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

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Abstract

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.

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Funding

This study was partially supported by Ankara Yıldırım Beyazıt University’s Research Foundation.

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Authors and Affiliations

  1. Department of Clinical Microbiology, Medical Faculty, Hacettepe University, Altındağ, 06230, Ankara, Turkey

    Banu Sancak

  2. Ankara Yıldırım Beyazıt University Central Research Laboratory, Ankara, Turkey

    Oguz Arı

  3. Department of Clinical Microbiology, Medical Faculty, Ankara Yıldırım Beyazıt University, Ankara, Turkey

    Rıza Durmaz

Authors
  1. Banu Sancak
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  2. Oguz Arı
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  3. Rıza Durmaz
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Contributions

BS collected and identified clinical isolates, performed susceptibility testing and PAP analyses, and drafted the manuscript. RD participated in the design of the molecular study and the analysis of the sequencing data, and drafted the manuscript. OA performed the molecular methods, participated in the sequence analysis, and drafted the manuscript.

Corresponding author

Correspondence to Banu Sancak.

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Conflict of interest

The authors declare that they have no conflict of interest.

Ethical Approval

The study was approved by the institutional ethical committee of Hacettepe University (GO 19/317, 16969557–448, February 28, 2019, 2019/06).

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Sancak, B., Arı, O. & Durmaz, R. Whole-Genome Sequence Analysis of Carbapenem-Heteroresistant Klebsiella pneumoniae and Escherichia coli Isolates. Curr Microbiol 79, 384 (2022). https://doi.org/10.1007/s00284-022-03087-x

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  • DOI: https://doi.org/10.1007/s00284-022-03087-x

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