Molecular evolution of Klebsiella pneumoniae ST278 harboring blaNDM-7 involved in nosocomial transmission

Abstract

During 2013, ST278 Klebsiella pneumoniae with blaNDM-7 was isolated from the urine (KpN01) and rectum (KpN02) of a patient in Calgary, Canada. The same strain (KpN04) was subsequently isolated from another patient in the same unit. Interestingly, a carbapenem-susceptible ST278 (KpN06) was obtained one month later from the blood of the second patient. Next generation sequencing (NGS) revealed that the loss of carbapenem-resistance in KpN06 was due to a 5-kb deletion on the blaNDM-7-harboring IncX3 plasmid. In addition, an IncFIB plasmid in KpN06 had a 27 kb deletion that removed genes encoding for heavy metal resistance. Phylogenetic analysis showed that the ST278 K. pneumoniae from patient 2 were likely descendants of KpN02 and that KpN06 was a close progenitor of an environmental ST278. It is unclear whether KpN06 lost the blaNDM-7 gene in vivo. This study detailed the remarkable plasticity and speed of evolutionary changes in multidrug resistance K. pneumoniae demonstrating the highly recombinant nature of this species. It also highlights the ability of NGS to clarify molecular micro-evolutionary events within antibiotic-resistant organisms.