Sequence Analysis of the Variable Number Tandem Repeat in Staphylococcus aureus Protein A Gene - Bacterial Pathogenesis: Methods and Protocols - page 281

extent of homogeneity of the given species and on the level of discrimination
needed to answer a given epidemiological or evolutionary hypothesis. Among
monomorphic species such as M. tuberculosis or B. anthracis , where the genetic
clock-speed or rate of change in housekeeping genes is relatively slow, the
discriminatory power of MLST is limited. In contrast, S. aureus is an ideal
species for MLST analysis as it is relatively diverse, with limited evidence of
recombination (27) . Consequently, MLST is able to address global epidemio-
logical questions where the isolates have had substantial time to diversify but
is less discriminating in detecting changes in closely related strains. It should
also be stressed that due to the sequencing of seven housekeeping genes for
S. aureus MLST analysis, this method, while objective and highly portable, is
also labor-intensive, time-consuming, and costly to use routinely in a clinical
or surveillance setting. In contrast, the results generated by spa typing have
been shown to approximate the population structure of S. aureus afforded by
MLST analysis while remaining objective, highly portable, and significantly
less costly.
3.6. Discussion
As a single locus sequence-based typing method, spa typing has many advan-
tages over other genotyping methods including cost, labor, ease of analysis,
and quality assurance. Initial concerns that spa typing was too variable and
not rooted in the phylogeny of S. aureus led to its limited acceptance as a
robust genotyping method, especially in regard to population-based studies.
However, numerous comparative genotyping studies have repeatedly showed
that spa typing is concordant with classical MLEE typing, MLST analysis, and
genome-wide microarray data. In fact, spa typing has proven to be superior to
MLST in discriminating MRSA strains, as its faster molecular clock provides
higher resolution that approaches the level provided by PFGE. For example, the
two closely related CA-MRSA clones, termed USA300 and USA500 by PFGE,
are distinguished by spa typing as types 1 and 7, respectively, but clustered
together as sequence type 8 (ST8) by MLST (3) ( see Figs. 4 and 5 ). Consistent
with the fact that these two clones are members of the same clonal complex and
descendants of a common ancestral strain, the sequence of the 10 repeats in spa
types 1 and 7 are highly conserved and differ only by a single non-synonymous
point mutation (21,33) . Figure 5 (bubble) shows an example where spa typing
is able to further resolve the MLST grouping among ST8 strains.
A current limitation of spa typing involves understanding the relatedness
among types with similar repeat organization, along with the weighting of