Table 3.
A panel of serovar-specific genes for typing the ten most frequent serovars in Australia.
| Serovar | Gene 1 | Gene 2 | Gene 3 | Gene 4 | Gene 5 | Gene 6 | Gene 7 | Gene 8 | Gene 9 | Gene 10 | Gene 11 | Gene 12 | Gene 13 | Gene 14 | Gene 15 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Typhimurium | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
| Enteritidis-B | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - |
| Enteritidis-A/C | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - |
| Virchow | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - |
| Saintpaul-I | - | - | - | - | + | - | - | - | [+] | - | - | - | - | - | - |
| Saintpaul-II | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - |
| Saintpaul-III | [+] | - | - | - | - | - | + | - | - | - | - | - | - | - | - |
| Infantis | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - |
| Paratyphi B-I&II | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - |
| Paratyphi B-III | [+] | - | - | - | - | - | - | - | - | + | - | - | - | - | - |
| Chester | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - |
| Hvittingfoss-I&II | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - |
| Hvittingfoss-III | [+] | - | - | - | - | - | - | - | - | - | - | - | + | - | - |
| Muenchen-I | - | - | - | - | - | - | [+] | - | - | - | - | - | - | + | - |
| Muenchen-II | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + |
| Error rate | 2.4 | 0 | 1.5 | 0 | 2.9 | 0 | 0.2 | 0 | 1 | 0 | 2.2 | 0 | 0 | 0 | 0.9 |
| Specificity | 97.6 | 100 | 98.5 | 100 | 97.1 | 100 | 99.8 | 100 | 99 | 100 | 97.8 | 100 | 100 | 100 | 99.1 |
“+”: true positives (TP); “-”: true negatives (TN); [+]: false positives (FP) in a subset of genomes. Gene 1 = STM4494 (Typhimurium); Gene 2 = SEN1384 (Enteritidis-clade B); Gene 3 = R561_RS18155 (Enteritidis-clade A/C); Gene 4 = SEV_RS01820 (Virchow); Gene 5 = SESPA_RS08460 (Saintpaul-I); Gene 6 = SeSPB_A1749 (Saintpaul-II); Gene 7 = Saintpaul-III; Gene 8 = L287_RS37190 (Infantis); Gene 9 = SPAB_01124 (Paratyphi B-I&II); Gene 10 = SPAB_01338 (Paratyphi B-III); Gene 11 = SEECH997_RS20295 (Chester); Gene 12 = LFZ15_01345 (Hvittingfoss-I&II); Gene 13 = LFZ15_20305 (Hvittingfoss-III); Gene 14 = L098_RS21065 (Muenchen-I); Gene 15 = Muenchen-II. See Supplementary Table S2 for gene details. The potential error rate of serovar-specific genes was defined by the formula: (Number of FPs)∗(The frequency of that serovar in a given region)/(Total of genomes of that serovar). The specificity of typing rate was equal to (1 – potential error rate).