Genome-scale metabolic modelling of trimethoprim's mode of action reveals free ATP salvaged to restore purine pool

Trimethoprim is a clinically important antibiotic for treating urinary tract infections yet its mechanism of killing remains elusive due to a cascade of effected metabolic reactions. Metabolites available in growth media can selectively counteract trimethoprim which affects the interpretation of results. We sought to understand the full scope of trimethoprim's impact on Escherichia coli metabolism and how metabolite availability affects trimethoprim outcomes. We applied flux balance analysis on a genome-scale metabolic model of E. coli to simulate trimethoprim activity under bacteriostatic and bactericidal conditions. Our results suggested that in the absence of environmental purines or nucleosides, trimethoprim induces salvage of ATP to repair DNA. We experimentally validated the result with ATP bioluminescence screening of 96 clinical E. coli isolates. Therefore, the choice of growth media composition significantly changes the outcome of trimethoprim challenge and should be taken into consideration when interpreting trimethoprim's activity.