A Strategic Target Rescues Trimethoprim Sensitivity in <i>Escherichia coli</i>

Abstract

Trimethoprim, a preferred choice for treating urinary tract infections, is becoming obsolete due to the rapid dissemination of resistant E. coli. Although, direct resistance mechanisms such as mutation and overexpression of the target are well characterized, associated alterations that drive or sustain resistance are unknown. We identify the repertoire of resistance associated perturbations by constructing and interrogating a transcriptome integrated functional interactome. The perturbations in stress response and metabolic pathways are seen to form a connected network, from which we identify the critical dependence on serine hydroxymethyltransferase (GlyA) as an emergent vulnerability. Through its deletion, we demonstrate that GlyA is necessary to sustain high levels of resistance in both laboratory-evolved resistant E. coli and a multidrug-resistant clinical isolate of uropathogenic E. coli. Through comparative evolution, we observe that the absence of GlyA activity decelerates the acquisition of resistance in E. coli. Put together, our results identify GlyA as a promising target for tackling trimethoprim resistance, providing a basis for the rational design of drug combinations.