Table 2.
Key characteristics of the SBSEC-MLST scheme for S. equinus, Sgg and Sgm
| S. equinus (n = 10) | Sgg (n = 6) | Sgm (n = 7) | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Index of association1 | IA | 2.092 | 2.093 | 0.329 | ||||||||||
| IA S | 0.232 | 0.233 | 0.037 | |||||||||||
| Gene | Gene product | A3 [bp] | A [no] | dN/dS | pms [No (%)] | SID | A [no] | dN/dS | pms [No (%)] | SID | A [no] | dN/dS | pms [No (%)] | SID |
| ddlA | D-alanine-D-alanine ligase | 489 | 8 | 0.093 | 52 (10.6) | 0.956 (0.894–1.018) | 6 | 0.098 | 8 (1.6) | 1.000 (NaN7-NaN) | 2 | 2.070 | 4 (0.8) | 0.286 (-0.092–0.664) |
| gki | glucokinase | 438 | 8 | 0.061 | 32 (7.3) | 0.956 (0.894–1.018) | 3 | 0.000 | 6 (1.4) | 0.600 (0.215–0.985) | 3 | −6 | 6 (1.4) | 0.714 (0.563–0.865) |
| glnA | glutamine synthetase | 396 | 2 | 0.000 | 1 (0.3) | 0.200 (-0.104–0.504) | 2 | 0.000 | 3 (0.8) | 0.600 (0.600–0.600) | 1 | −6 | 0 (0) | 0 (0.000–0.000) |
| mutS | DNA mismatch repair ATPase | 552 | 10 | 0.015 | 43 (7.8) | 1.000 (NaN7-NaN) | 3 | 0.037 | 17 (3.1) | 0.600 (0.215–0.985) | 4 | 0.123 | 6 (1.1) | 0.810 (0.630–0.989) |
| mutS2 | mismatch repair ATPase | 495 | 10 | 0.010 | 28 (5.7) | 1.000 (NaN7-NaN) | 5 | 0.017 | 13 (2.6) | 0.933 (0.805–1.062) | 2 | 0.000 | 2 (0.4) | 0.571 (0.465–0.678) |
| pheS | phenylalanyl tRNA synthetase | 480 | 8 | 0.075 | 14 (2.9) | 0.956 (0.894–1.018) | 3 | 0.000 | 11 (2.3) | 0.600 (0.215–0.985) | 2 | −6 | 1 (0.2) | 0.286 (-0.092–0.664) |
| proS | prolyl tRNA synthetase | 417 | 9 | 0.046 | 59 (14.1) | 0.978 (0.927–1.028) | 4 | 0.000 | 5 (1.2) | 0.800 (0.528–1.072) | 1 | −6 | 0 (0) | 0 .000 (0.000–0.000) |
| pyrE | orotate phosphoribosyl transferase | 393 | 7 | 0.040 | 21 (5.3) | 0.933 (0.871–0.995) | 5 | 0.000 | 4 (1) | 0.933 (0.805–1.062) | 3 | 0.042 | 16 (4.1) | 0.762 (0.655–0.869) |
| thrS | threonyl tRNA synthetase | 573 | 7 | 0.000 | 17 (3) | 0.933 (0.871–0.995) | 4 | 0.032 | 18 (3.1) | 0.800 (0.528–1.072) | 2 | 0.096 | 87 (15.2) | 0.286 (-0.092–0.664) |
| tpiA | triosephosphate isomerase | 408 | 3 | 0.049 | 7 (1.7) | 0.511 (0.200–0.822) | 2 | 0.000 | 1 (0.2) | 0.533 (0.277–0.790) | 2 | 0.000 | 1 (0.2) | 0.476 (0.183–0.769) |
| Mean (95 % CI) | 0.842 (0.307–1.378) | 0.74 (0.393–1.087) | 0.419 (−0.173–1.011) | |||||||||||
1Index of association based on one strain per ST: IA: calculated using classical Maynard Smith approach, IA S: standardized according to Haubold
2SBSEC: includes also 3 S. gallolyticus subsp. pasteurianus and 1 S. alactolyticus strains not listed separately
3 A allele
4 Pms polymorphic sites
5SID (95 % CI): Simpson’s index of diversity with 95 % confidence interval (CI) calculated from SID+/− 2*Standard deviation
6no dN/dS calculation due to limited allele numbers and differences
7NaN: maximum diversity, no CI calculcated. Values were calculated for the entire SBSEC and individual (sub)species, including all 10 target genes and Simpson’s index of diversity (SID) as an indication for the differentiation power among strains