Arbitrarily primed PCR (AP-PCR) or random amplified polymorphic DNA (RAPD) are methods of creating genomic fingerprints from species, even if little is known about the target sequence to be amplified (MacGowan et al., 1993; Welsh et al., 1994; Woods et al., 1994; van Belkum et al., 1995; Grattard et al., 1996; Matsui et al., 1998). Strain-specific arrays of amplicons (fingerprints) are generated by PCR amplification using arbitrary, or random sequence oligonucleotides that are often less than 10 nucleotides in length, and low-temperature annealing. A single primer is often used, because it will anneal in both orientations.

Detectable PCR product is generated when the primers anneal at the proper orientation and within a reasonable distance of one another. In spite of the arbitrary nature of the assay and amplification conditions that are relatively nonspecific, these methods have been shown to generate reproducible DNA banding patterns. These same characteristics make these methods suitable for a wide range of bacteria.

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