Brettanomyces is a yeast. Lactobacillus and Pediococcus are bacteria. If your cleaning and sanitizing regimen kills off all of the Saccharomyces (brewers) yeast, then it should do the same for the Brettanomyces. Bacteria can be a little more difficult to kill off, and it is probably a good idea to keep separate plastic equipment when using these microbes.
That being said, it isn't that hard to have a separate set of hoses to use for Brettanomyces, and it is cheap insurance.