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Most problems like that come from the industrialized food supply. You'd be pretty hard pressed to get e coli from spinach you grew yourself.

Even if you have chickens walking around and pooping throughout your garden?

If you have chickens in your garden, you won't have any spinach left. Chickens _love_ fresh greens.

You should never use manure that hasn't been properly composted. I don't think anyone who grows chickens and their own crops would not know this.