title: A whole-genome single nucleotide polymorphism-based approach to trace and identify outbreaks linked to a common Salmonella enterica subsp. enterica serovar Montevideo pulsed-field gel electrophoresis type.
abstract: In this study, we report a whole-genome single nucleotide polymorphism (SNP)-based evolutionary approach to study the epidemiology of a multistate outbreak of Salmonella enterica subsp. enterica serovar Montevideo. This outbreak included 272 cases that occurred in 44 states between July 2009 and April 2010. A case-control study linked the consumption of salami made with contaminated black and red pepper to the outbreak. We sequenced, on the SOLiD System, 47 isolates with XbaI PFGE pattern JIXX01.0011, a common pulsed-field gel electrophoresis (PFGE) pattern associated with isolates from the outbreak. These isolates represented 20 isolates collected from human sources during the period of the outbreak and 27 control isolates collected from human, food, animal, and environmental sources before the outbreak. Based on 253 high-confidence SNPs, we were able to reconstruct a tip-dated molecular clock phylogeny of the isolates and to assign four human isolates to the actual outbreak. We developed an SNP typing assay to rapidly discriminate between outbreak-related cases and non-outbreak-related cases and tested this assay on an extended panel of 112 isolates. These results suggest that only a very small percentage of the human isolates with the outbreak PFGE pattern and obtained during the outbreak period could be attributed to the actual pepper-related outbreak (20%), while the majority (80%) of the putative cases represented background cases. This study demonstrates that next-generation-based SNP typing provides the resolution and accuracy needed for outbreak investigations of food-borne pathogens that cannot be distinguished by currently used subtyping methods.
authors: Department of Food Science, Cornell University, Ithaca, New York 14853, USA. hcd5@cornell.edu
authors: Henk C den
authors: HC
authors: Bakker
authors: Andrea I Moreno
authors: AI
authors: Switt
authors: Craig A
authors: CA
authors: Cummings
authors: Karin
authors: K
authors: Hoelzer
authors: Lovorka
authors: L
authors: Degoricija
authors: Lorraine D
authors: LD
authors: Rodriguez-Rivera
authors: Emily M
authors: EM
authors: Wright
authors: Rixun
authors: R
authors: Fang
authors: Margaret
authors: M
authors: Davis
authors: Tim
authors: T
authors: Root
authors: Dianna
authors: D
authors: Schoonmaker-Bopp
authors: Kimberlee A
authors: KA
authors: Musser
authors: Elizabeth
authors: E
authors: Villamil
authors: Haena
authors: H
authors: Waechter
authors: Laura
authors: L
authors: Kornstein
authors: Manohar R
authors: MR
authors: Furtado
authors: Martin
authors: M
authors: Wiedmann
mesh_terms: D016000:Cluster Analysis; D004196:Disease Outbreaks; D016521:Electrophoresis, Gel, Pulsed-Field; D005517:Foodborne Diseases / Q000453:epidemiology* / Q000382:microbiology; D005838:Genotype; D006801:Humans; D017720:Molecular Epidemiology / Q000379:methods; D058889:Molecular Typing / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D012480:Salmonella Infections / Q000453:epidemiology* / Q000382:microbiology; D019779:Salmonella enterica / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification