STKP embodiment for S. aureus genotyping using SNPs: distribution of primers into eight tubesa

Tube no.LocusPossible polymorphsPolymorph for STKPPrimer combination
1 arcC210C,TCS1, U1
2 tpi241 + 243GA,GG,AGGAS2, U6
3 arcC162A,TAS1, U8
4 gmk318A,TTS3, U9
5 pta294A,CAS4, U11
6 pta383A,TTS6, U16
7 tpi36*C,TCS5, U15
8 tpi36*C,TTS5, 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.