Abstract

Antibiotic resistant bacteria are on the rise and pose a major health problem with more people dying of multi-drug resistant infections than of AIDS in the US since 2005. One approach to combat this issue is to improve the efficacy of existing antibiotics by finding “co-drugs” that increase the cell’s sensitivity to specific antibiotics. Potential targets for such “co-drugs” would be bacterial proteins that provide intrinsic antibiotic resistance. We have tested the entire KEIO collection of close to 4,000 single gene knockouts in Escherichia coli to identify genes whose loss increases sensitivity to one of twelve different antibiotics (ciprofloxacin, CPR; rifampicin, RIF, vancomycin, VAN, ampicillin, AMP; sulfamethoxazole, SFX, gentamicin, GEN; metronidazole, MET; streptomycin, STR; fusidic acid, FUS; tetracycline, TET; chloramphenicol, CAM; and erythromycin, ERY). We used high through-put screening of one or more subinhibitory concentrations of each antibiotic, and reduced more than 75,000 data points to a set of 160 strains that display significantly increased sensitivity to at least one of the antibiotics. These strains allow one to rapidly define a “sensitivity profile” fingerprint for each additional antibiotic to be tested and characterize these antibiotics with respect to their mechanisms of action. We used this redacted set of strains to define such a profile for nine additional antibiotics (spectinomycin, SPC; cephradine, CEP; aztreonam, AZT; colistin, COL; nitrofurantoin, NIT; neomycin, NEO; enoxacin, ENO; tobramycin, TOB; and cefoxitin, CEF). Comparison of the profiles for the 21 antibiotics reveals several patterns. Although some of the gene knockout mutants are relatively specific to the type of antibiotic tested, others are hypersensitive to more than one antibiotic. Collectively, these data provide targets for the design of “co-drugs” that can potentiate existing antibiotics and increase bacterial killing efficiencies at levels less toxic to humans.