I need any diseases, either bacterial or viral, that have the following two qualities:
1) It is not tested for (or cannot be tested for) before an organ transplant.
2) It will kill someone before they are off the operating table (if the guy wakes up, he will take the donor's germ-controlling power, and won't die. She can speed up the incubation period so that's not an issue; it needs to be something that has ridiculously high fatality rate.)
It doesn't need to be just one; a combination of things would be good.
I'm not a medical person at all, so I don't really know where to start searching for this.
(Story/RP background: my germ-controlling mutant is trying to kill someone by having her own organs harvested for a transplant that the villain needs. She'd never survive getting close enough to him to infect him, and germs are one of his few vulnerabilities. The germs can be anything bacterial or viral - she has access to an entire anti-bio-terrorism research lab. They can order anything and claim it's for research. Also, money is not an obstacle. The germs recognize her as symbiotic, so they wouldn't destroy the transplant organ even after it's out of her system.)
She could also make something fast-acting by giving specific commands to the germs, so we can speed things up a bit.
Edited for clarity on topic 2 - see first set of comments for the reasoning.