Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction

Interspersed repetitive sequences in prokaryotic genomes can be used as oligonucleotide primer binding sites for polymerase chain reaction (PCR)-mediated genomic fingerprinting (rep-PCR). rep-PCR is based on the observation that outwardly facing oligonucleotide primers, complementary to interspersed repeated sequences, enable the amplification of differently sized DNA fragments, consisting of sequences lying between these elements. Multiple amplicons of different sizes can be fractionated by electrophoresis and enable the establishment of DNA fingerprint patterns specific for individual bacterial strains. Several of these interspersed repetitive elements are conserved in diverse genera of bacteria and, therefore, enable single primer sets to be used for DNA fingerprinting many different microorganisms. Purified genomic DNA, crude bacterial cell lysates, or infected samples can be used directly in rep-PCR to generate DNA fingerprint profiles for comparative analyses. Detection and analysis of differently sized rep-PCR products include visual inspection of ethidium bromide-stained gets, computer-assisted detection and data storage methods, or laser scanning detection of fluorophore-labeled amplification products. DNA fingerprint patterns can be compared to estimate relative degrees of similarity between isolates and help determine whether isolates are clonally related.