There are a combination of things that are creating these different strains of germs.
Darwin's theory of evolution is a good explanation of one reason for the "stronger" germs. Antibiotics and antibacterial "stuff" eliminates the common types of bacteria.
The ones that resist are what remain and through mutation new types of bacteria are left. A lot of times these newer bacteria seem "stronger" because they are immune to our antibiotics.
Our bodies are also not accustomed to these newer strains of bacteria.
It's not necessarily a "stronger" bacteria, it's a different strain that has become immune to the antibiotics that are overused.