Multidrug-resistant Klebsiella pneumoniae harboring extended spectrum β-lactamase encoding genes isolated from human septicemias

PLoS One. 2021 May 4;16(5):e0250525. doi: 10.1371/journal.pone.0250525. eCollection 2021.

Abstract

Klebsiella pneumoniae is a major pathogen implicated in nosocomial infections. Extended-spectrum β-lactamase (ESBL)-producing K. pneumoniae isolates are a public health concern. We aim to characterize the type of β-lactamases and the associated resistance mechanisms in ESBL-producing K. pneumoniae isolates obtained from blood cultures in a Portuguese hospital, as well as to determine the circulating clones. Twenty-two cefotaxime/ceftazidime-resistant (CTX/CAZR) K. pneumoniae isolates were included in the study. Identification was performed by MALDI-TOF MS and the antimicrobial susceptibility testing by disk-diffusion. The screening test for ESBL-production was performed and ESBL-producer isolates were further characterized. The presence of different beta-lactamase genes (blaCTX-M, blaSHV, blaTEM, blaKPC, blaNDM, blaVIM, blaOXA-48, blaCMY-2, blaDHA-1, blaFOX, blaMOX, and blaACC) was analyzed by PCR/sequencing in ESBL-producer isolates, as well as the presence of other resistance genes (aac(6')-Ib-cr, tetA/B, dfrA, qnrA/B/S, sul1/2/3) or integron-related genes (int1/2/3). Multilocus-sequence-typing (MLST) was performed for selected isolates. ESBL activity was detected in 12 of the 22 CTX/CAZR K. pneumoniae isolates and 11 of them carried the blaCTX-M-15 gene (together with blaTEM), and the remaining isolate carried the blaSHV-106 gene. All the blaCTX-M-15 harboring isolates also contained a blaSHV gene (blaSHV-1, blaSHV-11 or blaSHV-27 variants). Both blaSHV-27 and blaSHV-106 genes correspond to ESBL-variants. Two of the CTX-M-15 producing isolates carried a carbapenemase gene (blaKPC2/3 and blaOXA-48) and showed imipenem resistance. The majority of the ESBL-producing isolates carried the int1 gene, as well as sulphonamide-resistance genes (sul2 and/or sul3); the tetA gene was detected in all eight tetracycline-resistant isolates. Three different genetic lineages were found in selected isolates: ST348 (one CTX-M-15/TEM/SHV-27/KPC-2/3-producer isolate), ST11 (two CTX-M-15/TEM/SHV-1- and CTX-M-15-TEM-SHV-11-OXA-48-producer isolates) and ST15 (one SHV-106/TEM-producer isolate). ESBL enzymes of CTX-M-15 or SHV-type are detected among blood K. pneumoniae isolates, in some cases in association with carbapenemases of KPC or OXA-48 type.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Bacterial Agents / therapeutic use
  • Cefotaxime / therapeutic use*
  • Ceftazidime / therapeutic use*
  • Cross Infection / drug therapy
  • Cross Infection / genetics
  • Cross Infection / microbiology
  • Cross Infection / pathology
  • Drug Resistance, Multiple, Bacterial*
  • Humans
  • Klebsiella Infections / drug therapy
  • Klebsiella Infections / genetics
  • Klebsiella Infections / microbiology
  • Klebsiella Infections / pathology*
  • Klebsiella pneumoniae / drug effects
  • Klebsiella pneumoniae / genetics*
  • Klebsiella pneumoniae / isolation & purification
  • Microbial Sensitivity Tests
  • Multilocus Sequence Typing / methods
  • Sepsis / drug therapy
  • Sepsis / genetics
  • Sepsis / microbiology
  • Sepsis / pathology*
  • Sequence Analysis, DNA / methods
  • beta-Lactamases / genetics*

Substances

  • Anti-Bacterial Agents
  • Ceftazidime
  • beta-Lactamases
  • Cefotaxime

Grants and funding

I.C. gratefully acknowledges the financial support of “Fundação para a Ciência e Tecnologia” (FCT – Portugal) from European Union (EU) through PhD grant SFRH/BD/133266/2017 (Medicina Clínica e Ciências da Saúde), as well as MCTES (Ministério da Ciência, Tecnologia e Ensino Superior) and Fundo Social Europeu (FSE). The experimental work performed in the University of La Rioja was financed by the project SAF2016-76571-R from the Agencia Estatal de Investigation (AEI) of Spain and FEDER of EU. N.S.C. was awarded a grant for the year 2018, from the Algerian Ministry of Higher Education and Scientific Research (The PNE Program), under the direction of Prof. Carmen Torres. V.S. acknowledges the financial support of “Fundação para a Ciência e Tecnologia” (FCT – Portugal) through PhD grant SFRH/BD/137947/2018 (Medicina Clínica e Ciências da Saúde). This work was supported by the Associate Laboratory for Green Chemistry - LAQV which is financed by national funds from FCT/MCTES (UIDB/50006/2020 and UIDP/50006/2020).