Assume a supernatural character, who has control over billions of billions of virus and bacteria. It's not always an interesting concept, ss infections typically spread slow, and moreover, the nature of this ability does not provide efficient self-defense.
Would it be possible to control virus and bacteria to perform lethal actions that take short amount of time? If yes, how?
1) The limitations of an actual virus: One of the reasons that viruses are "slow" to reach lethality is that they're unintelligent. They have to operate on chemical reactions, rather than actual decision making.
2) Instant lethality of a supernaturally controlled virus: However, if this supernatural Character can control viruses and bacteria, they can force them to swarm a specific organ (such as the brain), and essentially disassemble or shred it at the cellular level while replicating as quickly as possible to overwhelm any immune system response.
3) Sustainability: An actual virus which acted so quickly would likely go extinct by killing it's only host before being able to propagate. The supernatural character could circumvent this by growing the virus within their own body. Since they control the virus, they would be in no danger of suffering any ill effects, and could send it into a target at will.
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.
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.
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...).
Easy. The GI tract is loaded with trillions of bacteria. If you could "command" them to escape the gut and flood the bloodstream, this would be almost immediately fatal. Normally, in healthy GI tracts, these bacteria are prevented from invading the gut wall by a mucosal layer and the tight seal of endothelial cells lining the GI tract that selectively pass nutrients and water but block organisms. But if you could "command" bacteria, even the normal gut bacteria could move through the mucosal layer and disrupt the GI cell lining, allowing bacterial to slip past and get into the blood stream.
This is a long, technical read (http://cmr.asm.org/content/20/4/593.full) but it pretty clearly lists how a normally beneficial gut bacteria, the Bacteroides family, can become pathogenic by switching to a more aggressive form that can bind to the endothelial cell surface, breakdown the junction between cells, and stimulate a large immune response that doesn't kill the bacteria, but rather affects the tissues around it. If this process could be remotely initiated in the trillions of bacteria all at once, it would create a pretty significant gut failure that would trigger sepsis and death in short order.
The key to this type of attack is overwhelming response. Instead of just a few bacteria "going bad" that the immune system can deal with, this is a huge assault. Since bacterial don't have (as we understand it) sentience, they are basically organic robots. They have few options other than (mostly) blind movement, changing receptors on their surface in order to interact with their surroundings, and secreting substances (some of which can be fatal to humans). So you need a normally occurring bacteria that already has all the tools for a lethal attack so you don't have to try to infect the target with something like C. botulinum and have to wait for it to grow and secrete the botulism toxin. Bacteroides certainly fits the bill and should be present in sufficient numbers in all humans (though I suppose someone could carefully sterilize their GI tract in an attempt to counter this type of attack, but that would be incompatible with life for more than a few days).
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