Dear you may get some insight at the link below: https://www.researchgate.net/publication/260433705_Microbial_Genetics_Questioned_to_Understand?ev=prf_pub
I guess you mean to say E.coli a not one E.coli, you see different methods can be used depending on your objectives. May if you tell me your objectives, I may be able to guide. But in the absence of that, you can consider the use of RAPD, SSR etc