U can go for Medical microbiology but then only with MSc in it will not get u a job and neither u get paid well...With MSc , u can work in hospitals where u get a less pay..
But "if u want to become a medical microbiologist then u need to be a doctorate" and do a PhD..
with a PhD u can grab higher positions and also job is very lucrative..Even u can work abroad...
so try out giving GRE exam and going abroad for further studies or u can try for IISC-Bangalore,
TIFR-Mumbai or JNU-Delhi..
Very good luck..