title: Clonal or not clonal? Investigating hospital outbreaks of KPC-producing Klebsiella pneumoniae with whole-genome sequencing.
abstract: OBJECTIVE
  Whole-genome sequencing (WGS) is a promising tool for identifying transmission pathways in outbreaks caused by multidrug-resistant bacteria. However, it is uncertain how the data produced by WGS can be best integrated into epidemiologic investigations.
  
  
  METHODS
  We tested various genomic analyses to identify clonal groups in two distinct outbreaks of Klebsiella pneumoniae carbapenemase-producing K. pneumoniae that occurred in Switzerland in 2013 and 2015. In blinded fashion, we sequenced 12 strains involved in the two outbreaks, respectively, and six that were epidemiologically unrelated. We analysed genomic commonalities from conserved genes to plasmid-borne antibiotic resistance genes (ARGs) and contrasted these results with available epidemiologic evidence.
  
  
  RESULTS
  Using WGS, blinded analysts correctly identified the two clusters of strains from the two outbreaks. Nonetheless, the 2015 index strain was found to be slightly different (1-3 single nucleotide variants) from the strains recovered from secondary cases, likely because prior long-term carriage (3 years) by the index patient allowed for genetic mutations over time. Also, we observed occasional loss of ARG-bearing plasmidic fragments in outbreak-causing strains.
  
  
  CONCLUSIONS
  Retrospective WGS analysis was successful in identifying clonal groups in both outbreaks. Still, data should be analysed with caution in cases of previous long-term carriage of the studied bacteria.
authors.affiliation: Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland. Electronic address: etienne.ruppe@hcuge.ch.
authors.forename: E
authors.initials: E
authors.lastname: Ruppé
authors.affiliation: Infection Control Program, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland.
authors.forename: F
authors.initials: F
authors.lastname: Olearo
authors.affiliation: Infection Control Program, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland; Department of Infectious Diseases, Centro Hospitalar Lisboa Norte and Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal.
authors.forename: D
authors.initials: D
authors.lastname: Pires
authors.affiliation: Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.
authors.forename: D
authors.initials: D
authors.lastname: Baud
authors.affiliation: Bacteriology Laboratory, Service of Laboratory Medicine, Department of Genetics and Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland.
authors.forename: G
authors.initials: G
authors.lastname: Renzi
authors.affiliation: Bacteriology Laboratory, Service of Laboratory Medicine, Department of Genetics and Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland.
authors.forename: A
authors.initials: A
authors.lastname: Cherkaoui
authors.affiliation: Division of Clinical Microbiology, University Hospital Basel, Basel, Switzerland.
authors.forename: D
authors.initials: D
authors.lastname: Goldenberger
authors.affiliation: Infection Control Program, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland.
authors.forename: A
authors.initials: A
authors.lastname: Huttner
authors.affiliation: Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.
authors.forename: P
authors.initials: P
authors.lastname: François
authors.affiliation: Infection Control Program, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland.
authors.forename: S
authors.initials: S
authors.lastname: Harbarth
authors.affiliation: Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland; Bacteriology Laboratory, Service of Laboratory Medicine, Department of Genetics and Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland.
authors.forename: J
authors.initials: J
authors.lastname: Schrenzel
mesh_terms: D000368:Aged; D001426:Bacterial Proteins / Q000378:metabolism*; D016000:Cluster Analysis; D003428:Cross Infection / Q000453:epidemiology* / Q000382:microbiology; D004196:Disease Outbreaks; D018562:Disease Transmission, Infectious; D005838:Genotype; D006801:Humans; D007710:Klebsiella Infections / Q000453:epidemiology* / Q000382:microbiology; D007711:Klebsiella pneumoniae / Q000145:classification* / Q000201:enzymology / Q000302:isolation & purification; D008297:Male; D017720:Molecular Epidemiology / Q000379:methods; D058889:Molecular Typing / Q000379:methods*; D012189:Retrospective Studies; D013557:Switzerland / Q000453:epidemiology; D000073336:Whole Genome Sequencing / Q000379:methods*; D001618:beta-Lactamases / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D001618:beta-Lactamases; C063912:carbapenemase
keywords: Carbapenemase; Clone; Evolution; Genomics; Klebsiella pneumoniae; Molecular typing; Outbreak; Whole-genome sequencing (WGS)