Did the infection come from the pigs?
When Jeff and Bert go out investigating they stumble upon that random woman in the woods slaughtering the pigs. After they spot each other she then says something along the lines of "these g#@amn animals have been running around infecting everything"! So was it the pigs who had some sort of contagious disease infecting the water in the system causing the flesh eating bacteria? What do you think?!
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