Since you posted in the STDs forum, I assume you are concerned primarily about STDs. You can't get an STD by licking a shoe or by putting it in your mouth. STDs are passed by sexual/bodily contact, person-to-person.
If you seek to minimize your risk for other bacterial infections, use a new, unworn shoe, and swab it with alcohol. Then, let the alcohol evaporate before putting the shoe in your mouth. There is no guaranteed way to avoid bacterial infections, but you can minimize your risk. Mouthwash won't do the trick, because you will inevitably swallow some bacteria.
If anyone knew of something that guaranteed avoidance of disease we wouldn't have disease anymore. Don't know what you're using as an antiseptic, but do know that using too much of anything in or on your body that kills anything is toxic to beneficial organisms that live with us and protect us from disease. Ever seen people putting bactericides on them all the time? Not actually good for you -- too much will harm your immune system more than it is able to kill bacteria. Just like taking too many antibiotics. The only real protection is a strong immune system and avoiding things that are higher than needed risk, but total avoidance? Doesn't exist.