Nontargeted Metabolomics Reveals the Multilevel Response to Antibiotic Perturbations

Abstract

Microbes have shown a remarkable ability in evading the killing actions of antimicrobial agents, such that treatment of bacterial infections represents once more an urgent global challenge. Understanding the initial bacterial response to antimicrobials may reveal intrinsic tolerance mechanisms to antibiotics and suggest alternative and less conventional therapeutic strategies. Here, we used mass spectrometry-based metabolomics to monitor the immediate metabolic response of Escherichia coli to a variety of antibiotic perturbations. We show that rapid metabolic changes can reflect drug mechanisms of action and reveal the active role of metabolism in mediating the first stress response to antimicrobials. We uncovered a role for ammonium imbalance in aggravating chloramphenicol toxicity and the essential function of deoxythymidine 5'-diphosphate (dTDP)-rhamnose synthesis for the immediate transcriptional upregulation of GyrA in response to quinolone antibiotics. Our results suggest bacterial metabolism as an attractive target to interfere with the early bacterial response to antibiotic treatments and reduce the probability for survival and eventual evolution of antibiotic resistance.

Thinking Outside the Box—Novel Antibacterials To Tackle the Resistance Crisis

“…[119] There are numerous examples in which A(f)BPP revealed the molecular targets of small molecules in eukaryotic and prokaryotic cells. [132] Thea uthors quantified changes in about 750 metabolites upon exposure to the antibiotic and could see concentration-and compoundspecific changes of distinct metabolic pathways.I mportantly, Figure 5. [127] Promysalin is an effective antibacterial compound in P. aeurigonsa;however, its mode of action was poorly understood.…”

“…[129][130][131] Recent advancements have established mass spectrometry as awidely used and very powerful tool for the analysis of cellular metabolic (metabolomics) or protein (proteomics) networks.T his includes the identification of functional pathways that are affected upon treatment with antibacterial compounds.I narecent study by Zampieri et al,anontargeted metabolomics approach was applied to monitor the immediate short-term metabolic response of E. coli to av ariety of antibiotic perturbations. [132] Thea uthors quantified changes in about 750 metabolites upon exposure to the antibiotic and could see concentration-and compoundspecific changes of distinct metabolic pathways.I mportantly, this profiling approach cannot only be used to predict the MoA of new compounds,i ta lso aids the identification of novel druggable targets,a sr ecently shown in M. tuberculosis. [133] Thermal proteome profiling allows an unbiased search of protein targets in live cells using parent drugs without the need for modification.…”

Antibiotic efficacy — context matters

“…Targeted metabolomic studies have revealed significant changes in intracellular energy metabolites following antibiotic treatment [29-31], corroborated by live-cell imaging experiments directly measuring transient changes in ATP [32]. Experiments using the Seahorse XF Analyzer have captured real-time increases to cellular respiration by bactericidal antibiotics [33-35], complementing real-time measurements of overflow ROS production using electrochemical [36] or genetically encoded biosensors [33].…”

Acidification of Cytoplasmic pH inEscherichia coliProvides a Strategy to Cope with Stress and Facilitates Development of Antibiotic Resistance

“…Bacteria can acquire resistance to antibiotics by horizontal gene transfer, activation of regulatory loci and genetic mutations that modify the drug target, increase drug efflux, and activate the expression of drug inactivating enzymes (5)(6)(7)(8). High-level, clinically relevant resistant strains usually result from the accumulation of several mutations that, at times, involve changes in their metabolic status, thus altering diverse biochemical reactions (9)(10)(11).…”