Molecular Characterization of Bacterial Isolates

Pulsed-field gel electrophoresis (PFGE) was performed using the SmaI restriction enzyme (New England Biolabs, UK) [18] (link). Banding patterns were analysed using BioNumerics software version 6.01 (Applied Maths, Sint-Martens-Latem, Belgium) as described [19] (link). A similarity coefficient of 80% was used to define PFGE types [18] (link). DNA was extracted and MLST was performed as described elsewhere [2] (link), [6] (link), [20] (link). Sequence types (ST) were assigned using the MLST database (www.mlst.net) [20] (link). Phylogenetic analysis of concatenated MSLT data was performed using ClustalW for the alignment and the maximum likelihood method for construction of the phylogenetic tree in MEGA version 6. Two multiplex PCR assays were used to detect the presence of virulence and other genes (assay 1 for tst, eta, etb, sea, seb, sec, sed, see[21] (link), assay 2 for mecA and pvl) [22] (link).