Can't do bubkes about flu or HIV, but there is a vaccine for TB (BCG) and there is a promising vaccine in development for malaria; some of these diseases might have to be kicked in the ass with a vaccine. I suspect trying to make vaccines against these microbes will become more important as antibiotics become less effective. Certainly, a vaccine would have a higher likelihood of getting rid of these diseases for good.
EDIT: Microbio lesson. There are two basic 'types' of bacteria: Gram-positive and Gram-negative. This classification is based on a bacterium's reaction to a substance called the Gram stain. If a bacterium is Gram-positive, it has a thick cell wall over one membrane (the cell wall has peptidoglycan, which reacts with the Gram stain, and it is thick enough to retain it). If a bacterium is Gram-negative, it has two membranes, and the cell wall is too thin to retain the Gram stain.
Some cells are also Gram-variable, which means that it's sort of a crapshoot. One of these is TB!
Gram-negative bacteria are prone to being resistant to a lot of antibiotics, because they have two membranes instead of one.
There are four main mechanisms of drug resistance:
- Drug inactivation or modification: for example, enzymatic deactivation of penicillin G in some penicillin-resistant bacteria through the production of β-lactamases.
- Alteration of target site: for example, alteration of PBP—the binding target site of penicillins—in MRSA and other penicillin-resistant bacteria
- Alteration of metabolic pathway: for example, some sulfonamide-resistant bacteria do not require para-aminobenzoic acid (PABA), an important precursor for the synthesis of folic acid and nucleic acids in bacteria inhibited by sulfonamides, instead, like mammalian cells, they turn to using preformed folic acid.
- Reduced drug accumulation: by decreasing drug permeability or increasing active efflux (pumping out) of the drugs across the cell surface
I don't know enough about agents used against eukaryotes to say much about them.
The key thing here is that this is happening in a nosocomial context. Hospitals are places where it is VERY easy to pass around infections that mutate quickly, since it's a place where sick people go. There needs to be a veritable crusade to quash the likelihood of stuff like MRSA and UTIs getting passed around, before they even infect someone. Antibiotics can do a crapload (or could), but the linchpin of a healthy environment is stuff like handwashing, functional toilets, and a clean surface.
I am not super-confident that people who not only probably didn't go to school in ag or bio so don't understand the concept of bacterial evolution of resistance but are also monetarily invested in making bank from this are going to ditch antibiotics so easy, and I am also not super-confident that Big Ag gives much of a shit about the long term sustainability of their business model (answer: not sustainable in the long term, "let's have short term gobs of profit but burn out later!").