Table 2 |.

overview of techniques used for molecular characterization of Staphylococcus aureus

Technique	Methodology	Advantages	Disadvantages
Pulsed-field gel electrophoresis	DNA is fragmented by restriction enzymes, and the resulting fragments are then separated by an electric field that periodically changes direction179	Highly discriminatory, widely available and relatively low cost	Laborious, technically challenging, interlaboratory variability, not well suited for long-term or global epidemiology180
MLST	Comparison of partial sequences from seven housekeeping genes; alleles for each are defined by a standardized MLST database, and strains are defined by particular combinations of alleles181	Highly discriminatory and reproducible, well suited to long-term global epidemiology; eBurst algorithm was designed and validated for use with MLST data182	Expensive and laborious
Spa typing	Sequence-based analysis of 24 bp variable number tandem repeats 3′ of polymorphic X or the short sequence repeat region of the spa gene; sequences are referenced to one of two large international databases (Ridom or eGenomics)183	Rapid and well suited to outbreak investigations	Moderately expensive (though less costly than MLST)
Multilocus variable number of tandem repeat analysis	DNA profiling by assessment of variation in number of tandem short repeat sequences184	High-throughput and inexpensive	Newer technique with variable protocols; discriminatory power yet to be well evaluated
SCCmec typing	PCR-based technique in which unique SCCmec types are assigned to particular allotypes of the ccr and mecA genes	Less expensive than MLST or whole genome sequencing	Use confined to MRSA; divergent and evolving SCCmec types have been discovered that are not detected by current methods185
Repetitive element palindromic PCR	PCR fingerprinting method targeting repetitive DNA sequences scattered throughout the MRSA genome	Inexpensive, commercially available, easy to use and rapid	Less discriminatory — perhaps most suitable for initial screening186
Whole genome sequencing	Analysis of entire genome sequence for single-nucleotide variants187	Precise and highly discriminatory	Expensive; extensive data analysis and knowledge of bioinformatics required
STAR gene restriction profile analysis	STAR is PCR amplified and then digested with restriction enzymes to produce restriction profiles that vary based on variation in sequence and copy number of intergenic regions within the PCR product188	Rapid, easy to perform and reproducible	Discriminatory power varies by enzymes used — may be better suited for initial screening189

MLST, multilocus sequence typing; SCCmec, staphylococcal cassette chromosome mec; STAR, Staphylococcus aureus repetitive element.