title: Use of WGS data for investigation of a long-term NDM-1-producing Citrobacter freundii outbreak and secondary in vivo spread of blaNDM-1 to Escherichia coli, Klebsiella pneumoniae and Klebsiella oxytoca.
abstract: An outbreak of NDM-1-producing Citrobacter freundii and possible secondary in vivo spread of blaNDM-1to other Enterobacteriaceae were investigated.
  
  
  
  From October 2012 to March 2015, meropenem-resistant Enterobacteriaceae were detected in 45 samples from seven patients at Aalborg University Hospital, Aalborg, Denmark. In silico resistance genes, Inc plasmid types and STs (MLST) were obtained from WGS data from 24 meropenem-resistant isolates (13 C. freundii, 6 Klebsiella pneumoniae, 4 Escherichia coli and 1 Klebsiella oxytoca) and 1 meropenem-susceptible K. oxytoca. The sequences of the meropenem-resistant C. freundii isolates were compared by phylogenetic analyses. In vitro susceptibility to 21 antimicrobial agents was tested. Furthermore, in vitro conjugation and plasmid characterization was performed.
  
  
  
  From the seven patients, 13 highly clonal ST18 NDM-1-producing C. freundii were isolated. The ST18 NDM-1-producing C. freundii isolates were only susceptible to tetracycline, tigecycline, colistin and fosfomycin (except for the C. freundii isolates from Patient 2 and Patient 7, which were additionally resistant to tetracycline). The E. coli and K. pneumoniae from different patients belonged to different STs, indicating in vivo transfer of blaNDM-1in the individual patients. This was further supported by in vitro conjugation and detection of a 154 kb IncA/C2 plasmid with blaNDM-1. Patient screenings failed to reveal any additional cases. None of the patients had a history of recent travel abroad and the source of the blaNDM-1plasmid was unknown.
  
  
  
  To our knowledge, this is the first report of an NDM-1-producing C. freundii outbreak and secondary in vivo spread of an IncA/C2 plasmid with blaNDM-1to other Enterobacteriaceae.
authors: Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark ama@ssi.dk.
authors: Anette M
authors: AM
authors: Hammerum
authors: Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark.
authors: Frank
authors: F
authors: Hansen
authors: Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark.
authors: Hans Linde
authors: HL
authors: Nielsen
authors: Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark.
authors: Lotte
authors: L
authors: Jakobsen
authors: Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark.|Pathogen Genomics Division, Translational Genomics Research Institute (TGen), Flagstaff, AZ, USA.
authors: Marc
authors: M
authors: Stegger
authors: Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark.|Pathogen Genomics Division, Translational Genomics Research Institute (TGen), Flagstaff, AZ, USA.|Veterinary Disease Biology, University of Copenhagen, Copenhagen, Denmark.
authors: Paal S
authors: PS
authors: Andersen
authors: Department of Haematology, Aalborg University Hospital, Aalborg, Denmark.
authors: Paw
authors: P
authors: Jensen
authors: Department of Environmental Science, Aarhus University, Roskilde, Denmark.
authors: Tue Kjærgaard
authors: TK
authors: Nielsen
authors: Department of Environmental Science, Aarhus University, Roskilde, Denmark.
authors: Lars Hestbjerg
authors: LH
authors: Hansen
authors: Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark.
authors: Henrik
authors: H
authors: Hasman
authors: Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark.
authors: David
authors: D
authors: Fuglsang-Damgaard
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D016971:Citrobacter freundii / Q000145:classification / Q000201:enzymology* / Q000235:genetics / Q000302:isolation & purification; D003718:Denmark / Q000453:epidemiology; D004196:Disease Outbreaks; D004756:Enterobacteriaceae Infections / Q000453:epidemiology* / Q000382:microbiology; D004926:Escherichia coli / Q000201:enzymology* / Q000235:genetics / Q000302:isolation & purification; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D005838:Genotype; D006801:Humans; D007709:Klebsiella / Q000201:enzymology* / Q000235:genetics / Q000302:isolation & purification; D000077731:Meropenem; D008826:Microbial Sensitivity Tests; D010802:Phylogeny; D010957:Plasmids / Q000032:analysis / Q000145:classification; D017422:Sequence Analysis, DNA; D013845:Thienamycins / Q000494:pharmacology; D018440:beta-Lactam Resistance; D001618:beta-Lactamases / Q000235:genetics / Q000378:metabolism*
chemical_list: D000900:Anti-Bacterial Agents; D013845:Thienamycins; D001618:beta-Lactamases; C552864:beta-lactamase NDM-1; D000077731:Meropenem