title: Application of Molecular Typing Results in Source Attribution Models: The Case of Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) of Salmonella Isolates Obtained from Integrated Surveillance in Denmark.
abstract: Salmonella is an important cause of bacterial foodborne infections in Denmark. To identify the main animal-food sources of human salmonellosis, risk managers have relied on a routine application of a microbial subtyping-based source attribution model since 1995. In 2013, multiple locus variable number tandem repeat analysis (MLVA) substituted phage typing as the subtyping method for surveillance of S. Enteritidis and S. Typhimurium isolated from animals, food, and humans in Denmark. The purpose of this study was to develop a modeling approach applying a combination of serovars, MLVA types, and antibiotic resistance profiles for the Salmonella source attribution, and assess the utility of the results for the food safety decisionmakers. Full and simplified MLVA schemes from surveillance data were tested, and model fit and consistency of results were assessed using statistical measures. We conclude that loci schemes STTR5/STTR10/STTR3 for S. Typhimurium and SE9/SE5/SE2/SE1/SE3 for S. Enteritidis can be used in microbial subtyping-based source attribution models. Based on the results, we discuss that an adjustment of the discriminatory level of the subtyping method applied often will be required to fit the purpose of the study and the available data. The issues discussed are also considered highly relevant when applying, e.g., extended multi-locus sequence typing or next-generation sequencing techniques.
authors.affiliation: Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: Leonardo V
authors.initials: LV
authors.lastname: de Knegt
authors.affiliation: Research Group for Risk-Benefit, National Food Institute, Technical University of Denmark, Søborg, Denmark.
authors.forename: Sara M
authors.initials: SM
authors.lastname: Pires
authors.affiliation: Research Group for Diagnostic Engineering, National Food Institute, Technical University of Denmark, Søborg, Denmark.
authors.forename: Charlotta
authors.initials: C
authors.lastname: Löfström
authors.affiliation: Research Group for Diagnostic Engineering, National Food Institute, Technical University of Denmark, Søborg, Denmark.
authors.forename: Gitte
authors.initials: G
authors.lastname: Sørensen
authors.affiliation: Section for Bacteriology, Pathology and Parasitology, National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark.
authors.forename: Karl
authors.initials: K
authors.lastname: Pedersen
authors.affiliation: Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark.
authors.forename: Mia
authors.initials: M
authors.lastname: Torpdahl
authors.affiliation: Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark.
authors.forename: Eva M
authors.initials: EM
authors.lastname: Nielsen
authors.affiliation: Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: Tine
authors.initials: T
authors.lastname: Hald
mesh_terms: D000818:Animals; D016477:Artifacts; D001434:Bacteriophage Typing; D002645:Chickens; D003718:Denmark; D004196:Disease Outbreaks; D004372:Ducks; D059022:Food Safety; D006801:Humans; D008460:Meat; D018598:Minisatellite Repeats; D015233:Models, Statistical; D058885:Multilocus Sequence Typing / Q000379:methods*; D012478:Salmonella Food Poisoning / Q000175:diagnosis* / Q000382:microbiology*; D012480:Salmonella Infections; D012477:Salmonella enteritidis / Q000302:isolation & purification*; D012486:Salmonella typhimurium / Q000302:isolation & purification*; D013552:Swine; D014422:Turkeys
keywords: Bayesian inference; MLVA; Salmonella; source attribution; surveillance