Bacteria can share DNA [wikipedia.org] with other bacteria. (I don't know if it applies here, but I don't know that it doesn't) If the DNA for this toxin jumps to a different strain of bacteria (say... Pseudomonas aeruginosa) and becomes an infection... We need to ask what this toxin does to human tissue. If it isn't harmless, we could be building a drug resistant, toxin spewing bacteria!
That's one thing that could go wrong.
(No, I didn't read the article. I'm just assuming it doesn't cover this eventuality.)
Source: http://rss.slashdot.org/~r/Slashdot/slashdotScience/~3/lE2N1Www2nc/story01.htm
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