Those same conditions are ideal for bacterial growth. Beuchat said the seeds can become contaminated with a pathogen anywhere in a long trail. Birds can carry Salmonella. Animals, including deer, can carry E. coli. Manure that hasn't been properly composted can be contaminated.
Harmful organisms can get onto the seeds after they leave the field, too.
The real problem starts then. A pathogen on a dry seed is just there. But once you hydrate it and put it in the sprout production process, the organism is going to reproduce during that entire time. Once the sprouts are mature, they're washed, packaged and distributed to stores and restaurants. They're often refrigerated during that time, which limits further bacterial growth.