Molecular Evolution of a Klebsiella pneumoniae ST278 Isolate Harboring blaNDM-7 and Involved in Nosocomial Transmission.
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.
Division of Microbiology, Calgary Laboratory Services Department of Pathology and Laboratory Medicine Snyder Institute for Chronic Diseases, Cummings School of Medicine, University of Calgary, Canada.
Tarah
T
Lynch
Public Health Research Institute Tuberculosis Center, Rutgers University, Newark, New Jersey.
Liang
L
Chen
Division of Microbiology, Calgary Laboratory Services Department of Pathology and Laboratory Medicine.
Gisele
G
Peirano
Division of Microbiology, Calgary Laboratory Services Department of Pathology and Laboratory Medicine Department of Medicine Snyder Institute for Chronic Diseases, Cummings School of Medicine, University of Calgary, Canada.
Dan B
DB
Gregson
Division of Microbiology, Calgary Laboratory Services Department of Pathology and Laboratory Medicine Department of Medicine Snyder Institute for Chronic Diseases, Cummings School of Medicine, University of Calgary, Canada.
Deirdre L
DL
Church
Division of Microbiology, Calgary Laboratory Services Department of Pathology and Laboratory Medicine Department of Microbiology, Immunology, and Infectious Diseases Department of Medicine Snyder Institute for Chronic Diseases, Cummings School of Medicine, University of Calgary, Canada.
John
J
Conly
Public Health Research Institute Tuberculosis Center, Rutgers University, Newark, New Jersey.
Barry N
BN
Kreiswirth
Division of Microbiology, Calgary Laboratory Services Department of Pathology and Laboratory Medicine Department of Microbiology, Immunology, and Infectious Diseases Snyder Institute for Chronic Diseases, Cummings School of Medicine, University of Calgary, Canada Department of Medical Microbiology, University of Pretoria, South Africa.
Johann D
JD
Pitout
D000368:Aged; D002170:Canada; D003428:Cross Infection / Q000453:epidemiology* / Q000382:microbiology / Q000635:transmission; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D005260:Female; D005838:Genotype; D006801:Humans; D007710:Klebsiella Infections / Q000453:epidemiology* / Q000382:microbiology / Q000635:transmission; D007711:Klebsiella pneumoniae / Q000145:classification* / Q000201:enzymology / Q000235:genetics* / Q000302:isolation & purification; D010802:Phylogeny; D010957:Plasmids; D017422:Sequence Analysis, DNA; D017384:Sequence Deletion; D017385:Sequence Homology; D001618:beta-Lactamases / Q000235:genetics / Q000378:metabolism*
D004269:DNA, Bacterial; D001618:beta-Lactamases; C552864:beta-lactamase NDM-1
K. pneumoniae; ST278; blaNDM-7; carbapenemases; microevolution; plasmid