ABSTRACT
Until recently, the major emphasis in determining bacterial relatedness was placed on techniques that assessed one or more phenotypic markers. These included methods such as serotyping, phage typing, biotyping, antibiotic susceptibility testing, and bacteriocin typing. It is now well known that at the bacterial species level, there is sufficient genetic diversity to allow identification of different clones (genetically identical organisms descended from a single common ancestor) by means of molecular typing methods that incorporate genotypic and chemotypic techniques. These can be broadly defined as methods used to physically characterize bacteria on the basis of their DNA composition (genotyping) or production of proteins, fatty acids, carbohydrates, or other biochemical content (phenotyping or chemotyping). The most common genotypic typing methods currently used include chromosomal DNA restriction analysis, plasmid typing, DNA probe-based hybridizations such as ribotyping, pulsed-field gel electrophoresis, and PCR-based methods such as randomly amplified polymorphic DNA (RAPD), rep-PCR, PCR-ribotyping and PCR-restriction fragment length polymorphism (PCR-RFLP). There are also commercially available kits for DNA probing and PCR analysis. Those methods involving PCR primer technology and hybridizations with chemiluminescent DNA probes have been referred to as DNA fingerprinting techniques because the patterns generated are a result of interaction with the genome of the microorganism. The most common chemical typing methods include pyrolysis mass spectrometry (Py-MS), Fourier transform infrared spectroscopy (FTIR), gas-liquid chromatography (GLC), and electrophoretic protein typing. These methods for the most part have been referred to as chemical imaging techniques, because the operational fingerprint or pattern that is generated is based on the interaction with biochemical structures. The exception is electrophoretic protein analysis, where the patterns generated are based on some larger molecular content and are thus generally referred to as molecular fingerprints. Listings of some of the characteristics of bacterial typing methods are in Table 8.1 and Table 8.2.
