This is very in depth and informative.
Like JuliusSqueezer, I do not like to jump straight to antibiotics. When the time comes to use them I always have a culture done to see what will be most affective. Certain bacteria can have adverse affects when treated with certain antibiotics and start to grow rapidly.
I once had a boa that had 3 gram negative bacteria, when one drug would work on one it would make the other two grow. We ended up going to avian antibiotics and that still didn't work. Aspergillosis was also present. $4,000 later It had to be put down.
When a snake is ill it is definately a good factor to keep the cage clean, husbandry at its best. I keep them on newspaper and change it every day with a good cleaning of nolvasan. Like eyespy said, Bacteria can grow very rapidly in an enclosure even though you can not see it.
A bad year with reptiles is better than a good year without em.