The spinach-packaging company in the cross hairs of an investigation into a nationwide E. coli outbreak has struggled to manage its wastewater and is in violation of a state water disposal permit, according to public records and state officials.

The Sacramento Bee reports that there is no indication these problems at Natural Selection Foods contributed to the current outbreak; by Wednesday investigators had not pinpointed a single source. But federal officials said wastewater management and processing habits at Natural Selection and other companies have not been ruled out.