Using Genetic Distance from Archived Samples for the Prediction of Antibiotic Resistance in Escherichia coli

Antimicrob Agents Chemother. 2020 Apr 21;64(5):e02417-19. doi: 10.1128/AAC.02417-19. Print 2020 Apr 21.


The rising rates of antibiotic resistance increasingly compromise empirical treatment. Knowing the antibiotic susceptibility of a pathogen's close genetic relative(s) may improve empirical antibiotic selection. Using genomic and phenotypic data for Escherichia coli isolates from three separate clinically derived databases, we evaluated multiple genomic methods and statistical models for predicting antibiotic susceptibility, focusing on potentially rapidly available information, such as lineage or genetic distance from archived isolates. We applied these methods to derive and validate the prediction of antibiotic susceptibility to common antibiotics. We evaluated 968 separate episodes of suspected and confirmed infection with Escherichia coli from three geographically and temporally separated databases in Ontario, Canada, from 2010 to 2018. Across all approaches, model performance (area under the curve [AUC]) ranges for predicting antibiotic susceptibility were the greatest for ciprofloxacin (AUC, 0.76 to 0.97) and the lowest for trimethoprim-sulfamethoxazole (AUC, 0.51 to 0.80). When a model predicted that an isolate was susceptible, the resulting (posttest) probabilities of susceptibility were sufficient to warrant empirical therapy for most antibiotics (mean, 92%). An approach combining multiple models could permit the use of narrower-spectrum oral agents in 2 out of every 3 patients while maintaining high treatment adequacy (∼90%). Methods based on genetic relatedness to archived samples of E. coli could be used to predict antibiotic resistance and improve antibiotic selection.

Keywords: Gram-negative bacteria; antibiotic-resistant organisms; antibiotics; empirical antibiotics; genomics; rapid diagnostics.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Bacterial Agents / pharmacology
  • Anti-Bacterial Agents / therapeutic use
  • Area Under Curve
  • Databases, Genetic
  • Drug Resistance, Bacterial / genetics*
  • Escherichia coli / drug effects*
  • Escherichia coli / genetics*
  • Escherichia coli Infections / drug therapy
  • Escherichia coli Infections / microbiology
  • Genome, Bacterial / genetics
  • Genomics
  • Humans
  • Microbial Sensitivity Tests
  • Models, Biological
  • Ontario
  • Predictive Value of Tests
  • Retrospective Studies
  • Trimethoprim, Sulfamethoxazole Drug Combination / pharmacology


  • Anti-Bacterial Agents
  • Trimethoprim, Sulfamethoxazole Drug Combination