You could be dealing with bacteria, mold or both. Antibacterial disinfecting wipes can be used for bacterial issues. get all surfaces good and damp and let air dry. Dipping in a bleach solution would also work but might not be appropriate for all shoes. For fungi/mold, take the insoles out and open the top of the shoes as wide as possible to promote air circulation. Dust both sides of the insoles and the inside of the shoes with fungicidal foot powder like those that they use for athlete's foot. Wipe the outside of the shoes with disinfecting wipes and let them dry completely. After a day or so, wash the shoes and dry them quickly and completely with warm, not hot, airflow. If the insoles are still smelly, replace them. Pulling the insoles out of the shoes after any use where they become damp from the environment or sweat, and dusting with antifungal foot powder will inhibit new growth and keep your shoes from stinking. Antifungal sprays would also work and could help prevent foot infections as well.