacterial / genetics
  • DNA, Bacterial / isolation & purification
  • Databases, Nucleic Acid
  • Genetics, Microbial / methods
  • Genome, Bacterial
  • Genotype
  • Humans
  • Inverted Repeat Sequences*
  • Molecular Epidemiology / methods*
  • Polymerase Chain Reaction
  • Polymorphism, Genetic
  • Species Specificity
  • Yersinia pestis / genetics


  • DNA, Bacterial