Plasmid dynamics in Klebsiella pneumoniae during an outbreak of a carbapenemase-producing Klebsiella pneumoniae.. Plasmid dynamics in KPC-producing K. pneumoniae

The increase in Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae is a worldwide threat. The gene encoding the KPC-enzyme (blaKPC) is generally located on large conjugative plasmids. Most studies describing the dynamics of these plasmids during an outbreak setting or during long term colonization only include the KPC-producing Enterobacteriaceae in their analysis. Thereby, potentially missing the loss of the blaKPC containing plasmid itself. In this study, we describe an outbreak of KPC-producing K. pneumoniae in which all K. pneumoniae isolates were collected for each patient colonized with a KPC-producing K. pneumoniae and plasmid dynamics were studied in the collected K. pneumoniae isolates. Moreover, the plasmid dynamics in these isolates were analyzed using short-read whole-genome sequencing only and using a combined short-read and long-read (hybrid) whole-genome sequencing approach. In the isolates of two patients, plasmid loss was detected by both approaches. However, the prediction of what different plasmids were present in each of the isolates did differ between the short-read only and the hybrid approach. Moreover, the hybrid assembly identified a recombination event between two plasmids in the same isolate. These findings demonstrate the plasticity of plasmid distribution in K. pneumoniae during an outbreak and the value of different genomic methods in understanding these genomic changes.