Figure 3.

Accessory genome of cluster 2. All strains of cluster 2 (n = 59) are shown. Heatmap visualization with gene presence indicated by black bars and gene absence by white bars. Frames contain genes pertaining to AG group I, II, and III (in green, violet, and blue, respectively) and are presented in magnification inserts (B–D) next to the heatmap (A). An overview of AG groups and gene blocks is given in the table insert (D). (A) X axis: accessory genes are consecutively numbered, beginning with 1 through 474. Left Y axis: indication of (i) the source of the strains [P, patient (bold) or E, environment (italic)] (“P/E”), (ii) the MLST type (“MLST”), (iii) day of sampling (“sample day”) consecutively counted with the day of sampling of the oldest strain in this study (strain ID 57) set to 1, (iv) strain identification number (“strain ID”), chronologically ordered by timepoint of sampling descending from early to late, and (v) AG groups I, II and III (“AG group”). Right Y axis: assignment of the strains to three time groups corresponding to early, middle and late time periods of sampling (yellow, orange and red, respectively). (B–D) Magnification inserts: AG group I, II and III (in green, violet, and blue, respectively) with indication of gene blocks 1–0 and the number of genes contained within these. Missing gene blocks are framed in the respective color, whereas additional gene blocks are filled in the respective color. Genes not belonging to one of the gene blocks are filled in black color. For AG groups I and II, some additional strains (without genes belonging to one of the gene blocks) are displayed in the magnification inserts for comparative visualization and are filled in black color. Abbreviations: AG group, accessory genome group; MLST, multi-locus sequence typing.