My 15 year son was prescribed clindamycin phosphate gel 1% for acne three months ago. It worked well but suddenly does not work anymore. Why?

That's common. Nobody knows why though resistance may be part of the picture, or his testosterone surge may be getting even greater. There are a variety of meds for acne; topical spironolactone is a little-known option. I'm glad you're concerned, and if junior needs Isotretinoin after he's gotten his full growth, please consider it.