Gelcompar 2 software 6

Pulsed-field gel electrophoresis (PFGE) XbaI (New England Biolabs, Beverly, MA, USA)-digested genomic DNA was conducted to delineate the genetic relatedness of the isolates using procedures described previously [40 (link)]. PFGE patterns were interpreted in accordance with the criteria of Tenover et al. [41 (link)]. Restriction fragments were analyzed using GelCompar II software 6.5 (Applied Maths, Austin, TX, USA), and dendrograms of the patterns were constructed using the unweighted pair group method with arithmetic mean (UPGMA) based on the Dice similarity index.

Clonal relatedness of Enterobacter isolates was determined using PFGE, which was performed according to a previously described protocol [57 (link)]. The restriction enzyme XbaI (New England Biolabs Inc., MA, USA) was used at the temperature suggested by the manufacturer. Restriction fragments were analyzed using GelCompar II software 6.5 (Applied Maths, Austin, TX, USA), and dendrograms of the patterns were constructed using the unweighted pair group method with the arithmetic mean based on the Dice similarity index. PFGE patterns were interpreted in accordance with the criteria of Tenover et al. [58 (link)]. Isolates with >85% similarity in PFGE banding patterns were designated as a pulsotype.

The presence of the mecA gene in cefoxitin-resistant S. aureus was confirmed by PCR^{50 (link)}. Methicillin-resistant S. aureus genotyping was performed using several methods including SCCmec typing^{51 (link)}, restriction and modification (RM) testing^{52 (link),53 (link)}, pulsed-field gel electrophoresis (PFGE) of the SmaI-fragmented DNA^{54 (link)}, and multilocus sequence typing (MLST)^{55 (link)}. Dendrograms were generated from the PFGE patterns using GelCompar II software 6.5 (Applied Maths, Sint-Martens-Latem, Belgium). To assign the MLST sequence types, the allele sequences were trimmed and analyzed using the Public Database for Molecular Typing and Microbial Genome Diversity (http://pubmlst.org). Detection of lukSF-PV genes was performed using a PCR-based method described previously^{56 (link)}.