Can a e. coli colony contain flu viruses or other viruses inside the bacteria?

Not exactly: You're right to prompt the question, in that bacteria can be made more virulent by uptake of "signals" from a bacteriophage. Also, an e.Coli infection does not preclude a superimposed or secondary viral illness--which together compromises the host patient more than a single infection might. However, flu viruses can not live within e.Coli.