The binding of Magnetic nanoparticles to microbes is in its infancy, although established. I doubt if you will be able to achieve this with dead E. coli cells. Reason being that the binding of MNP to bacteria may be dependent on the surface chemistry (& morphology?) of the bacterial cell wall. How this changes in a dead bacteria, I am unsure. I believe there is literature which speaks about functionalizing the MNP with, for example, vancomycin. Please check the links below.