Figure 1.
Minimum Spanning trees (MSTs) of 133 P. aeruginosa isolates based on MLVA, MLST, PFGE and DiversiLab data.
Each network represents its own genetic relatedness among isolates and displays its relative concordance against MLVA-CC and MLST-CC. A; Clustering of MLVA profile was done using the categorical coefficient. Each circle represents an MT, the size of which indicates the number of isolates with this particular type. Black lines connecting pairs of MTs indicate that they differ in one VNTR locus (thick lines), two VNTR locus (thin), or three to 15 VNTR locus (dashed). Grey zones surround MTs that belong to the same MLVA-CC. B; Clustering was done using MLST character data. Each circle represents an ST, the size of each circle indicates the number of isolates with this type. Black lines connecting pairs of STs indicate that they differ in one allele locus (thick lines), two alleles locus (thin), or three to seven (dashed). Grey zones surround STs that belong to the same MLST-CC. C; MST with permutation resampling with majority summary based on band matching class, each single node represents a distinct PFGE-type, the collapsed nodes represent closely related patterns with ≤6 band class differences. D; MST with permutation resampling with majority summary based on band matching class, each single node represents a distinct DL pattern, the collapsed nodes represent closely related patterns with ≤2 band class differences.
Table 1.
Number of genotypes, clonal complexes and singletons retrieved from the four genotyping schemes.
Figure 2.
Graphical representation of 44 isolates belonging to MLST-CC235 analyzed by PFGE, DL, MLST and MLVA.
A; Dendrogram generated by PFGE banding pattern, the clustering was done by UPGMA using the Dice coefficient with a tolerance position of 1%. 19 PFGE types were obtained with a cut-off of 80% of similarity. B; Dendrogram generated by the Pearson cluster analysis of rep-PCR results. PFGE-type, ST, MT and virtual gel are shown for each isolate. STs are depicted in colored boxes. A similarity index cut-off value of 95% was used by the DiversiLab® software to define genetic classification and to highlight the 9 DL-types. C; Minimum Spanning Tree illustrating the clonal complex MLST-CC235, the predominant ST235 is the primary founder surrounded by its SLVs (STs 976, 230, 989 and 227). Each color was assigned to each distinct ST. D; Minimum Spanning Tree of MLST-CC235 isolates typed by MLVA, Each circle represents an MT and 13 different colors were assigned to each distinct MT.
Table 2.
Simpson's index of diversity of the different typing methods.
Table 3.
Congruence between typing methods determined by the Adjusted Wallace coefficient [95% CI].