Rapid Evolution of Reduced Susceptibility against a Balanced Dual-Targeting Antibiotic through Stepping-Stone Mutations

Antimicrob Agents Chemother. 2019 Aug 23;63(9):e00207-19. doi: 10.1128/AAC.00207-19. Print 2019 Sep.

Abstract

Multitargeting antibiotics, i.e., single compounds capable of inhibiting two or more bacterial targets, are generally considered to be a promising therapeutic strategy against resistance evolution. The rationale for this theory is that multitargeting antibiotics demand the simultaneous acquisition of multiple mutations at their respective target genes to achieve significant resistance. The theory presumes that individual mutations provide little or no benefit to the bacterial host. Here, we propose that such individual stepping-stone mutations can be prevalent in clinical bacterial isolates, as they provide significant resistance to other antimicrobial agents. To test this possibility, we focused on gepotidacin, an antibiotic candidate that selectively inhibits both bacterial DNA gyrase and topoisomerase IV. In a susceptible organism, Klebsiella pneumoniae, a combination of two specific mutations in these target proteins provide an >2,000-fold reduction in susceptibility, while individually, none of these mutations affect resistance significantly. Alarmingly, strains with decreased susceptibility against gepotidacin are found to be as virulent as the wild-type Klebsiella pneumoniae strain in a murine model. Moreover, numerous pathogenic isolates carry mutations which could promote the evolution of clinically significant reduction of susceptibility against gepotidacin in the future. As might be expected, prolonged exposure to ciprofloxacin, a clinically widely employed gyrase inhibitor, coselected for reduced susceptibility against gepotidacin. We conclude that extensive antibiotic usage could select for mutations that serve as stepping-stones toward resistance against antimicrobial compounds still under development. Our research indicates that even balanced multitargeting antibiotics are prone to resistance evolution.

Keywords: antibiotic resistance; genome engineering; gepotidacin.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acenaphthenes / chemistry
  • Acenaphthenes / pharmacology
  • Animals
  • Anti-Bacterial Agents / pharmacology*
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Ciprofloxacin / pharmacology
  • DNA Gyrase / chemistry
  • DNA Gyrase / genetics
  • DNA Gyrase / metabolism
  • Directed Molecular Evolution
  • Drug Resistance, Bacterial / drug effects*
  • Drug Resistance, Bacterial / genetics*
  • Escherichia coli / drug effects
  • Escherichia coli / genetics
  • Fluoroquinolones / pharmacology
  • Genetic Fitness
  • Heterocyclic Compounds, 3-Ring / chemistry
  • Heterocyclic Compounds, 3-Ring / pharmacology
  • Klebsiella Infections / microbiology
  • Klebsiella pneumoniae / drug effects*
  • Klebsiella pneumoniae / genetics
  • Klebsiella pneumoniae / pathogenicity
  • Mice
  • Microbial Sensitivity Tests
  • Molecular Dynamics Simulation
  • Mutation*
  • Virulence / genetics

Substances

  • Acenaphthenes
  • Anti-Bacterial Agents
  • Bacterial Proteins
  • Fluoroquinolones
  • Heterocyclic Compounds, 3-Ring
  • Ciprofloxacin
  • gepotidacin
  • DNA Gyrase