There would be three things:
1/ Identification of the pathogen
2/ Finding a remedy that is sensistive to a therapy which means what substance has the highest probability of killing the organisms
3/ Addressing the resistant factor of the efflux pump. Goldenseal Leaf (not root) has many constituents that can disable the efflux pump. Using this in combination with a substance that is known to kill the organism is key.
Look at a product that is Lyme Nosode C128, there appears to be some success with this. Deseret Biologicals has a number of products geared towards Lyme and co-infections.