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

the Antibacterial Resistance Leadership Group

Research output: Contribution to journalArticle

1 Scopus citations

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%.

Original languageEnglish (US)
Article number114996
JournalDiagnostic Microbiology and Infectious Disease
Volume97
Issue number1
DOIs
StatePublished - May 2020

Keywords

  • Core genome multilocus sequence typing
  • Klebsiella pneumoniae
  • Pulse field gel electrophoresis
  • Whole genome sequencing

ASJC Scopus subject areas

  • Microbiology (medical)
  • Infectious Diseases

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