Genomic Characterization of Colistin Heteroresistance in Klebsiella pneumoniae during a Nosocomial Outbreak.
Klebsiella pneumoniae is emerging as an important nosocomial pathogen due to its rapidly increasing multidrug resistance, which has led to a renewed interest in polymyxin antibiotics, such as colistin, as antibiotics of last resort. However, heteroresistance (i.e., the presence of a subpopulation of resistant bacteria in an otherwise susceptible culture) may hamper the effectiveness of colistin treatment in patients. In a previous study, we showed that colistin resistance among extended-spectrum-beta-lactamase (ESBL)-producing K. pneumoniae isolates emerged after the introduction of selective digestive tract decontamination (SDD) in an intensive care unit (ICU). In this study, we investigated heteroresistance to colistin among ESBL-producing K. pneumoniae isolates by using population analysis profiles (PAPs). We used whole-genome sequencing (WGS) to identify the mutations that were associated with the emergence of colistin resistance in these K. pneumoniae isolates. We found five heteroresistant subpopulations, with colistin MICs ranging from 8 to 64 mg/liter, which were derived from five clonally related, colistin-susceptible clinical isolates. WGS revealed the presence of mutations in the lpxM, mgrB, phoQ, and yciM genes in colistin-resistant K. pneumoniae isolates. In two strains, mgrB was inactivated by an IS3-like or ISKpn14 insertion sequence element. Complementation in trans with the wild-type mgrB gene resulted in these strains reverting to colistin susceptibility. The MICs for colistin-susceptible strains increased 2- to 4-fold in the presence of the mutated phoQ, lpxM, and yciM alleles. In conclusion, the present study indicates that heteroresistant K. pneumoniae subpopulations may be selected for upon exposure to colistin. Mutations in mgrB and phoQ have previously been associated with colistin resistance, but we provide experimental evidence for roles of mutations in the yciM and lpxM genes in the emergence of colistin resistance in K. pneumoniae.
Laboratory for Medical Microbiology and Public Health, Hengelo, The Netherlands t.halaby@labmicta.nl.|Department of Intensive Care, Medisch Spectrum Twente, Enschede, The Netherlands.
Teysir
T
Halaby
Laboratory for Medical Microbiology and Public Health, Hengelo, The Netherlands.|Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
Emre
E
Kucukkose
Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
Axel B
AB
Janssen
Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
Malbert R C
MR
Rogers
Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
Dennis J
DJ
Doorduijn
Laboratory for Medical Microbiology and Public Health, Hengelo, The Netherlands.
Adri G M
AG
van der Zanden
Laboratory for Medical Microbiology and Public Health, Hengelo, The Netherlands.|Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands.
Nashwan
N
Al Naiemi
Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands.
Christina M J E
CM
Vandenbroucke-Grauls
Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
Willem
W
van Schaik
D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001426:Bacterial Proteins / Q000235:genetics; D003091:Colistin / Q000494:pharmacology*; D003428:Cross Infection / Q000188:drug therapy / Q000453:epidemiology* / Q000382:microbiology; D004196:Disease Outbreaks; D024881:Drug Resistance, Bacterial / Q000187:drug effects / Q000235:genetics*; D016680:Genome, Bacterial; D006801:Humans; D007710:Klebsiella Infections / Q000188:drug therapy / Q000453:epidemiology* / Q000382:microbiology; D007711:Klebsiella pneumoniae / Q000187:drug effects* / Q000235:genetics; D008826:Microbial Sensitivity Tests; D009154:Mutation; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D001618:beta-Lactamases / Q000235:genetics / Q000378:metabolism
D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; C079792:PhoQ protein, Bacteria; D001618:beta-Lactamases; D003091:Colistin