It's very important to run a clean reptile room, and I'll provide some insight to things I've learned over the years that have helped me and I believe may help you, too.
1. Gloves and Hand Washing
While gloves are not a cure all for preventing the spread of disease, they do help tip the odds in your favor. Gloves are relatively inexpensive, disposable, and you can store a lot of them without taking up too much space. Make sure there is a trash receptacle in the room where they are used for disposal and that it is emptied often. The proper technique of removing gloves must also be used for them to be effective. First, ensure you open the glove box using the perforated area and carefully pull out the gloves so as not to contaminate the entire box. Secondly, when removing the gloves, you will have to remove the second glove with your ungloved hand. Be sure to place your bare fingers inside the second glove when peeling it off so that your bare fingers never touch the outside of the glove. This is for general glove use, other protocols are needed for "sterile glove technique" but honestly if you have something known to be contagious you should have a vet advising you in any event. You should also be aware that amphibians are sensitive to some gloves, especially larval amphibians. Even with gloves you still need to regularly wash your hands, and I do so between species. Be sure you are washing your hands properly with soap for at least 20 seconds.
Here are some inexpensive gloves (note: get the 1000 pack even if you do not need a lot, they are much cheaper this way)
2. Change Water Bowls Often
One of the biggest pitfalls one can run into is failure to keep fresh and clean water at all times. Sadly, even experienced keepers have had a water bowl run dry unexpectedly. For most species, it is recommended to have water available at all times and it is very important that the water be clean. I do use a few ceramic water dishes which I regularly wash and put in the oven at 200ishF for 20 minutes to help reduce germs. What I really like using are disposable plastic deli cups. The 8 ounce for small snakes that cannot tip them over and later the 16 ounce cups. With medium sized snakes, you'll need to get a 4" PVC coupler or cut PVC pipe to size to keep the cups from tipping over. Occasionally, you'll have a problem snake that will also push those around and you may find you need to take further measures to hold it in place. I have found the best deals on webstaurantstore.com but the best deal changes frequently so check the site carefully. They usually come in cases of 500.
3. Remove wastes
Although this one is obvious, it is very important. Leaving food and poop in your cages will invite flies which can help spread disease, foul smells, allow parasites to complete their life cycles, and allow ammonia levels to rise inside the enclosure. None of these things are healthy for your reptile collection. The most important thing is to change the substrate and wash away any wastes with soap and water (this is for reptiles -- special considerations and other protocols are needed for amphibians). The decision as to whether or not to use a disinfectant is of lesser importance to the primary concern which is removing all wastes. Disinfectants will be needed when you've had disease or parasites involved and many of these things require specific types of disinfectants so a general comment is difficult to make. There is no disinfectant that is effective across all manner of disease causing organisms regardless of whatever the marketing materials may wish you to believe. I will make a more detailed post about this in the future. A shop vac may prove useful for sucking up bits of substrate. I use inexpensive ones from HomeDepot that sit on top of a bucket.
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