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Emerg Infect Dis. 2014 Aug;20(8):1306-14. doi: 10.3201/eid2008.131399.

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.

KEYWORDS:

Salmonella enterica serovar Enteritidis; bacteria; high-throughput nucleotide sequencing; infectious disease outbreaks; public health laboratory surveillance; pulsed-field gel electrophoresis; whole-genome sequencing

PMID:
25062035
PMCID:
PMC4111163
DOI:
10.3201/eid2008.131399
[Indexed for MEDLINE]
Free PMC Article

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