The epidemiological analysis of nosocomial pathogens is a subject of long-standing clinical interest. In recent years, molecular techniques have received increasing attention as a means of analyzing epidemiological interrelationships, thus leading to use of the term molecular epidemiology. Since chromosomal DNA represents a fundamental molecule of cellular identity, there has been particular interest in assessing chromosomal similarity as a measure of epidemiological relatedness.
One attractive approach has been to digest chromosomal DNA with restriction enzymes, resulting in a series of different sized fragments that form patterns when comparatively analyzed by agarose gel electrophoresis. In this context, differences in fragment patterns commonly are referred to as restriction-fragment length polymorphisms (RFLPs). Enzymes commonly used to cleave DNA typically recognize numerous sites within the bacterial chromosome. With such enzymes, restriction digestion of DNA from different bacterial isolates results in fragments that are too numerous to compare accurately after conventional agarose gel electrophoresis.