But conquistadors and Aztecs were both human. According to Seth Shostak, senior engineer from SETI, bacteria are limited to the life forms they are biochemically related to. Our germs have evolved to survive on our unique DNA.
Even viruses and bacterial infections that infect one species on our planet will only rarely spread to another. Dogs don’t routinely get the ‘flu, for example. Any alien life form that invaded earth will likely be immune to earthly diseases, so don’t expect a War of the Worlds solution.