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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.

Original publication




Journal article


Emerg Infect Dis

Publication Date





1306 - 1314


Salmonella enterica serovar Enteritidis, bacteria, high-throughput nucleotide sequencing, infectious disease outbreaks, public health laboratory surveillance, pulsed-field gel electrophoresis, whole-genome sequencing, Electrophoresis, Gel, Pulsed-Field, Genome, Bacterial, Genotype, Humans, Phylogeny, Polymorphism, Single Nucleotide, Population Surveillance, Prospective Studies, Retrospective Studies, Salmonella Infections, Salmonella enteritidis, Sequence Analysis, DNA