Barbara,
There have actually been studies done by one of the top manufacturer's of CPAP equipment, and they found that bacteria are actually too large to be born along the airflow into your lungs. There used to be myths flying around that said you could get a nasty respiratory infection from unclean humidifier tanks/water, but we now know this isn't true. CPAP airflow can include dust, pollen, or smoke that irritates the lungs (just change filters regularly to avoid this!), but respiratory infections will not be caused this way (or exacerbated). Keep using the machine! =)