"
So unless robots poop I suppose less E Coli in the lettuce? Chipotle may yet survive."
Manure is present in all farming. Granted, farmers choose as to which method of processing the manure goes through, before they buy it or otherwise use it.
Even human manure is used, especially in east Asia. Today, though, it is properly processed to safeguard against bad germs and parasites if used very soon (e.g. proper composting in the correct temperature range).
Humanure Handbook, 3rd Edition
In most climates, it takes at least two years for human manure simply buried shallowly in earth to be safe enough as fertilizer for vegetables consumed by humans. For cattle manure, it must be in the field for at least six months (earlier in some climates).