Sequence Analysis of the Variable Number Tandem Repeat in Staphylococcus aureus Protein A Gene - Bacterial Pathogenesis: Methods and Protocols - page 279

similar algorithms to identify and name repeats and assign spa types; however,
they use different nomenclature. It is important to note that the numerical
notation used to express the various spa types is not an index of relatedness.
That is, spa types 1, 2, 3, and so on are named in the order that they were
analyzed. Different nomenclature systems can confuse the literature and make
interlaboratory comparison more difficult, therefore a consensus nomenclature
method is needed. Furthermore, a consensus nomenclature that indicates, along
with the spa type, information on the phylogenetic position of a particular
strain within the overall population structure of S. aureus would be helpful
in furthering our understanding of the relationship between the micro- and
macrovariation within this species.
3.5. Other Genotyping Techniques
The early 1980s witnessed the initial integration of molecular techniques to
discriminate between different isolates of S. aureus . While previous methods
that have historically relied on characterizing phenotypic properties such as
colony morphology, serology, phage typing, toxin production, and antibiotic
susceptibility profiles were useful, they did not provide sufficient discrim-
ination, thereby limiting their application in epidemiological studies. The
transition from phenotypic characterization to genotyping saw the introduction
of numerous DNA-based methods, including plasmid profiling, electrophoretic
profiling of restriction enzyme digests of the chromosome, and random PCR
typing. Southern blot hybridization using a rRNA gene probe, or ribotyping, has
become a commonly used genotyping method as it is applicable to all bacteria
although the limited number of ribosomal gene copies in most species limits the
number of restriction fragment length polymorphisms and the overall discrimi-
natory capabilities. Given the array of molecular tools available, it is important
to choose an appropriate method(s) to address a particular study question, for
example, outbreak investigations, transmission dynamics, or phylogenetics. In
general, key aspects of choosing a molecular technique to study S. aureus
epidemiology include the observed rate of polymorphism(s) of the biomarker,
the genetic diversity of the strains in the population and the spatial and temporal
distance between the study isolates.
3.5.1. PFGE
The most accepted bacterial genotyping method is PFGE, as it is applicable
to all bacteria and the DNA fingerprints are highly discriminating. In this
approach, restriction enzymes that cut infrequently in a given species are used
to generate a macrorestriction profile of the entire bacterial chromosome. The
resulting DNA fingerprint patterns are excellent tools in outbreak investigations,