DOI: https://doi.org/10.22263/2312-4156.2021.5.34
Petrovskaya T.A.1, Karpova E.V.1, Tapalski D.V.1, Mozharovskaya L.V.2, Baranov O.Y.2
Molecular-genetic mechanisms of resistance of nosocomial Klebsiella pneumoniae strains to polymyxins and antibiotics of other groups according to whole genome sequencing data
1Gomel State Medical University, Gomel, Republic of Belarus
2Forest Institute of the National Academy of Sciences of Belarus, Gomel, Republic of Belarus
Vestnik VGMU. 2021;20(5):34-41.
Abstract.
Identification of numerous mechanisms of resistance to colistin and other antibiotics is possible using whole genome sequencing.
Objectives. To assess the molecular-genetic mechanisms of resistance to polymyxins and antibiotics of other groups in nosocomial Klebsiella pneumoniae strains.
Material and methods. For 13 multidrug- and extensively drug-resistant K. pneumoniae strains semiconductor sequencing was performed in the Ion PGM System genomic sequencer (Thermo Fisher Scientific, USA). The assembly of genomic sequences and their annotation were carried out. The PROVEAN software tool was used to predict the influence of nucleotide replacements on the structure of amino acid sequences and functional activity of proteins. The identification of antibiotic resistance genes and the search for efflux mechanisms were performed by the ResFinder v.4.1 and CARD web resources.
Results. Several types of β-lactamase genes were detected simultaneously in all strains, as well as genes of resistance to fosfomycin. Genes of resistance to aminoglycosides were identified in 11 strains, to chloramphenicol – in 10, to rifampicin – in 5, to macrolides – in 4. The mcr phosphoethanolamine transferase genes were absent in all strains. Functionally significant substitutions were revealed in the pmrB gene (D150Y, T157P, G207S) comparing the studied samples with the reference K. pneumoniae strain ATCC 700603. Changes in the mgrB gene were also found in colistin-resistant strains (W20R replacement, insertional inactivation of the gene by transposons of the IS1, IS4 and IS5 families).
Conclusions. The results of whole genome sequencing represent the significant resistance of nosocomial Klebsiella pneumoniae strains to the majority of antibiotics including β-lactams, aminoglycosides, fluoroquinolones, fosfomycin, chloramphenicol, polymyxins. Genetic determinants of colistin resistance were revealed (insertional inactivation and deletion of the mgrB gene; D150Y, T157P and G207S substitutions in the pmrB gene) in strains with colistin MIC 64-128 mg/l and their absence in colistin-susceptible strains.
Key words: Klebsiella pneumoniae, colistin, antibiotic resistance, whole genome sequencing.
Funding sources. This study was performed as a part of the task «Study of biological and molecular genetic mechanisms of the formation of resistance to polymyxins in extensively drug-resistant gram-negative bacteria and the rationale for combined antibiotic therapy of infections caused by them» SPSI «Basic and applied sciences – medicine», 2016-2020.
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Information about authors:
Petrovskaya T.A. – senior lecturer of the Chair of Microbiology, Virology and Immunology, Gomel State Medical University,
ORCID: https://orcid.org/0000-0001-6580-3603
Karpova E.V. – lecturer of the Chair of Microbiology, Virology and Immunology, Gomel State Medical University,
ORCID: https://orcid.org/0000-0002-3952-6187
Tapalski D.V. – Doctor of Medical Sciences, associate professor, head of the Chair of Microbiology, Virology and Immunology, Gomel State Medical University,
ORCID: https://orcid.org/0000-0002-9484-7848
Mozharovskaya L.V. – researcher of the Laboratory of Genomic Research and Bioinformatics, Forest Institute of the National Academy of Sciences of Belarus,
ORCID: https://orcid.org/0000-0001-9106-1877
Baranov O.Y. – Doctor of Biological Sciences, associate professor, head of the Laboratory of Genomic Research and Bioinformatics, Forest Institute of the National Academy of Sciences of Belarus,
ORCID: https://orcid.org/0000-0002-0665-0093
Correspondence address: Republic of Belarus, 246050, Gomel, 5 Lange str., Gomel State Medical University, Chair of Microbiology, Virology and Immunology. E-mail: Этот адрес электронной почты защищён от спам-ботов. У вас должен быть включен JavaScript для просмотра. – Dmitry V. Tapalski.
