If one truly believes in transubstantiation, the very basis of our religion... that the bread and wine are truly changed into the Body and Blood of Christ, then you need not worry about getting sick from drinking from the chalice. Furthermore, the Eucharist is suppose to be a re-enactment, so to speak, of the Last Supper at which Christ shared the bread and wine with his disciples, He passed the bread and passed the cup as opposed to "feeding" the disciples the bread....
When I was a child I always felt that if I wasn't feeling well and took Communion, I would hope that I would be cured. As you say, it is the Body and Blood of Jesus.
It is more than a reenactment of the Last Supper. We believe that the Sacrifice is actually happening again. It is much like Passover. At the supper the family says "memory" but memory in Judaism is the event actually occurring again.
It is really difficult to explain.