Clones are defined as indistinguishable isolates, derived from the same parent strain. Subsequent generations of organisms often begin to diverge from the parent. As divergence occurs progeny strains will share most characteristics with the parent, but differences will appear. These progeny strains may be termed clonally-related to the parent.

It follows that isolates which are clones or clonally-related may be part of an outbreak. Thus, strain typing helps the epidemiologist determine when to initiate additional investigation. Related organisms may be derived from a point source such as a contaminated solution, fomite or colonized health care worker. They could also be transmitted from patient-to-patient via health care worker hands or medical equipment. It is easy to understand the role that culture and characterization of microbes, including those from non-patient sources, may play in helping the infection control team plan appropriate interventions in outbreak settings. On the other hand, when organisms are shown to be unrelated, an outbreak of a single strain type may be ruled-out.

In addition to outbreak investigation, strain typing can help the epidemiologist track a particular strain within a given institution and through the wider health care community. Clinicians have also applied these techniques to assess whether multiple infections with the same species over time represents persistent infection or acquisition of a new strain. Determining whether multiple positive blood cultures are caused by the same organism or several different strains of a skin contaminant is another clinical use for these methods.

A number of different laboratory methods have been developed for strain delineation. Simple phenotypic tests such as biochemical profiling, serotyping and antibiotic susceptibility patterns characterize bacteria based on the expression of genes and are an important first screen of relatedness. However, many organisms share phenotypic traits, yet are genetically distinct. Susceptibility of a bacterium to a panel of antibiotics (the antibiogram) is probably the most useful of this class of tests because these data are readily available at the time of organism identification. If isolates have different antibiotic susceptibilities, they are probably not closely related. Many outbreaks, however, are caused by strains with similar antibiograms such as the highly resistant methicillin resistant Staphylococcus aureus (MRSA) and vancomycin resistant Enterococcus. The limited variability in susceptibility patterns for such strains necessitates the use of a molecular method.

Genotypic or molecular methods are based on differences in the presence, size and sequence of genetic material. A number of techniques have been developed to analyze and compare the chromosome or plasmid content of strains. Most of these tests have been designed to yield fragments of DNA of variable lengths which are then separated by gel electrophoresis to give an array of bands called the "DNA fingerprint."

The techniques used most commonly for nosocomial pathogens include: pulsed-field gel electrophoresis (PFGE), restriction fragment length polymorphism (RFLP), Ribotyping, and PCR amplification of random (RAPD) or extra-genic sequences. The first three techniques are examples of methods used in our laboratory.