S.aureus is one of the bacteria that's found on our skin naturally. It can live there for years and not cause any problems. It's only when it gets inside our bodies that it causes infections, usually through a wound. Most of these can be treated without too much trouble using antibiotics, but some strains of the bug are resistant to the common antibiotics.
We've brought a lot of this on ourselves because doctors have been throwing antibiotics at every disease and infection since they were first discovered whether it was necessary or not. Another problem is that patients feel better after a few days on antibiotics so they don't finish the course. If your doc gives you a two week course, finish it unless you have side-effects, and even then, don't stop taking them without consulting your doctor. Bugs have their own ways of responding to antibiotics and antivirals the same way we have an immune system to defend against them. Bacteria that survive antibiotic exposure often become resistant to that antibiotic. What's worse is they can transfer resistance between each other. It's along the lines of, say your cousin has measles and recovers, he or she becomes immune to it and can pass that immunity on to you or anyone else in your family. Shame we can't do that, eh?
We have an immune system for a reason. It will take care of most infections by itself, but occasionally it needs a little help. With most bugs (bacteria, viruses, etc), you're sick for a week or two, but then you recover and you'll never be bothered by that strain again because you're immune to it. Different strain of the same bug, different story, unless you're lucky enough to have antibodies to something it has in common with the bug you've just recovered from (without going into too much detail about immunology). In some cases your system needs a bit of help. There are bugs which will kill you before your immune system even gets going because, for example, they produce toxins. Some bugs change their coats regularly to fool the immune system. That's what happens in diseases like malaria. Others go dormant or hide inside cells and come out every now and again for one reason or another. That's what happes with herpes. These are the types of diseases that need antibiotics and extra treatments in heathy individuals, or if an infection doesn't start improving within a few days. If your immune system is compromised, then, yes, antibiotics are necessary.
Hospitals should be as clean as possible, ideally sterile, but there's no way to achieve that yet. However, standards of cleanliness should be high. Sadly, they're being dropped to cut costs. A lot of hosptial-acquired infections have been passed on by doctors and nurses not washing their hands between patients. I'm reminded of a bit of advice I was given to me when I began my microbiology degree: "A wise microbiologist washes his hands before and after going to the toilet."
Living in a sterile environment is all well and good, but that can lead to problems in itself. If your immune system isn't being challenged it can become hyper-reactive. That's one of the reasons being put forward for an increase in the number of patients with severe allergies. The immune system can also turn on the body, which is happening in many auto-immune diseases. That has again been attributed to it becoming, in effect, "bored" at having nothing to do. Each time you fight off an infection, you become immune to it. If you've never had any diseases, you won't have any immunity. You can produce hundreds of different antibodies to different bugs and the various antigens on them. Those will give you some degree of protection from other related bugs, so, ideally, what you want is to become immune to as many diseases as possible - ideally without getting too sick in the process. So, don't stop your kids crawling around on the floor or playing with worms etc. Do get your dogs and cats wormed though and there are a couple of nasty diseases they can catch from them too.
