Hi,
All the three courses you have mentioned have their own advantages. They may merge into one in some cases when you try for jobs or in research. MSc Biotechnology will have special papers in microbiology as well. Clinical research also includes some biotech and microbiological aspects. Some of the earlier discussions in this section will be useful to you, so please go through them as well.

Clinical and therapeutic research is a growing area and you can find better research/job prospects in that field also. I would suggest you to think of your comfort zone in Biotech or Clinical research, and chose one of them.
Regards,
Suresh