Best I can tell germs are always there. Some create worse deseises then others, while some are unnoticed because our body is good at combating them.
The worst 2 kinds of deseise that I am aware of are immune deficiency deseises like AIDS, and autoimmune deseises where your immune system fights parts of your own body. In one case any germ is enough to wreck havoc on you, while in the other case your own over active immune system goes to war with one type of body tissue or organ. Though I'm sure there are deseises that bring on worse conditions to live through, or die from, I can't really image a worse deseise state then having no immune system, or have a war within you waged by the immune system.
As for where germs come from... I think there's studies out there on how long certian germs can live in the air, or on a surface before dying. Some can't survive very long outside of a body they infect. Others unfortunately can stand a longer time. Gives me all the more reason to cover my sneezes as best I can.