The other outbreaks were E. coli related that involved either sprouts or cucumbers in California, Idaho, Michigan, Montana, Utah, Washington or Colorado, CNN reported.
The government agencies said the company had not corrected its supply chain for the long run to make sure that the ingredients used are safe.
But changes have recently been made, the company said.
Jimmy John's President James North told USA Today that no more sprouts will be sold at all locations across the country until further notice. But company President James North said the stoppage was "out of the abundance of caution and was not initiated by any known, immediate threat," CNN reported.
The FDA said Jimmy John's must provide the steps it is taking to address the issues within 15 days of the letter and if it does not correct the violations, there could be "a seizure and/or injunction," CNN reported.