For most infectious diseases, incubation time is counted in days. Pretty much never in hours.
Why? The simplest explanation is that the bacteria or virus actually needs the person to stay alive long enough to infect other people. An infection killing in a matter of minutes would die in a matter of hours (basically, people around patient zero).
Now, let's suppose you have your super-bacteria or your super-virus. If you have the mean to control them, you also have the mean to have theme do a "suicide attack" and you can probably kill someone in minutes. Here are a few ideas of how.
There are lots of poisons around, some are highly lethal in very small doses. If your bacteria holds pockets of poison that they are ready to release, you can do a lot of damage very quickly that way. Poison targeting one specific organ (I'd suggest the lungs, but that's up to you) could be lethal very quickly.
Note that this would mean the character would need to carry poison inside of him all the time. Better be sure of his control over his microminions.
2. Slow infection, coordinated attack
This does not exactly answer your question but is worth suggesting I think. Basically, you let your virus/bacteria slowly install itself within the enemy's body, passing as a harmless parasite (most of our body is made out of harmless parasite after all). Then make all of your bacterias to attack at the same time. This could do some interesting visual, like the character talking to / fighting someone for minutes until his foe suddenly dies from all of his body.
3. Brute force
This one may be a physical burden to the character, because it requires him to produce a lot of viruses/bacterias. Mostly, we die from infection when the assailant is so numerous it can't be beaten. But in nature, the assailant needs to reproduce in the infected body. You don't need that. Just spam a mucosa with aggressive bacterias, constantly renewed. You just need an easy way to transmit your bacterias (a very visual deathly kiss, a less classy spitting...).