Why is everyone concentrating on viruses when the OP asks for germs generally?
I agree the chances of being infected with an alien virus is pretty remote. The chances of an lien species having DNA, much less anything we would recognise as virus, is so remote as to be ludicrous.
However other alien microbes of the bacterial/fungal type are far more likely prospect. The evolution of lifeforms that excrete exozymes and simply abosrb any nutrients around them is pretty much garaunteed it’s such an efficient, adaptable and
elegant design.
So then we have to figure out what these things can digest.
Given that any alien lifeform will probbaly be carbon based we can assume that any long-chain hydrocarbons will be on the eating list just as they are on Earth. Beyond that it’s hard to say. Things like sugars and proteins are more likely to be shared between unrelated groups than something ascomplex as DNA/RNA. It’s odds on that any alien microbe will be able to digest at least some of the componenets of the human body. Mabe not efficiently, but as well as some microbes can digest syntehtic polymers. So they could pose a risk.
Then we have to ask whether our immune system could effectively deal with them. I’d say unlikely. Our immune systems are geared towards terrestrial lifeforms. It locks in largely on recognised sugars and proteins. Anything that isn’t a ‘recognised’ sugar or a protein tends to be largely ignored by the immune system and instead is detoxified by the liver or excreted in the kidneys. That’s how most drugs retain effectiveness. Aspirin may be a complex molecule, but it doesn’t cause an immune reaction. Alien bugs aren’t likely to have any recognisable antigens, even if they are composed of something analogous to carbohydrates and protein.
So we have an alien bug with, for arguments sake, a poly-cyclopropane/chlorinated hydrocarbon shell instead of a carbohydrate/lipopolysaccharide shell and producing ‘enzymes’ composed not of organic amino acids, but of organic phosphoric acids. There’s nothing there for our immune systems to recognise. The creature’s surface coating is going to be immunologically ‘inert’ or at best provoke a very minor immune response. The damaging exozymes that are melting us from the inside out are also probably immunologically inert. Even if they aren’t, I don’t think we have anything in our arsenal to denature phopsphoric acid proteins.
But even if they do provoke an immune response and they do get denatured, what sort of physiological effect will be produced by having fragments of phosphoric acids floating around in our bloodstreams? The same is true of the microbes cell walls. So we can kill the microbes. They then lyse and release PCBs and cyclopropanes into our systems. That ain’t good.
This is of course all guesswork. But it does show some of the problems associated with compleyely alien bugs. They will most likely be able to use us as a food supply. Our immune systems are not geared to fight them, and may not be able to deal with them at all. The secondary metabolites of these creatures may well be dangerous to us simply by chance.
So yeah, on the balance of probabilities some alien microbes will be able to infect us. Odds are they will have a hard time digesting us and become annoying tinea/thrush type infections. Worst case they can digest us with relative ease and produce even moderately toxic secondary metabolites.
The biggest factors will be that any alien organism will probably have evolved to cope with temperatures and gas mixtures very different to anything found in the human body. But that isn’t garaunteed. Opportunistic Earth microbes like Clostridium tetani also evolved with very differebt gas mixtures, but they still kill people. They also have the capacity to operate at very wide range of temperatures.