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

Abstract Whole genome sequencing 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 whole genome sequencing (WGS) data to predict phenotypic antimicrobial susceptibility (AST). 31/40 ARLG K. pneumoniae isolates belonged to the same PFGE type, all of which, alongside three 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%.