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S. aureus
is attributed to a remarkable array of cell-associated and
secreted virulence factors involved in pathogenesis, many of which are acquired
on mobile genetic elements. The control and prevention of
S. aureus
infections
in recent years have been further complicated by the wide spread of multidrug-
resistant
S. aureus
strains known as methicillin-resistant
S. aureus
(MRSA) in
nosocomial settings. Since the introduction of methicillin into clinical use in
1961, the occurrence of MRSA has steadily increased in health care institu-
tions worldwide
(1)
. Recently, the epidemiology of MRSA, which is typically
associated with nosocomial environments, has changed dramatically, causing an
inordinate number of skin and soft tissue infections among an otherwise healthy
population in the community
(3,4)
. Referred to as community acquired (CA-)
MRSA, it represents a contemporary epidemic of increasing global occurrence.
Control and prevention methods for methicillin-susceptible
S. aureus
(MSSA) and MRSA have relied largely on prompt and appropriate antibiotic
treatment, use of universal precautions, and cohorting. The introduction of
molecular typing methods to sub-speciate and track strains of
S. aureus
in institutional settings (e.g., hospital, nursing home) or in the community
has had a dramatic impact on epidemiologic analysis and in elucidating
transmission pathways, thereby aiding control efforts. Differentiation of
S.
aureus
isolates not only clarifies the epidemiologic scenario but also sets the
stage to pose biological questions about mechanisms of resistance, molecular
evolution, and pathogenesis. As such, the last decade has seen a plethora of
molecular tools become available for the sub-speciation of pathogens including
S. aureus
. Common techniques include pulsed-field gel electrophoresis (PFGE)
of genomic macrorestriction fragments and multilocus sequence typing (MLST)
methods
(5,6)
. The former is often used in short-term epidemiologic investi-
gations (e.g., outbreaks) while the later is applied to long-term epidemiologic
studies (e.g., phylogenetic studies). Recently, genotyping based on repetitive
DNA, and specifically the analysis of variable number tandem repeats (VNTRs),
has been used to provide resolution for both short- and long-term studies. In this
chapter, we focus on the methods, analysis, and application of VNTR analysis
in
S. aureus
.
1.1. Variable Number Tandem Repeats
The recent availability of numerous annotated bacterial genome sequences
has generated a rich source of data for the recognition of new and robust
genotyping targets. Many of these targets have given rise to methodological
approaches that are amenable to rapid, affordable, and high-throughput systems
that facilitate data storage and interlaboratory comparisons. However, a current
challenge is to identify a single-locus sequencing target that is conserved in a
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