J.L.
Hello- Unfortunately all mold guidelines suggest removal of carpet. I do mold consulting as part of my job- and there is not a good way to remove mold or stop it from coming back. You can bleach hard surfaces, but not carpet or padding. I would suggest removing it and just keeping a solid concrete floor until you can either replace (if it is an on-going problem- I would not replace with carpet) or use tile. You could also just use rugs that could be laundered easily if soiled. If the basement is flooding because of a sewage backup- the carpet and padding should definitely be removed. Hope it helps- although I know it's not the answer you were hoping.