Once the DNA is released, then the agarose and DNA suspension (also known as a plug) is treated as follows: The DNA, immobilized in the agarose, is cut with molecular scissors (restriction enzymes) at specific locations (restriction sites). Microbiologists select these restriction enzymes to generate a small number of DNA pieces that can be separated based on size. The treated plugs are then loaded onto an agarose gel, and the DNA pieces are separated based on size using an electric field. This produces a DNA fingerprint with a specific pattern. The figure shows an example of an agarose gel where each lane represents a DNA fingerprint or pattern. PFGE is different from conventional DNA electrophoresis because PFGE can separate very large fragments to generate a fingerprint by constantly changing the direction of the electric field.
Once a DNA fingerprint is created, the public health laboratory analyzes the fingerprint pattern using a software program known as BioNumerics*. After analysis, the laboratory uploads its pattern to the national database, where PulseNet Central’s database managers will investigate the pattern to see if it is causing an outbreak or it is part of an ongoing outbreak. If so, these database managers will work with the public health microbiologists and epidemiologists to further investigate the outbreak.