An introduction to molecular hospital epidemiology.

One of the primary goals of the hospital epidemiologist is the identification and characterization of nosocomial outbreaks. Outbreaks usually are identified by the recovery of a unique strain from a cluster of patients infected with a nosocomially acquired pathogen. Until recently, the microbiologic tools available to any hospital epidemiologist permitted identification of novel strains by speciation and antibiogram. Thus, most outbreak descriptions consisted of the identification of an unusual species or the appearance of a new antibiotic resistance phenotype in a recognized nosocomial pathogen. The emergence of enterococci in this decade or the emergence of methicillin-resistant Staphylococcus aureus (MRSA) in the 1970s are notable examples. Where resources have existed, additional methods have been used for further discrimination. Outbreak and endemic strains have been compared by phage typing, serologic typing, and capsular typing. For example, beta-hemolytic streptococci may be grouped by Lancefield antisera, and Staphylococcus aureus may be grouped by phage typing. However, certain Lancefield groups and certain phage groups are common among epidemic and endemic isolates, which may prevent identification of a specific epidemic strain. Molecular techniques often can discriminate among strains of the same serologic type or phage type and may offer other advantages over these older typing methods. With molecular methods, there is no need to maintain stocks of antisera or lysate cultures, and with the proper technique all strains may be typed. Plasmid profile comparison was an early attempt at molecular differentiation. In this method, plasmid DNA is isolated from bacterial cultures and separated by electrophoresis in an agarose gel. Plasmids of similar size migrate the same distance through the gel. However, the different configurations of plasmid DNA, which migrate different distances, and the ease with which plasmids may be gained or lost during an epidemic limit comparisons to those strains with identical profiles. Different configurations of plasmid DNA may be resolved by cutting the plasmids with restriction endonuclease enzymes. Each enzyme recognizes a unique sequence of base pairs (restriction site) within a segment of DNA and cleaves the DNA at that site. Two identical plasmids would be cut into the same number of co-migrating fragments by a given restriction enzyme regardless of the configuration of the plasmid DNA. However, strains without plasmids are "untypable." Newer methods potentially can type any strain by using the chromosomal DNA present in all bacteria and fungi. Three such methods analyze differences in chromosomal DNA organization: genomic (chromosomal) digests, restriction fragment length polymorphisms (RFLPs), and pulsed-field gel electrophoresis (PFGE). Many investigators have compared strains by cleavage of chromosomal DNA using a restriction enzyme that acts at numerous sites. However, gel electrophoresis of such DNA results in bands so numerous that it is almost impossible to resolve individual fragments. General pattern differences may be visible, but the appearance of these differences is highly dependent on DNA concentration and technique. Therefore, it is difficult to determine precise similarities or differences among more han three or four strains using this method. RFLP relies upon the variability in location of certain common genes such as the genes for ribosomal RNA,1 methicillin resistance, or erythromycin resistance.2 This method requires that the gene to be