Core genome MLST and resistome analysis of Klebsiella pneumoniae using a clinically amenable workflow

Diagn Microbiol Infect Dis. 2020 May;97(1):114996. doi: 10.1016/j.diagmicrobio.2020.114996. Epub 2020 Jan 21.

Abstract

Whole genome sequencing (WGS) is replacing traditional microbiological typing methods for investigation of outbreaks in clinical settings. Here, we used a clinical microbiology laboratory core genome multilocus sequence typing (cgMLST) workflow to analyze 40 isolates of K. pneumoniae which are part of the Antimicrobial Resistance Leadership Group (ARLG) isolate collection, alongside 10 Mayo Clinic K. pneumoniae isolates, comparing results to those of pulsed-field gel electrophoresis (PFGE). Additionally, we used the WGS data to predict phenotypic antimicrobial susceptibility (AST). Thirty-one of 40 ARLG K. pneumoniae isolates belonged to the same PFGE type, all of which, alongside 3 isolates of different PFGE types, formed a large cluster by cgMLST. PFGE and cgMLST were completely concordant for the 10 Mayo Clinic K. pneumoniae isolates. For AST prediction, the overall agreement between phenotypic AST and genotypic prediction was 95.6%.

Keywords: Core genome multilocus sequence typing; Klebsiella pneumoniae; Pulse field gel electrophoresis; Whole genome sequencing.

MeSH terms

  • Anti-Bacterial Agents / pharmacology*
  • Bacterial Typing Techniques
  • Electrophoresis, Gel, Pulsed-Field
  • Genome, Bacterial*
  • Genotype
  • Humans
  • Klebsiella Infections / diagnosis*
  • Klebsiella Infections / microbiology
  • Klebsiella pneumoniae / classification*
  • Klebsiella pneumoniae / drug effects*
  • Klebsiella pneumoniae / enzymology
  • Microbial Sensitivity Tests
  • Multilocus Sequence Typing*
  • Phenotype
  • Whole Genome Sequencing
  • Workflow
  • beta-Lactamases

Substances

  • Anti-Bacterial Agents
  • beta-Lactamases