TABLE 3.
Sequence variation in seven MLST loci from 38 STs
| MLST locus | Amplicon size (bp) | No. of major alleles | No. of variable sites | dS × 100 (mean ± SE) | dN × 100 (mean ± SE) | dN/dS (95% CI)a | Phi Pb |
|---|---|---|---|---|---|---|---|
| adhP | 498 | 10 | 11 | 1.61 ± 0.66 | 0.23 ± 0.11 | 0.20 (0.06, 0.47) | 1.0 |
| atr | 501 | 8 | 12 | 2.33 ± 0.74 | 0.26 ± 0.15 | 0.09 (0.02, 0.23) | 1.0 |
| glcK | 459 | 8 | 10 | 1.91 ± 0.75 | 0.23 ± 0.13 | 0.13 (0.03, 0.33) | 1.0 |
| glnA | 498 | 8 | 9 | 1.36 ± 0.55 | 0.21 ± 0.12 | 0.11 (0.03, 0.29) | 1.0 |
| pheS | 501 | 7 | 8 | 1.46 ± 0.69 | 0.32 ± 0.19 | 0.13 (0.03, 0.33) | 0.04c |
| sdhA | 519 | 6 | 12 | 2.58 ± 0.91 | 0.47 ± 0.23 | 0.18 (0.07, 0.39) | 0.16 |
| tkt | 480 | 8 | 10 | 0.89 ± 0.54 | 0.68 ± 0.30 | 0.67 (0.31, 1.24) | 0.16 |
| Avg | 493.7 | 7.9 | 10.3 | 1.73 ± 0.69 | 0.34 ± 0.18 | 0.22 (0.08, 0.47) | |
| Totald | 3,546 | 38 | 72 | 1.48 ± 0.26 | 0.20 ± 0.05 | 0.13 (0.10, 0.18) | 6.5 × 10−10 |
a
95% CI, 95% confidence interval.
b
Phi P, pairwise homoplasy index P value.
c
Despite evidence for recombination using the Phi in SplitsTree (26), a more thorough analysis using the GARD approach (32) failed to identify any recombination breakpoints in pheS.
d
Represents all 38 STs with concatenated gene data.