title: Investigation of a possible outbreak of carbapenem-resistant Acinetobacter baumannii in Odense, Denmark using PFGE, MLST and whole-genome-based SNPs.
abstract: OBJECTIVE
  The objectives were to study a possible outbreak of carbapenem-resistant Acinetobacter baumannii by comparing three different typing methods (PFGE, MLST and whole-genome SNPs) and to compare the resistance gene profiles of the isolates.
  
  
  METHODS
  From December 2012 to October 2013, eight carbapenem-resistant A. baumannii were detected at Odense University Hospital, Odense, Denmark. These isolates were typed by PFGE, with ApaI and SmaI, respectively, and subjected to WGS. The WGS data were used for in silico extraction of MLST types using two different schemes, resistance genes and SNPs, to which 31 publicly available A. baumannii genomes were added.
  
  
  RESULTS
  Using ApaI, the eight isolates had four different PFGE profiles, which were further differentiated using SmaI, separating one of the profiles into two distinct PFGE types. Five ST2 (Pasteur MLST) OXA-23-producing isolates, two ST1 OXA-72-producing isolates and one ST158 OXA-23-producing isolate were detected. The five ST2 isolates were subdivided into ST195, ST208 and ST218 using the Oxford MLST scheme. The phylogenetic analysis based on the core genome showed that six of the eight Danish A. baumannii isolates were located in three distinct clusters. The two remaining isolates did not cluster with other Danish or international isolates included in the study. Isolates that clustered using PFGE, Oxford MLST and phylogenetic analysis also shared similar resistance gene profiles.
  
  
  CONCLUSIONS
  The SNP profile, Oxford MLST, PFGE and resistance gene profiles clearly indicated spread of three different A. baumannii strains.
authors: Statens Serum Institut, Copenhagen S, Denmark ama@ssi.dk.
authors: Anette M
authors: AM
authors: Hammerum
authors: Statens Serum Institut, Copenhagen S, Denmark.
authors: Frank
authors: F
authors: Hansen
authors: Department of Clinical Microbiology, Odense University Hospital, Odense C, Denmark.
authors: Marianne N
authors: MN
authors: Skov
authors: Statens Serum Institut, Copenhagen S, Denmark Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, USA.
authors: Marc
authors: M
authors: Stegger
authors: Statens Serum Institut, Copenhagen S, Denmark Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, USA Veterinary Disease Biology, University of Copenhagen, Copenhagen, Denmark.
authors: Paal S
authors: PS
authors: Andersen
authors: Department of Clinical Microbiology, Odense University Hospital, Odense C, Denmark.
authors: Anette
authors: A
authors: Holm
authors: Statens Serum Institut, Copenhagen S, Denmark.
authors: Lotte
authors: L
authors: Jakobsen
authors: Department of Clinical Microbiology, Odense University Hospital, Odense C, Denmark.
authors: Ulrik S
authors: US
authors: Justesen
mesh_terms: D000151:Acinetobacter Infections / Q000453:epidemiology* / Q000382:microbiology; D040981:Acinetobacter baumannii / Q000145:classification* / Q000187:drug effects / Q000235:genetics / Q000302:isolation & purification; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D015780:Carbapenems / Q000494:pharmacology*; D003718:Denmark / Q000453:epidemiology; D004196:Disease Outbreaks; D014644:Genetic Variation; D005838:Genotype; D006785:Hospitals, University; D006801:Humans; D017720:Molecular Epidemiology; D058889:Molecular Typing; D020641:Polymorphism, Single Nucleotide; D018440:beta-Lactam Resistance
chemical_list: D000900:Anti-Bacterial Agents; D015780:Carbapenems
keywords: antimicrobial resistance; antimicrobial resistance epidemiology; carbapenems