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There already is a method, decades old: bacteriophages [1] in phage therapy [2]. Put them with bacteria that have resistance and they'll evolve along with them. It's cheap and will always be effective.

[1] https://en.wikipedia.org/wiki/Bacteriophage [2] https://en.wikipedia.org/wiki/Phage_therapy




Apparently we (and other animals) have evolved some mucus-strategies for capturing bacteriophages for our own use.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3696810/




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