“Is there any way to keep secondary infections at bay for people on the ventilator?”

Foreign bodies in our body increases the risk for secondary infections. We can't completely avoid secondary infections, especially if the foreign body like tracheostomy tube is going to be kept permanently. There are many measures we could take to reduce the rate of infection. Some of the measures are maintaining upright posture while feeding, regular cleaning of breathing tubes, chest physical therapy, optimizing the feeding/fluids rate to avoid fluid overload, regular oral care, avoiding sick contacts, and many more. For further details, recommend you to reach out to your sister's lung doctor, respiratory therapist, or primary doctor.