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

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

doi:10.3201/eid2008.131399

i

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

Supporting Files Public Domain

Aug 2014
By den Bakker, Henk C. ; Allard, Marc W. ; Bopp, Dianna ; ...

Details

Alternative Title:

Emerg Infect Dis
Personal Author:

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

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.
Subjects:

Bacteria High-throughput Nucleotide Sequencing Infectious Disease Outbreaks Public Health Laboratory Surveillance Pulsed-field Gel Electrophoresis Research Salmonella Enterica Serovar Enteritidis Whole-genome Sequencing
Source:

Emerg Infect Dis. 20(8):1306-1314.
Document Type:

Journal Article
Volume:

20
Issue:

8
Collection(s):

Emerging Infectious Diseases
Main Document Checksum:

urn:sha256:60c2019423c56d4d8b3b293ea5045a72ab303582c1c93d0656c84d23dba271d1
Download URL:

https://stacks.cdc.gov/view/cdc/24488/cdc_24488_DS1.pdf
File Type:

[PDF - 1.06 MB ]

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