Molecular Evolution of a Klebsiella pneumoniae ST278 Isolate Harboring blaNDM-7 and Involved in Nosocomial Transmission

J Infect Dis. 2016 Sep 1;214(5):798-806. doi: 10.1093/infdis/jiw240. Epub 2016 Jun 9.


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 K. pneumoniae ST278 (KpN06) was obtained 1 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 K. pneumoniae ST278 from patient 2 was likely a descendant 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-resistant K. pneumoniae, demonstrating the highly recombinant nature of this species. It also highlights the ability of NGS to clarify molecular microevolutionary events within antibiotic-resistant organisms.

Keywords: K. pneumoniae; ST278; blaNDM-7; carbapenemases; microevolution; plasmid.

Publication types

  • Case Reports

MeSH terms

  • Aged
  • Canada
  • Cross Infection / epidemiology*
  • Cross Infection / microbiology
  • Cross Infection / transmission
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / genetics
  • Evolution, Molecular*
  • Female
  • Genotype*
  • Humans
  • Klebsiella Infections / epidemiology*
  • Klebsiella Infections / microbiology
  • Klebsiella Infections / transmission
  • Klebsiella pneumoniae / classification*
  • Klebsiella pneumoniae / enzymology
  • Klebsiella pneumoniae / genetics*
  • Klebsiella pneumoniae / isolation & purification
  • Phylogeny
  • Plasmids
  • Sequence Analysis, DNA
  • Sequence Deletion
  • Sequence Homology
  • beta-Lactamases / genetics
  • beta-Lactamases / metabolism*


  • DNA, Bacterial
  • beta-Lactamases
  • beta-lactamase NDM-1