First report of Klebsiella quasipneumoniae harboring blaKPC-2 in Saudi Arabia

Antimicrob Resist Infect Control. 2019 Dec 19:8:203. doi: 10.1186/s13756-019-0653-9. eCollection 2019.

Abstract

Background: Nosocomial infections caused by multi-drug resistant Enterobacteriaceae are a global public health threat that ought to be promptly identified, reported, and addressed accurately. Many carbapenem-resistant Enterobacteriaceae-associated genes have been identified in Saudi Arabia but not the endemic Klebsiella pneumoniae carbapenemases (KPCs), which are encoded by blaKPC-type genes. KPCs are known for their exceptional spreading potential.

Methods: We collected n = 286 multi-drug resistant (MDR) Klebsiella spp. isolates as part of screening for resistant patterns from a tertiary hospital in Saudi Arabia between 2014 and 2018. Antimicrobial susceptibility testing was carried out using both VITEK II and the broth microdilution of all collected isolates. Detection of resistance-conferring genes was carried out using Illumina whole-genome shotgun sequencing and PacBio SMRT sequencing protocols.

Results: A Carbapenem-resistant Enterobacteriaceae (CRE) Klebsiella quasipneumoniae subsp. similipneumoniae strain was identified as a novel ST-3510 carrying a blaKPC-2 carbapenemase encoding gene. The isolate, designated as NGKPC-421, was obtained from shotgun Whole Genome Sequencing (WGS) surveillance of 286 MDR Klebsiella spp. clinical isolates. The NGKPC-421 isolate was collected from a septic patient in late 2017 and was initially misidentified as K. pneumoniae. The sequencing and assembly of the NGKPC-421 genome resulted in the identification of a putative ~ 39.4 kb IncX6 plasmid harboring a blaKPC-2 gene, flanked by transposable elements (ISKpn6-blaKPC-2-ISKpn27).

Conclusion: This is the first identification of a KPC-2-producing CRE in the Gulf region. The impact on this finding is of major concern to the public health in Saudi Arabia, considering that it is the religious epicenter with a continuous mass influx of pilgrims from across the world. Our study strongly highlights the importance of implementing rapid sequencing-based technologies in clinical microbiology for precise taxonomic classification and monitoring of antimicrobial resistance patterns.

Keywords: Carbapenemases; KPC-2; Klebsiella quasipneumoniae; MDR; Tn3; blaKPC-2.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aged
  • Anti-Bacterial Agents / pharmacology
  • Drug Resistance, Multiple, Bacterial*
  • Humans
  • Klebsiella / drug effects
  • Klebsiella / genetics*
  • Klebsiella / isolation & purification*
  • Klebsiella Infections / microbiology*
  • Male
  • Microbial Sensitivity Tests
  • Phylogeny
  • Plasmids / genetics
  • Public Health
  • Saudi Arabia
  • Tertiary Care Centers
  • Whole Genome Sequencing
  • beta-Lactamases / genetics*

Substances

  • Anti-Bacterial Agents
  • beta-Lactamases
  • beta-lactamase KPC-2, Klebsiella pneumoniae

Supplementary concepts

  • Klebsiella quasipneumoniae