Table 3.
The pangenome composition of ST131 clades and subclades showed stable core, soft core and shell genomes with open pangenomes (alpha).
| Clades | All | A | B | C | C1_6 | C2_4 | C2_9 |
|---|---|---|---|---|---|---|---|
| #isolates | 4,071 | 414 | 433 | 3,200 | 1,113 | 384 | 1,651 |
| alpha | 0.823 | 0.807 | 0.762 | 0.806 | 0.755 | 0.696 | 0.822 |
| Average alpha | 0.812 | 0.780 | 0.796 | 0.766 | 0.749 | 0.754 | 0.799 |
| Total genes | 26,479 | 12,163 | 16,323 | 21,304 | 16,490 | 10,322 | 15,485 |
| Core genes | 3,712 | 3,798 | 3,771 | 3,916 | 3,843 | 4,109 | 4,019 |
| Soft core genes | 242 | 292 | 281 | 334 | 424 | 380 | 354 |
| Shell genes | 1,018 | 764 | 1,437 | 731 | 571 | 642 | 566 |
| Cloud genes | 21,507 | 7,309 | 10,834 | 16,323 | 11,652 | 5,191 | 10,546 |
The average alpha was determined for sample sizes from 30 to the maximum per group (see Fig. 6): for all ST131 this was 0.812 ± 0.024 (mean ± standard deviation); for A 0.780 ± 0.045; B 0.796 ± 0.046; C 0.766 ± 0.031; C1_6 0.749 ± 0.017; C2_4 0.754 ± 0.077; and C2_9 0.799 ± 0.038. The groups’ cloud gene rates correlated with sample size following a power law model. B0 (n = 13) was included with B. Eight C1_10 and 16 C2_6/C2_10 isolates not assigned to clear Fastbaps clusters were not examined.