Most brewers have heard horror stories about wild yeast and certain bacteria, like Lactobacillus and Pediococcus, setting up camp in a brewery and contaminating everything in sight. I think these stories originated from times when brewing equipment was very difficult to clean. Wooden vessels, poor valve designs, threaded fittings, open fermenters and the like were commonly seen in older breweries. In this type of environment, it is easy to understand how an unwanted population of microorganisms would be very difficult to expel.
Things are much different when brewing at home. Unlike commercial breweries, homebrewers do not always have multiple batches of beer moving through the brewing process where cross-contamination from one batch is a real possibility, especially if every piece of equipment is not cleaned after every use. If one of the batches contains something bad, like a contaminant, then this can easily and quickly be spread throughout the brewery. Most modern brewery designs have eliminated these problems, but the thought of contamination still scares commercial brewers. At home it is fairly easy to keep batches separated, clean your brewing tools and give them an appropriate dip in a sanitizer before every use.
I can guarantee that you can brew beers containing Brettanomyces at home without contaminating all of your brewing equipment and other beers. The key is to practice good sanitation and some common sense. Anything that has a non-porous surface can be cleaned and sanitized and will not retain wild yeast or bacteria. That means you can use glass carboys, metal spoons, etc for all of your brewing and do not need to duplicate your equipment stock. Plastic hoses, buckets, gaskets and wooden barrels are another story, and I would suggest not using these items on both your regular and wild beers. Barrels are a well-known vector for Brettanomyces in the wine industry. Once a barrel has Brettanomyces, it is nearly impossible to kill off the yeast.
I often view brewing through the eyes of a food microbiologist. Cross contamination is a big deal in food safety and keeping raw foods containing pathogenic microorganisms separated from foods that are ready to eat is crucial. Consumers deal with this issue on a regular basis when raw meat is stored in the refrigerator along with fruits and vegetables and when proper procedures are used, nothing bad happens. The same is true with brewing. If you think I am being too easy going on this issue, read the side of that yogurt container in the fridge next to your yeast culture; it’s full of Lactobacillus!