MLEE revealed 4 main phylogenetic groups designated A, B1, B2 and D. coli) reference collection, ECOR, consists of 72 strains that are representative of the genotypic diversity, as indexed by multilocus enzyme electrophoresis (MLEE), in the species as a whole. Combined VNTR loci with higher variability are useful markers for resolving closely related isolates, whereas combined loci with lower variability are suitable for establishing clear phylogenetic relationships between strains or clones that have evolved over a longer timescale. Accordingly, MLVA is a useful tool for the phylogenetic analysis of S.

A clustering analysis using the profiles of 18 loci with limited variability established clear phylogenetic relationships among IST clonal groups. The phylogenetic pattern for the closely related isolates determined using MLVA profiles of 8 highly variable loci was in agreement with that determined using the 26-locus profiles.

MLVA data for the 703 IST1 isolates revealed that diversification among the closely related isolates was attributed mainly to four highly variable loci. MLVA was carried out using 26 VNTR loci with a range of degrees of variability.

The global phylogenetic patterns determined by IST, PFGE, and MLVA were concordant. A panel of 916 isolates, including 703 closely related IST1 isolates, were characterized by inter-IS1 spacer typing (IST), pulsed-field gel electrophoresis (PFGE), and multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) to evaluate the utility of MLVA as a molecular tool for the phylogenetic analysis of Shigella sonnei.

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