title: WGS-based surveillance of third-generation cephalosporin-resistant Escherichia coli from bloodstream infections in Denmark.
abstract: To evaluate a genome-based surveillance of all Danish third-generation cephalosporin-resistant Escherichia coli (3GC-R Ec ) from bloodstream infections between 2014 and 2015, focusing on horizontally transferable resistance mechanisms.
  
  
  
  A collection of 552 3GC-R Ec isolates were whole-genome sequenced and characterized by using the batch uploader from the Center for Genomic Epidemiology (CGE) and automatically analysed using the CGE tools according to resistance profile, MLST, serotype and fimH subtype. Additionally, the phylogenetic relationship of the isolates was analysed by SNP analysis.
  
  
  
  The majority of the 552 isolates were ESBL producers (89%), with bla CTX-M-15 being the most prevalent (50%) gene, followed by bla CTX-M-14 (14%), bla CTX-M-27 (11%) and bla CTX-M-101 (5%). ST131 was detected in 50% of the E. coli isolates, with the remaining isolates belonging to 73 other STs, including globally disseminated STs (e.g. ST10, ST38, ST58, ST69 and ST410). Five of the bloodstream isolates were carbapenemase producers, carrying bla OXA-181 (3) and bla OXA-48 (2). Phylogenetic analysis revealed 15 possible national outbreaks during the 2 year period, one caused by a novel ST131/ bla CTX-M-101 clone, here observed for the first time in Denmark. Additionally, the analysis revealed three individual cases with possible persistence of closely related clones collected more than 13 months apart.
  
  
  
  Continuous WGS-based national surveillance of 3GC-R Ec , in combination with more detailed epidemiological information, can improve the ability to follow the population dynamics of 3GC-R Ec , thus allowing for the detection of potential outbreaks and the effects of changing treatment regimens in the future.
authors.affiliation: Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark.
authors.forename: Louise
authors.initials: L
authors.lastname: Roer
authors.affiliation: Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark.
authors.forename: Frank
authors.initials: F
authors.lastname: Hansen
authors.affiliation: Department of Systems Biology, Technical University of Denmark, Kgs Lyngby, Denmark.
authors.forename: Martin Christen Frølund
authors.initials: MCF
authors.lastname: Thomsen
authors.affiliation: Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark.
authors.forename: Jenny Dahl
authors.initials: JD
authors.lastname: Knudsen
authors.affiliation: Department of Clinical Microbiology, Herlev and Gentofte Hospital, Herlev, Denmark.
authors.forename: Dennis Schrøder
authors.initials: DS
authors.lastname: Hansen
authors.affiliation: Department of Clinical Microbiology, Aarhus University Hospital, Aarhus, Denmark.
authors.forename: Mikala
authors.initials: M
authors.lastname: Wang
authors.affiliation: Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark.
authors.forename: Jurgita
authors.initials: J
authors.lastname: Samulioniené
authors.affiliation: Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark.
authors.forename: Ulrik Stenz
authors.initials: US
authors.lastname: Justesen
authors.affiliation: Department of Clinical Microbiology, Slagelse Hospital, Slagelse, Denmark.
authors.forename: Bent L
authors.initials: BL
authors.lastname: Røder
authors.affiliation: Department of Clinical Microbiology, Aarhus University Hospital, Aarhus, Denmark.
authors.forename: Helga
authors.initials: H
authors.lastname: Schumacher
authors.affiliation: Department of Clinical Microbiology, Lillebaelt Hospital, Vejle, Denmark.
authors.forename: Claus
authors.initials: C
authors.lastname: Østergaard
authors.affiliation: Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark.
authors.forename: Leif Percival
authors.initials: LP
authors.lastname: Andersen
authors.affiliation: Department of Clinical Microbiology, Hospital South West Jutland, Esbjerg, Denmark.
authors.forename: Esad
authors.initials: E
authors.lastname: Dzajic
authors.affiliation: Department of Clinical Microbiology, Viborg Regional Hospital, Viborg, Denmark.
authors.forename: Turid Snekloth
authors.initials: TS
authors.lastname: Søndergaard
authors.affiliation: Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark.
authors.forename: Marc
authors.initials: M
authors.lastname: Stegger
authors.affiliation: Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark.
authors.forename: Anette M
authors.initials: AM
authors.lastname: Hammerum
authors.affiliation: Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark.
authors.forename: Henrik
authors.initials: H
authors.lastname: Hasman
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D016470:Bacteremia / Q000453:epidemiology / Q000382:microbiology*; D001426:Bacterial Proteins / Q000096:biosynthesis / Q000235:genetics; D018550:Cephalosporin Resistance / Q000235:genetics*; D002511:Cephalosporins / Q000494:pharmacology*; D016521:Electrophoresis, Gel, Pulsed-Field; D062665:Epidemiological Monitoring; D004926:Escherichia coli / Q000187:drug effects* / Q000201:enzymology / Q000235:genetics*; D004927:Escherichia coli Infections / Q000453:epidemiology / Q000382:microbiology*; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008826:Microbial Sensitivity Tests; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D001618:beta-Lactamases / Q000096:biosynthesis / Q000235:genetics
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D002511:Cephalosporins; D001618:beta-Lactamases; C063912:carbapenemase