The problem is growing leafy plants like lettuce and spinach in space can come with a side dish of bacteria, according to a new study from a team at the University of Delaware. In tests on plants grown in simulated microgravity, they were shown to actually be more susceptible than normal to the Salmonella enterica pathogen.
Sounds like not a big problem at all. Seems like they'll just have to use appropriate cleaning methods. Even in the worst case scenario they would probably just have to use food irradiation.
The ISS has a very strict cleaning regime. Essentially every work minute not spent on research or maintenance is for cleaning. I think to remember that they even have one day a week when all they do is clean.