You can get aircon decontaminator spray (Commonly refered to as an Aircon bomb!) You set your aircon to cold, fan on full power, on recirculating. Then you set the aerosol off in the passenger footwell aimed at the heater box and shut the door.
Leave it for 15 mins or so and that kills all the bacteria and removes nasty niffs.
You don't need to stick it on any drainage tube, just position it so it is sucked into the heater box.