title: Rapid whole-genome sequencing for surveillance of Salmonella enterica serovar enteritidis.
abstract: For Salmonella enterica serovar Enteritidis, 85% of isolates can be classified into 5 pulsed-field gel electrophoresis (PFGE) types. However, PFGE has limited discriminatory power for outbreak detection. Although whole-genome sequencing has been found to improve discrimination of outbreak clusters, whether this procedure can be used in real-time in a public health laboratory is not known. Therefore, we conducted a retrospective and prospective analysis. The retrospective study investigated isolates from 1 confirmed outbreak. Additional cases could be attributed to the outbreak strain on the basis of whole-genome data. The prospective study included 58 isolates obtained in 2012, including isolates from 1 epidemiologically defined outbreak. Whole-genome sequencing identified additional isolates that could be attributed to the outbreak, but which differed from the outbreak-associated PFGE type. Additional putative outbreak clusters were detected in the retrospective and prospective analyses. This study demonstrates the practicality of implementing this approach for outbreak surveillance in a state public health laboratory.
authors: Henk C
authors: HC
authors: den Bakker
authors: Marc W
authors: MW
authors: Allard
authors: Dianna
authors: D
authors: Bopp
authors: Eric W
authors: EW
authors: Brown
authors: John
authors: J
authors: Fontana
authors: Zamin
authors: Z
authors: Iqbal
authors: Aristea
authors: A
authors: Kinney
authors: Ronald
authors: R
authors: Limberger
authors: Kimberlee A
authors: KA
authors: Musser
authors: Matthew
authors: M
authors: Shudt
authors: Errol
authors: E
authors: Strain
authors: Martin
authors: M
authors: Wiedmann
authors: William J
authors: WJ
authors: Wolfgang
mesh_terms: D016521:Electrophoresis, Gel, Pulsed-Field; D016680:Genome, Bacterial; D005838:Genotype; D006801:Humans; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D011159:Population Surveillance; D011446:Prospective Studies; D012189:Retrospective Studies; D012480:Salmonella Infections / Q000453:epidemiology* / Q000382:microbiology*; D012477:Salmonella enteritidis / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D017422:Sequence Analysis, DNA
keywords: Salmonella enterica serovar Enteritidis; bacteria; high-throughput nucleotide sequencing; infectious disease outbreaks; public health laboratory surveillance; pulsed-field gel electrophoresis; whole-genome sequencing