The interviewed expert has very good credentials and clinical experience to be talking about what he is talking about, and his warnings should be taken seriously. But even at that, the fallacious teleological language he uses about biological evolution by natural selection suggests a way out of this problem. When he says, "Bacteria, like any living organism, want to survive," and "So anything that we do to try and ki…
That being said, I have no problem with the statement that bacteria want to survive. They most certainly have mechanisms that are engaged actively in order to increase chances of survival. Horizontal gene transfer (http://en.wikipedia.org/wiki/Horizontal_gene_transfer) allows bacteria to evolve in means other than traditional reproduction.
To add to my pedantic argument, it's not a conscious desire of theirs, but I'd argue that the basic things that humans do to survive (eat, drink, sleep, and have sex) are not conscious desires either. I'd argue that sexual reproduction is a mechanism that directly represents the biological success of greater genetic diversity and sharing of genes between organisms. We desire sex, and we desire sex with the best genetic candidates, and it's all a biological process encoded into our DNA that represents our desire for survival, so in that sense, bacteria desire survival as well.
And what does desire even mean? Does desire require consciousness and the ability to choose? It's a horribly imprecise term if you stare too long at it, so what I'm saying is that I don't think it's useful to pick on the doctor for his choice of words in this case.
Anyway, you have great points otherwise, but that first paragraph is not a point worth tripping over.