A recent study revealed cleaning a halter with warm water, soap and a disinfectant does not eliminate the highly contagious strangles bacteria. While the study only looked at the strangles bacteria (Streptococcus equi) it may be that other bacteria are hiding out in the porous fibers.
The only way researchers were able to eliminate the strangles bacteria from the nylon halters was by washing the halters in HOT (140 degree) water.
Interestingly enough, the bacteria on leather halters was no longer present after 6 days, even without cleaning. Cleaning them with soap, water, and a disinfectant eliminated the bacteria immediately.