E. coli in water isn't itself the threat. It's an indicator that human or animal poop has gotten into the water, along with whatever disease-causing bacteria and viruses one or more of the poop sources might be carrying. It's also a matter of degree, with concern rising with the amount of contamination (and, presumably, the number of sources). A town's entire sewage stream is much more likely to cause illness than a single home's. The illnesses of concern are those transmitted by the fecal-oral route, which is both yucky and common. Polio, for example, is transmitted this way.
If you boil E. coli-contaminated water for at least one minute you can make it biologically safe to drink. I'm guessing you're concerned about showering, and I'd be surprised if the water posed any extra threat to you because of the fistula, though I wouldn't intentionally try to push any water into the fistula. It might be wisest to avoid tub baths, but even that is an overabundance of caution. The organisms we worry about in E. coli-contaminated water aren't those likely to cause fistula trouble.