Restriction enzyme analysis of chromosomal DNA and its application in epidemiological studies

The ability to examine the bacterial genome directly eliminates the problems associated with the variable expression of proteins which may be encountered with protein-based typing or 'fingerprinting' techniques. Bacterial DNA is extracted by a rapid method, digested with a restriction endonuclease and the resulting fragments separated by gel electrophoresis to give a characteristic banding pattern. The choice of restriction endonuclease for a particular bacterial species is critical; an enzyme which cuts frequently results in an indistinct pattern which is difficult to interpret. A banding pattern consisting of a readily discernible number of discrete bands, usually about 20 or less in number, is preferable. Fragments in the 1-10 kb size range enable short separation times while larger fragments are desirable if interpretation is complicated by the presence of plasmid bands. This approach has enabled differentiation of isolates within Staphylococcus aureus (including methicillin-resistant S. aureus), non-typable Haemophilus influenzae, Neisseria meningitidis, Moraxella catarrhalis, Legionella pneumophila and enterococci, indistinguishable by conventional methods. Restriction enzyme digestion of chromosomal DNA provides a highly discriminatory method of bacterial characterization suitable for epidemiological studies.