Meat is by no means sterile, if by that you mean free from germs and
viruses. I read an estimate that cells often have viruses in them, numerous
ones. Bacteria are very small and meat can be teeming with them and still be
"fresh."

I agree that it is a problem when processing brings bacteria that belong in
a certain place (the gut) of an animal into contact with a place where it
doesn't belong (muscle meat.) Is this what you are talking about?

--Richard