I will boil my workout shoes a good 30 minutes after every workout (of course I take the shoes off before doing this...what, am I stupid?). And just to be sure that no death dealing fungi ever develops, sap them in a microwave, on high, for 15 minutes. This is standard policy where I train at in SoCal. Hope this helps and Good Luck.
Side Bar: or you could just spray them with a disinfectant when done.