Pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS) were evaluated as tools to aid in the investigation of a putative carbapenem-resistant Klebsiella pneumoniae (CRKP) transmission between 2 patients.

PFGE revealed a 1-band difference between the isolates recovered from the 2 patients, suggesting high degree of relatedness.

WGS revealed 22–24 single nucleotide variants between the CRKP from the 2 patients, which is more than the expected annual mutation rate in K. pneumoniae.

WGS also identified differences in plasmid content, which were related to phenotypic antimicrobial resistance.

Consensus guidelines for the performance and interpretation of WGS are required for this technology to aid in epidemiologic investigations.