The Interactions Between Fluoropyrimidines and the Gut Microbiome that Lead to Drug Resistance in Bacteria and Can Alter the Drug Efficacy in the Host

Abstract

Bacterial metabolism of host-targeting drugs can impact the success of host treatment. It has been found that host-targeting drugs may not only interact with the host cells but can inhibit growth of bacteria. With repeated exposure, this inadvertent impact on microbes can apply selective pressure leading to genetic adaptation of the host microbiome. This adaptation can, in turn, alter the bacterial metabolism of the drug and lead to a change in drug availability and toxicity in the host. One such set of drugs we explored are the fluoropyrimidines 5-fluorouracil (5-FU) and 5-fluoro-3’-deoxyuridine (FUDR) used to treat tumors. Using E. coli loss-of-function screens, we identified 5-FU resistant strains that decreased drug toxicity on the C. elegans host. Furthermore, the mechanisms of resistance developed after repeated exposure to 5-FU and FUDR converged to a select set of resistance mechanisms involving the nucleotide synthesis and salvage pathway. We also found bacteria evolved in nutrient-poor media reduced the host drug toxicity whereas bacteria evolved in nutrient-rich media did not alter the drug toxicity on the host. Next, we identified similar mechanisms of resistance in Comamonas aquatica. 5-FU evolved C. aquatica but not FUDR evolved C. aquatica decreased drug toxicity in a C. elegans host. Lastly, we explored the selective pressure of 5-FU treatment on the gut microbiome Using a murine model and the E. coli knock-out library, we identified that selection by the gut environment matches previously studied mechanisms in which some E. coli strains preferentially colonize the gut. Then, we found 5-FU treatment enriches for mutants known to provide 5-FU resistance in vitro. Overall, we found that bacteria can become resistant to fluoropyrimidines leading to changes in drug efficacy for the host. Additionally, 5-FU treatment in mice can also select for genotypes in the gut that provide resistance to 5-FU exposure.