There are about 50 colleges offering medical microbiology in India.Some of the colleges are
AIIMS ,New Delhi
CMC ,Vellore Chennai
Fergusson college
St.Xavier college
And many more

Following are some of the colleges in India offering MSC medical microbiology.

• Kasturba Medical College - [KMC] Mangalore , Karnataka (India)
• JSS Academy of Higher Education & Research - [JSS University] 
• KLE University
• Bharati Vidyapeeth University 
• Calicut University. 
• NIMS University.
• Sharda University 
• Chaudhary Charan Singh University 

Hello Praveen,
Some of the Colleges offereing M.Sc Medical Microbiology are-
University of Madras, Chennai
Jamia Hamdard, New Delhi
Sgt Medical College Hospital And Research Institute, Gurgaon
Jss Medical College And Hospital, Mysore
Good Luck!