My question is, is it acceptable or valid to detect plasmid mediated antimicrobial resistance genes via Rt-Qpcr. İs there any limitaitons to isolate RNA from plasmid and calculate gene expression?
Ibrahim, it depends on the question you are trying to answer. If you want to know whether the genes are being transcribed then RT-qPCR is fine. However that does not really tell you how much enzyme activity is present. However if you have a very reproducible environment with the same strain and you have done the controls to correlate mRNA levels to enzyme level, then it might be an acceptable proxy.