E. coli barcoded genetic screen in the presence of 186 drugs

Numerous host-targeted drugs, not typically prescribed as antibiotics, are potent antimicrobials at physiological concentrations. However, the mechanistic underpinning of this bacterial toxicity remains largely unknown. We systematically investigated the toxicity mechanisms of two hundred antibiotic and non-antibiotic drugs using pooled genetic screens with a barcoded collection of thousands of Escherichia coli knockout strains. We measured two million gene-drug interactions that revealed the genes and pathways underlying drug-specific toxicity. Graph-based analysis of drug-drug similarities revealed that antibiotics cluster into network modules consistent with established antibiotic classes, while non-antibiotics remained largely unconnected. Analysis focusing on non-antibiotics revealed that half of them clustered into modules with shared toxicity mechanisms that can potentially reveal unexploited targets for novel antimicrobials. Conversely, analysis focused on efflux systems showed they widely impact antibiotics and non-antibiotics alike, implying that administration of many non-antibiotics can inadvertently select for antibiotics resistance.