In silico comparison of different PFGE and wgMLST

Background: Pulsed field gel electrophoresis (PFGE) is acknowledged to be the ‘gold standard’ for the typing of strains of a number of bacterial species, including E. coli, and is used widely in clinical settings (van Belkum A., 2007). Methods & Materials: In silico PFGE analysis of 138 complete E.coli genomes using classical XbaI and 5 other enzymes (Sse8647I, ApaI, AclN, SrfI and SdiI) have been performed by Geneious (Biomatter). Images with gel pattern have been analyzed by TotalLab 1D (Nonlinear Dynamics) to produce band matrix. wgMLST scheme with 2216 loci have created with SeqSpere (Ridom). Discriminatory power and concordance between different PFGE and wgMLST have been estimated based on Simpson and adj.Rand and Wallace indices. Results: 138 genomes of E.coli have been used to produce different PFGE and wgMLST patterns. Sites of restriction, band (loci) numbers and discriminatory power are presented in Table 1. Table 2