Investigation of a suspected nosocomial transmission of blaKPC3-mediated carbapenem-resistant Klebsiella pneumoniae by whole genome sequencing

• 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.

Whole genome sequencing (WGS) was compared to pulse-field gel electrophoresis (PFGE) of XbaI-digested genomic DNA, as methods by which to evaluate a potential transmission of carbapenem-resistant Klebsiella pneumoniae between 2 hospital inpatients. PFGE result demonstrated only 1-band difference between the isolates, suggesting probable relatedness. In contrast, while WGS data demonstrated the same sequence type and very similar chromosomal sequences, over 20 single nucleotide variants were identified between the isolates, bringing into question whether there was a transmission event. WGS also identified an additional plasmid, with an XbaI restriction site in the isolates of the second patient that was not identified by PFGE. While WGS provided additional information that was not available by PFGE, in this study, neither method could definitively conclude the relatedness between the isolates.