Prediction of antibiotic resistance by gene expression profiles

Nat Commun. 2014 Dec 17;5:5792. doi: 10.1038/ncomms6792.


Although many mutations contributing to antibiotic resistance have been identified, the relationship between the mutations and the related phenotypic changes responsible for the resistance has yet to be fully elucidated. To better characterize phenotype-genotype mapping for drug resistance, here we analyse phenotypic and genotypic changes of antibiotic-resistant Escherichia coli strains obtained by laboratory evolution. We demonstrate that the resistances can be quantitatively predicted by the expression changes of a small number of genes. Several candidate mutations contributing to the resistances are identified, while phenotype-genotype mapping is suggested to be complex and includes various mutations that cause similar phenotypic changes. The integration of transcriptome and genome data enables us to extract essential phenotypic changes for drug resistances.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Bacterial Agents / classification
  • Anti-Bacterial Agents / pharmacology*
  • Drug Resistance, Multiple, Bacterial / genetics*
  • Escherichia coli / drug effects*
  • Escherichia coli / genetics
  • Escherichia coli / growth & development
  • Escherichia coli / metabolism
  • Gene Expression Profiling
  • Gene Expression Regulation, Bacterial*
  • Genes, Bacterial*
  • Genotype
  • Microbial Sensitivity Tests
  • Models, Statistical*
  • Mutation
  • Phenotype
  • Transcriptome


  • Anti-Bacterial Agents

Associated data

  • GEO/GSE59408
  • SRA/PRJDB2980