I'm surprised that the article doesn't mention LYMERix, the FDA-licensed vaccine that seems to be a casualty of anti-vaccine hysteria and a somewhat overzealous legal system. There seems to be a tiny suggestion that the vaccine might cause some issues, but all the studies seem to show that this isn't a problem.

Also, vaccinating dogs against Lyme disease is standard practice, and it doesn't seem to hurt the dogs.

Here are some references:

http://cid.oxfordjournals.org/content/52/suppl_3/s253.long

http://cid.oxfordjournals.org/content/52/suppl_3/s253.long