I have dealt with clostridia before and it is quite a persisitant bug so make sure you keep on top of any dire rear relapses, it can only be diagnosed fully by a stool sample (poo) but the good news is that it does respond to treatment, however repeat treatments are usually required if the bug is being particulairly persistant.
E coli is a nasty strep bug and is contageous, I have never dealt with it myself but again it is treatable and it seems you have managed to catch it quick enough.
Both bugs are likely to have come from dirty living conditions - I assume they are P@H piggies, I would contact them and make them aware of the problems you have had with cookie, chances are the same stock will also have it. It is highly unlikely that either of these two bugs could have come from your housing arrangements or food that you have fed.
I am so glad cookie is feeling better, lots of hugs and get well soon cookie