Repetitive Sequence-based PCR (rep-PCR) DNA Fingerprinting of Bacterial Genomes

Abstract

Bacterial chromosomes contain multiple interspersed repetitive sequences that occupy intergenic regions at sites dispersed throughout the genome. Such blocks of noncoding, repetitive sequences can serve as multiple genetic targets for oligonucleotide probes, enabling the generation of unique DNA profiles or fingerprints for individual bacterial strains. DNA fingerprinting requires the resolution of differently sized DNA fragments derived from chromosomal or plasmid DNA by restriction endonuclease-mediated digestion and/or DNA amplification to yield a band pattern that serves as a unique identifier. These unique ``bar codes'' or DNA fingerprints define each bacterial chromosome without the need for measuring gene expression or enzyme function. Genotypic or molecular approaches differ with respect to the level of resolution of individual bacterial species or strains into distinct categories (Figure 34-1).