**4. Molecular epidemiology**

In addition to the characterization of SCC*mec* types as an epidemiological tool, other methods are available for molecular epidemiology studies, such as Pulsed Field Gel Electrophoresis (PFGE), Multilocus Sequence Typing (MLST) and *spa* typing, which allow for the identification of circulating bacterial clones in hospitals and in the community.

PFGE is a method that uses restriction enzymes to cleave the extracted DNA, and in the case of the *Staphylococcus* genus, the enzyme used is *Sma*I. The fragments are separated in agarose gel. The direction of the electrical field is periodically changed, forming a 120º angle. This allows for fragments of up to 12mb to be separated, contrarily to conventional electrophoresis, which is not capable of separating fragments that are larger than 50kb (Herschleb et al., 2007). This method is generally used in local studies, such as in hospital outbreaks, which allows for identifying the circulating type.

The sequencing of constitutive bacterial genes can also be used as an important epidemiological tool. The method known as *spa* typing investigates polymorphisms on a single locus. It can discriminate between PFGE and MLST and is also applied in local studies and for detecting pandemic clones (Malachowa et al., 2005).

Another methodology that uses the sequencing and analysis of genetic polymorphisms is MLST. It analyzes the sequence of seven constitutive genes (*gmk, pta, dfp, gtr, mutS, pyrR,*  and *xpt*) and compares them with the sequences of each allele in the locus, which are previously numbered. The combination of the alleles identified in each gene determines the profile of the sample. (Aanensen & Spratt, 2005). It is the most adequate methodology for detecting pandemic clones given that the investigated genes are constitutive, with low mutation rates when compared to the analysis of the whole chromosome, in the case of PFGE (Miragaia et al., 2007).
