TABLE 3.
STKP embodiment for S. aureus genotyping using SNPs: distribution of primers into eight tubesa
| Tube no. | Locus | Possible polymorphs | Polymorph for STKP | Primer combination |
|---|---|---|---|---|
| 1 | arcC210 | C,T | C | S1, U1 |
| 2 | tpi241 + 243 | GA,GG,AG | GA | S2, U6 |
| 3 | arcC162 | A,T | A | S1, U8 |
| 4 | gmk318 | A,T | T | S3, U9 |
| 5 | pta294 | A,C | A | S4, U11 |
| 6 | pta383 | A,T | T | S6, U16 |
| 7 | tpi36* | C,T | C | S5, U15 |
| 8 | tpi36* | C,T | T | S5, U14 |
a
Conventional kinetic PCR requires the same number of reactions as there are polymorphs at a particular locus. In the full S. aureus kinetic PCR genotyping method, 17 reactions are required—two for each of 7 loci, except for arcC210, tpi241 + 243, and pta294, where three polymorphs are possible and consequently three reactions are required (see third column). Single-tube kinetic PCR uses a universal control reaction—in this case tpi36 in tubes 7 and 8—to normalize cycle times obtained so that polymorphs can be deduced from a single reaction per locus. *, “universal” control reaction.