Whole-Genome Sequence Analysis of Carbapenem-Heteroresistant Klebsiella pneumoniae and Escherichia coli Isolates

Curr Microbiol. 2022 Nov 3;79(12):384. doi: 10.1007/s00284-022-03087-x.


Carbapenem-heteroresistant isolates can be misclassified as susceptible by in vitro susceptibility tests, leading to treatment failure. The underlying mechanisms of heteroresistance, where the bacterial isolate harbors both resistant and susceptible subpopulations, are poorly understood. The aim of the current study was to clarify molecular mechanisms responsible for carbapenem heteroresistance. Whole-genome shotgun sequencing was performed for both resistant and susceptible subpopulations of three Klebsiella pneumoniae and one Escherichia coli blood isolates, which were identified as carbapenem-heteroresistant by the population analysis profile method. The software from the Center for Genomic Epidemiology was used to identify genomic similarities, antibiotic resistance genes, Multilocus Sequence Typing (MLST), and core-genome MLST(cgMLST). Both susceptible and resistant subpopulations of the E. coli strain had the same MLST profiles. MLST1/2 and cgMLST for E. coli were 46/736 and 119473, respectively. The susceptible and resistant subpopulations of each K. pneumoniae strain exhibited identical MLST profiles. The genetic background for antimicrobial resistance in three K. pneumoniae strains was almost similar between the colonies inside and outside the inhibition zone of each strain, however, there were remarkable differences between the three strains. The blaKPC-2 and blaOXA-48 genes were responsible for carbapenem resistance for E. coli and K. pneumoniae strains, respectively. This is the first study, which has demonstrated similar genotypic and resistant gene profiles in the resistant and susceptible subpopulations of each strain. Additional metabolic and transcriptomic investigations are needed to understand the mechanisms responsible for carbapenem heteroresistance.

MeSH terms

  • Anti-Bacterial Agents / pharmacology
  • Anti-Bacterial Agents / therapeutic use
  • Bacterial Proteins / genetics
  • Carbapenems / pharmacology
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Escherichia coli Infections* / drug therapy
  • Humans
  • Klebsiella Infections* / microbiology
  • Klebsiella pneumoniae / metabolism
  • Microbial Sensitivity Tests
  • Multilocus Sequence Typing
  • beta-Lactamases / genetics
  • beta-Lactamases / metabolism


  • Carbapenems
  • beta-Lactamases
  • Anti-Bacterial Agents
  • Bacterial Proteins