The use of defined primers for polymerase chain reaction (PCR) amplification of interspersed repetitive DNA elements present at distinct locations in prokaryotic genomes is referred to as repetitive element sequence based-polymerase chain reaction (rep-PCR). The initial discovery of repetitive extragenic palindromic (REP) elements occurred in the genomes ofEscherichia coliandSalmonella. The family of REP elements is generally between 33 and 40 bp in length, has 500 to 1,000 copies per genome, and comprises about 1% of the bacterial genomes ofE. coliorSalmonella. The amplified DNA fragments, when separated by electrophoresis, constitute a genomic fingerprint that can be employed for subspecies discrimination and strain delineation of bacteria and fungi. The application of rep-PCR to microbes has proven a discriminatory and reproducible tool for microbial subtype analyses and for microbial ecology investigations.
