title: What caused the outbreak of ESBL-producing Klebsiella pneumoniae in a neonatal intensive care unit, Germany 2009 to 2012? Reconstructing transmission with epidemiological analysis and whole-genome sequencing.
abstract: OBJECTIVE
  We aimed to retrospectively reconstruct the timing of transmission events and pathways in order to understand why extensive preventive measures and investigations were not sufficient to prevent new cases.
  
  
  METHODS
  We extracted available information from patient charts to describe cases and to compare them to the normal population of the ward. We conducted a cohort study to identify risk factors for pathogen acquisition. We sequenced the available isolates to determine the phylogenetic relatedness of Klebsiella pneumoniae isolates on the basis of their genome sequences.
  
  
  RESULTS
  The investigation comprises 37 cases and the 10 cases with ESBL (extended-spectrum beta-lactamase)-producing K. pneumoniae bloodstream infection. Descriptive epidemiology indicated that a continuous transmission from person to person was most likely. Results from the cohort study showed that 'frequent manipulation' (a proxy for increased exposure to medical procedures) was significantly associated with being a case (RR 1.44, 95% CI 1.02 to 2.19). Genome sequences revealed that all 48 bacterial isolates available for sequencing from 31 cases were closely related (maximum genetic distance, 12 single nucleotide polymorphisms). Based on our calculation of evolutionary rate and sequence diversity, we estimate that the outbreak strain was endemic since 2008.
  
  
  CONCLUSIONS
  Epidemiological and phylogenetic analyses consistently indicated that there were additional, undiscovered cases prior to the onset of microbiological screening and that the spread of the pathogen remained undetected over several years, driven predominantly by person-to-person transmission. Whole-genome sequencing provided valuable information on the onset, course and size of the outbreak, and on possible ways of transmission.
authors.affiliation: Postgraduate Training for Applied Epidemiology, Berlin, Germany, affiliated to the European Programme for Intervention Epidemiology Training, European Centre for Disease Prevention and Control, Stockholm, Sweden Division of Healthcare-Associated Infections, Surveillance of Antimicrobial Resistance and Consumption, Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Haller
authors.affiliation: Division of Nosocomial Pathogens and Antibiotic Resistances, Department for Infectious Diseases, Robert Koch Institute, Wernigerode, Germany Department of Laboratory Medicine, University Hospital Halle, Halle, Germany.
authors.forename: Christoph
authors.initials: C
authors.lastname: Eller
authors.affiliation: Division of Healthcare-Associated Infections, Surveillance of Antimicrobial Resistance and Consumption, Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany.
authors.forename: Julia
authors.initials: J
authors.lastname: Hermes
authors.affiliation: Department of Medical Microbiology, Ruhr-University Bochum, Bochum, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Kaase
authors.affiliation: Division of Nosocomial Pathogens and Antibiotic Resistances, Department for Infectious Diseases, Robert Koch Institute, Wernigerode, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Steglich
authors.affiliation: Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses, Robert Koch Institute, Berlin, Germany.
authors.forename: Aleksandar
authors.initials: A
authors.lastname: Radonić
authors.affiliation: Central Administration Department, Information Technology, Robert Koch Institute, Berlin, Germany.
authors.forename: Piotr Wojtek
authors.initials: PW
authors.lastname: Dabrowski
authors.affiliation: Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses, Robert Koch Institute, Berlin, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Nitsche
authors.affiliation: Division of Nosocomial Pathogens and Antibiotic Resistances, Department for Infectious Diseases, Robert Koch Institute, Wernigerode, Germany.
authors.forename: Yvonne
authors.initials: Y
authors.lastname: Pfeifer
authors.affiliation: Division of Nosocomial Pathogens and Antibiotic Resistances, Department for Infectious Diseases, Robert Koch Institute, Wernigerode, Germany.
authors.forename: Guido
authors.initials: G
authors.lastname: Werner
authors.affiliation: Department of Public Health, Gesundheitsamt Bremen (Local Public Health Service), Bremen, Germany.
authors.forename: Werner
authors.initials: W
authors.lastname: Wunderle
authors.affiliation: Division of Healthcare-Associated Infections, Surveillance of Antimicrobial Resistance and Consumption, Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany.
authors.forename: Edward
authors.initials: E
authors.lastname: Velasco
authors.affiliation: Division of Healthcare-Associated Infections, Surveillance of Antimicrobial Resistance and Consumption, Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany.
authors.forename: Muna
authors.initials: M
authors.lastname: Abu Sin
authors.affiliation: Division of Healthcare-Associated Infections, Surveillance of Antimicrobial Resistance and Consumption, Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany.
authors.forename: Tim
authors.initials: T
authors.lastname: Eckmanns
authors.affiliation: Division of Nosocomial Pathogens and Antibiotic Resistances, Department for Infectious Diseases, Robert Koch Institute, Wernigerode, Germany DZIF Group on Microbial Genome Research, Leibniz Institute DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen), Braunschweig, Germany.
authors.forename: Ulrich
authors.initials: U
authors.lastname: Nübel
mesh_terms: D005075:Biological Evolution; D015331:Cohort Studies; D004196:Disease Outbreaks; D019353:Endemic Diseases; D005260:Female; D016680:Genome, Bacterial; D005858:Germany / Q000453:epidemiology; D006801:Humans; D007231:Infant, Newborn; D007363:Intensive Care Units, Neonatal; D007710:Klebsiella Infections / Q000453:epidemiology / Q000382:microbiology / Q000635:transmission*; D007711:Klebsiella pneumoniae / Q000235:genetics / Q000378:metabolism; D008297:Male; D010802:Phylogeny; D012189:Retrospective Studies; D017422:Sequence Analysis, DNA; D001618:beta-Lactamases / Q000378:metabolism
chemical_list: D001618:beta-Lactamases
keywords: EPIDEMIOLOGY; INFECTIOUS DISEASES; MOLECULAR BIOLOGY