What do you mean? The presidency has enormous power at this point, and when it comes to enforcing regulation the power is actually granted by Congress
All the president has to do is convince these few companies that they're actually in danger of operations being shut down, even temporarily. They will respond a lawsuit to block this if they think that would be the easier path, but there's any number of ways to bring them in line. They'd lose an enormous amount of money for every day they're shut down... If they believe cleaning up their operations is going to be the cheaper path, they'll make changes unbelievably fast
The presidency also has enormous soft power... If the president calls a company out publicly for food safety, the share price will drop, grocers will switch suppliers if they can, and it'll affect sales
It all hinges on reputation though... It might take following through on a threat to bring the rest in line, but once they see food safety as the cost of doing business with no cheaper option, they'll absolutely fall in line