PCR is good. But if your sample does not contain any DNA, it can give false negative too. It seems that stool tests are not very sensitive and real doctor should not rely on one test. He must order as many test as he could. Swabbing the rectum is far more sensitive than collecting stool. Bugs live on the tissue. Stools are just excrements, They might or not contain some cysts if the technician is lucky to find any.
The charges against this doctor are lies and fallacies. I think they did not like the ozone treatment he was doing.
Most antidepressants are serotonin reuptake inhibitors or inhibitors of MOA which degrades serotonin. Parasites and fungus produce serotonin and it increases their virulence. Imagine if someone has a parasites an he is giving antidepressant. The infection will go wild and probably he will become more depressed.