Yes there are. A number of companies have developed anti-bacterial
inner linings and insoles for shoes. One such is Ortholite. While
the Ortholite website remains a tad cagey on the actual science
beyond their product, they do promise a patented formulation which
can fight the following.
You may remain somewhat skeptical of the above claims, but they
do have US approval from the EPA/FDA agencies to back up their claims.
Another option is to wear an anti-bacterial sock; BOVOSOX have
developed a range of hosiery products which feature the Ruco-Bac-AGP
based anti-microbial technology.