Hi T.,
The lab only needs a small smear to test. There may be enough left on his bottom when he "goes" so you can wipe what has not yet touched the diaper. Or you can "scoop" some off the top. I'm not really sure how a clean diaper can contaminate what the lab is doing....
Also if you see him going, put him in the tub,take his diaper off and try to get some.
If you are still having trouble I would say, call the pharmacist and see if they have a small syringe you can use to get some out...if you can stick a rectal thermometer up there, a very small syringe should do fine. Once again, the lab only needs a small smear to test.
If it's not a parasite or something foreign causing this, please let me know when you get the results. I had issues like this as a child and I can help steer you into handling this correctly the first time...
Regards,
M.