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Rapid Whole-Genome Sequencing for Surveillance of Salmonella enterica Serovar Enteritidis

2014; Centers for Disease Control and Prevention; Volume: 20; Issue: 8 Linguagem: Inglês

10.3201/eid2008.131399

1080-6059

Henk C. den Bakker, Marc W. Allard, Dianna J. Bopp, Eric W. Brown, John L. Fontana, Zamin Iqbal, Aristea Kinney, Ronald J. Limberger, Kimberlee A. Musser, Matthew Shudt, Errol Strain, Martin Wiedmann, William J. Wolfgang,

Bacterial Identification and Susceptibility Testing

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.