As I see it, you have a few options available to you and forgive me if you already know some of this;
1) ET tube: There have been studies showing that ET tubes coated/treated with silver reduce VAP rates.
2) Ventilator tubing: The newer F&P Evaqua tubing may help in that there is less build up of rain out in both the inspiratory and expiratory limbs.
3) Nebuliser:
a. Selection of nebulisers that sit ABOVE the circuit, e.g. vibrating mesh nebulisers mitigate the risk of bacteria-laden rain out spilling down into the nebuliser (e.g. Jet-type) and the subsequently being aerosolised in a highly respirable aerosol.
b. Placement of the nebuliser on the dry side of the humidifier. This mitigates the risk of any bacteria-laden rain out getting anywhere near the nebuliser.
Good suggestions from Ronan. This is unpublished data but I found that when a nebulizer was placed close to the "wye" connection point in a ventilator circuit, cultures showed moderate to heavy organism growth within 48 hours. When the nebulizer was placed on the dry side of the humidifier, no growth was found on any of the daily cultures for a period of four days. Placing the nebulizer in this position may also increase the amount of aerosol delivered (see the work from J Fink & A Ari in Respiratory Care Journal). Other suggestions to mitigate pathogen delivery to ventilated patients would include 1) only change the ventilator circuit when visibly soiled 2) avoid disconnecting the patient from the circuit 3) follow good hand hygiene practices 4) consider the use of heat moisture exchangers (I have experience with the Evaqua circuit that Ronan mentions and think it is a very good product) 5) minimize the duration of invasive mechanical ventilation.
The suggestions above are excellent. Here is a peds reference (which has the same recommendations) from the Solutions for Patient Safety Group that has the references included (that you can site in your paper). Hope it helps!