Genome-Wide Identification of Antimicrobial Intrinsic Resistance Determinants in Staphylococcus aureus

Abstract

The emergence of antimicrobial resistance severely threatens our ability to treat bacterial infections. While acquired resistance has received considerable attention, relatively little is known of intrinsic resistance that allows bacteria to naturally withstand antimicrobials. Gene products that confer intrinsic resistance to antimicrobial agents may be explored for alternative antimicrobial therapies, by potentiating the efficacy of existing antimicrobials. In this study, we identified the intrinsic resistome to a broad spectrum of antimicrobials in the human pathogen, Staphylococcus aureus. We screened the Nebraska Transposon Mutant Library of 1920 single-gene inactivations in S. aureus strain JE2, for increased susceptibility to the anti-staphylococcal antimicrobials (ciprofloxacin, oxacillin, linezolid, fosfomycin, daptomycin, mupirocin, vancomycin, and gentamicin). Sixty-eight mutants were confirmed by E-test to display at least twofold increased susceptibility to one or more antimicrobial agents. The majority of the identified genes have not previously been associated with antimicrobial susceptibility in S. aureus. For example, inactivation of genes encoding for subunits of the ATP synthase, atpA, atpB, atpG and atpH, reduced the minimum inhibitory concentration (MIC) of gentamicin 16-fold. To elucidate the potential of the screen, we examined treatment efficacy in the Galleria mellonella infection model. Gentamicin efficacy was significantly improved, when treating larvae infected with the atpA mutant compared to wild type cells with gentamicin at a clinically relevant concentration. Our results demonstrate that many gene products contribute to the intrinsic antimicrobial resistance of S. aureus. Knowledge of these intrinsic resistance determinants provides alternative targets for compounds that may potentiate the efficacy of existing antimicrobial agents against this important pathogen.

Mutational Evolution of Pseudomonas aeruginosa Resistance to Ribosome-Targeting Antibiotics

“…The present work provides information on the evolutionary trajectories leading to resistance to antibiotics belonging to different structural families but targeting the ribosome in P. aeruginosa. The results suggest that, although mutations in several genes may contribute to the development of antibiotic resistance ( Fajardo et al, 2008 ; Tamae et al, 2008 ; Alvarez-Ortega et al, 2011 ; Martinez, 2012 ; Vestergaard et al, 2016 ; Lopez-Causape et al, 2018a ), which may imply a large degree of stochasticity in the evolutionary trajectories, mutation-driven evolution toward resistance is partially deterministic, at least when bacteria grow in the same conditions. This opens up the possibility of predicting the appearance of antibiotic resistance ( Martinez et al, 2007 ).…”

Studies on Aminoglycoside Susceptibility Identify a Novel Function of KsgA To Secure Translational Fidelity during Antibiotic Stress

“…Efforts to combat antibiotic resistance may involve investigating the killing mechanism of current antibiotics and identifying new targets for the development of novel antibiotics or potentiators of existing drugs (3). High-throughput screening at the genome level for genetic determinants of bacterial survival upon antibiotic killing is an effective way for target identification in both Gram-negative and -positive bacteria (4)(5)(6)(7).…”

Analysis of the Pseudomonas aeruginosa Aminoglycoside Differential Resistomes Allows Defining Genes Simultaneously Involved in Intrinsic Antibiotic Resistance and Virulence

“…The shared intrinsic resistome to aminoglycosides of P. aeruginosa. Several publications on the intrinsic resistome of bacterial pathogens analyzed only one antibiotic belonging to each structural family in the understanding that the data obtained with one antibiotic might be extrapolated to other members in the family (14,(17)(18)(19). To decipher whether or not this was indeed the situation in our case, we included in the analysis genes whose inactivation has been previously reported to modify P. aeruginosa susceptibility to aminoglycosides (16,18).…”

“…tibility to antibiotics of this pathogen (13)(14)(15)(16)(17)(18). However, these studies are frequently performed using only one antibiotic for each studied group, under the assumption that the results can be extrapolated to other members of the same structural family of antimicrobials (14,(17)(18)(19). In the current article, we challenge this hypothesis by analyzing the susceptibility of a large set of P. aeruginosa mutants to four aminoglycosides, namely, tobramycin, amikacin, streptomycin, and kanamycin, by using data obtained from in-house screening and previously published data (16,18).…”