title: Comparison of whole genome sequencing typing results and epidemiological contact information from outbreaks of Salmonella Dublin in Swedish cattle herds.
abstract: BACKGROUND
  Whole genome sequencing (WGS) is becoming a routine tool for infectious disease outbreak investigations. The Swedish situation provides an excellent opportunity to test the usefulness of WGS for investigation of outbreaks with Salmonella Dublin (S. Dublin) as epidemiological investigations are always performed when Salmonella is detected in livestock production, and index isolates from all detected herds are stored and therefore available for analysis. This study was performed to evaluate WGS as a tool in forward and backward tracings from herds infected with S. Dublin.
  
  
  METHODS
  In this study, 28 isolates from 26 cattle herds were analysed and the WGS results were compared with results from the epidemiological investigations, for example, information on contacts between herds. The isolates originated from herds in three different outbreaks separated geographically and to some extent also in time, and from the only region in Sweden where S. Dublin is endemic (Öland).
  
  
  RESULTS
  The WGS results of isolates from the three non-endemic regions were reliably separated from each other and from the endemic isolates. Within the outbreaks, herds with known epidemiological contacts generally showed smaller differences between isolates as compared to when there were no known epidemiological contacts.
  
  
  CONCLUSIONS
  The results indicate that WGS can provide valuable supplemental information in S. Dublin outbreak investigations. The resolution of the WGS was sufficient to distinguish isolates from the different outbreaks and provided additional information to the investigations within an outbreak.
authors.affiliation: Department of Disease Control and Epidemiology, National Veterinary Institute, Uppsala, Sweden; estelle.agren@sva.se.
authors.forename: Estelle C C
authors.initials: EC
authors.lastname: Ågren
authors.affiliation: Department of Disease Control and Epidemiology, National Veterinary Institute, Uppsala, Sweden.
authors.forename: Helene
authors.initials: H
authors.lastname: Wahlström
authors.affiliation: Department of Disease Control and Epidemiology, National Veterinary Institute, Uppsala, Sweden.
authors.forename: Catrin
authors.initials: C
authors.lastname: Vesterlund-Carlson
authors.affiliation: Department of Disease Control and Epidemiology, National Veterinary Institute, Uppsala, Sweden.
authors.forename: Elina
authors.initials: E
authors.lastname: Lahti
authors.affiliation: Department of Microbiology, National Veterinary Institute, Uppsala, Sweden.
authors.forename: Lennart
authors.initials: L
authors.lastname: Melin
authors.affiliation: Department of Microbiology, National Veterinary Institute, Uppsala, Sweden.
authors.forename: Robert
authors.initials: R
authors.lastname: Söderlund
keywords: NGS; SNP; Sweden; WGS; molecular epidemiology; zoonosis