Genetical modifications

Hmm...using generalised statements that don't tell the whole story ey? First of all, generally viruses don't mutate at phenomenal rates. There a few that do, the more known ones being influenza and HIV due to specific mechanisms, such as its reverse transcriptase for HIV (if you want me to explain further, please ask). Most viruses don't have these mechanisms, so the mutation rate isn't fast at all.
Different bacteria and different viruses mutate at different rates, and it's also dependent on what they're exposed to. And only a very small percentage of mutations are beneficial. Yeah, I'm not disagreeing that the bacteria could have a mutation that could affect humans, but more deleterious mutations will accumulate. There also has to be a selection factor, which varies greatly among bacteria and viruses.

If you're talking about natural selection, well of course, that's how mutations appear and accumulate. Your example of lions and zebras is not explained correctly. Lions ran faster so zebras ran faster? The zebras that could run faster survived, hence had offspring that could run faster. If you want to read all about mutation and natural selection, i've already explained it here viewtopic.php?f=23&t=13067
It's my first post in it.
Did I ever mention or even imply that we would create immunity to something that doesn't even exist yet? I'm pretty sure this is what I wrote:

We create antibodies in response to the foreign matter. You can't create antibodies to defend against something that's not there. Going back to vaccines, we inject a safe form of a specific foreign matter (say hepatitis B ) that can cause damage, so the antibodies are produced to stop that safe form of hepatitis B. But they remain the body, so if our bodies are exposed to hepatitis B ), our antibodies will stop them. By genetically modifying our bodies to produce antibodies at a faster and more efficient rate, these would fight foreign matter and we would be able to fight diseases more easily. Take the common cold for example. The cold is caused by a virus. The cause of them are many different types of viruses, not just one specific one. So when you do get infected, there is no treatment for it. Your body has to produce specific antibodies, which prevent the viruses from entering the cell. The antibodies will then signal a macrophage (white blood cells) which will engulf the infected cell to stop further production of that virus. Viruses can't reproduce on their own, so the cold is then over within a few days, on average about a week. Now, if we genetically modified our immune response to be drastically faster, the common cold might be nothing more than a day's annoyance. The same can be said for many other things.
If you're talking about gaining resistance, how can you gain resistance against something that's created after it's infected you? Let's say, it does gain a specific resistance against the antibody. Your immune response would then produce a specific antibody to counter that 'super virus/bacteria' which wouldn't happen.
Bacteria gain resistance against antibiotics because if a bacteria has a mutation that makes it less susceptible to that antibiotic, it will survive the antibiotic and will multiply. Antibiotics work because they kill off bacteria, or make them weak enough for our immune system to finish them off. Bacteria can gain a resistance against this. So that's why it isn't good to take antibiotics for the common cold. It wouldn't do anything against the common cold, in fact, would probably help the bacteria in your throat become more resistant. Bacteria can't resist with a super immune system. The reason bacteria or viruses make us sick, is because they multiply and overwhelm the immune system before our immune system can attack in full force. Using vaccinations, our immune systems does have that head start. Using a super immune system, we may not ever need vaccinations again.

Generalised statement? Did you know certain people can resist certain strains of HIV? Different strains of HIV may target different cells. People with a certain mutation are able to stop HIV from binding to a specific receptor, which will then inhibit entry into the cell. Using genetic modification, we could stop HIV from adsorbing onto target cells.
HIV uses protease to get into the cell. Protease inhibitors are a specific antiretroviral drug, which will inhibit the protease, therefor stopping the HIV getting into the cell. If we genetically modified a human to produce the protease inhibitor drug in response to HIV, that would stop it from entering. I mentioned before that HIV uses the enzyme reverse transcriptase. It uses this to copy its genes into a cell. If we genetically modified a human to produce a protease inhibitor as well as a reverse transcriptase inhibitor, HIV would be fended off.
People with AIDS (basically it's a worse case of HIV, something that occurs when HIV is left untreated) as well as people with HIV are able to remove the virus from their blood completely. The only case in which it isn't completely removed is when the virus has copied itself into specific cells not able to be reached by the two drugs. If we had a rapid immune response, producing those two specific drugs, I reckon your perfect example isn't so perfect.