I've already tried primers targeting rpoB, pta, tpi and tuf genes. Despite the last ones, they were all designed for amplification in S. aureus.
Do you know any primers targeting sequence of constitutive genes enough conservative to obtain comparable Ct values in CNS and S. aureus ?
I don't know specifically for S.aureusa and Staphylococci. But i think the 16s rRNA gene can be used as reference gene as it is used for many of the bacterial northern blot analysis and can be used for qPCR and metabolic gene GAPDH can be used. But you have to check that its expression is mostly unaffected by the conditions you used.
What you can try is use 2 or 3 different housekeeping genes, that make arithmetic average and use this values. It is really comfortable for using other RT-PCR. You do not make housekeeping gene for all your genes separately. Only first time and then use values for all your analysis.
Validation of housekeeping genes for normalizing RNA expression in real-time PCR.
http://www.gene-quantification.de/dheda-bustin-hkg-2004.pdf
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