Diversilab strain typing system

The genetic relatedness of isolates was investigated by semi-automated rep-PCR on DiversiLab^™ Strain Typing System (bioMérieux, Marcy-L’Étoile, France) using the DiversiLab P. aeruginosa kit (Bacterial Barcodes, bioMérieux, Marcy-L’Étoile, France), according to the manufacturer’s instructions. Fingerprints were obtained by electrophoresis using microfluidic lab-on-a-chip on Agilent 2100 Bioanalyzer equipment (Agilent Technologies, Palo Alto, CA, USA) and analysis performed with DiversiLab on-line software (v 3.4) applying the Pearson correlation coefficient. Isolates were classified as in the same clonal group (genotypically indistinguishable) if the similarity was ≥97%, and as unique pattern if the similarity was <97%.

The genetic relationship between the E. coli strains was evaluated by repetitive sequence-based PCR (rep-PCR) using the DiversiLab^® strain typing system (bioMérieux). Results were interpreted with DiversiLab web-based software (bioMérieux) using the Pearson correlation and the modified Kullback–Leibler method. Isolates with identical strain patterns were considered indistinguishable if the similarity percentage was ≥95%.
Multi-Locus Sequence Typing (MLST) analysis was performed using the Achtman MLST scheme (pubmlst/org/mlst). Seven housekeeping genes (edk, fumH, gyrB, icd, mdh, recA and purA) were amplified according to this protocol.