Pathogens played a part in the fall of some civilizations?

Absolutely. Once vaccines and proper medicine came around, things did turn around. There were cases though where a sickness came in and ravaged small colonies /towns early in the US history. One such place was near here. Always had that thought in back of my mind about things brought back from space and what consequences that could mean for us.
 
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I am much more concerned with ancient pathogens suddenly coming out of melted perma-frost, than alien infections.

The Andromeda Strain is always a possibility, but the home-grown germs have evolved to target us, and are already here.