Can molecular methods discern live vs. dead DNA?

Yes. There are live-dead qPCR methods available from most qPCR reagent vendors.

One of the common objections to using qPCR for microbial testing is the fact that the method does not distinguish between live and dead DNA. PCR primers and probes will amplify any DNA in the sample that matches the target sequence, regardless of viability. This is what we call the Live-Dead problem. 

Many critics falsely assume DNA-based methods will fail more material than culture-based methods when it comes to threshold tests, such as Total Yeast and Mold and Total Aerobic Count, and leave growers hopeless to employ sterilization techniques. After all, sterilization kills the microbes but doesn’t eliminate the DNA, so dead organisms will inflate results. However, scientists, including the team at Medicinal Genomics, have developed techniques to solve the live-dead problem. Generally, these solutions fall into two categories: live-dead qPCR and before-after culture qPCR. 

Read More Here: https://www.medicinalgenomics.com/solving-the-live-dead-problem/