TY - JOUR
T1 - Rapid whole-genome sequencing for surveillance of salmonella enterica serovar Enteritidis
AU - den Bakker, Henk C.
AU - Allard, Marc W.
AU - Bopp, Dianna
AU - Brown, Eric W.
AU - Fontana, John
AU - Iqbal, Zamin
AU - Kinney, Aristea
AU - Limberger, Ronald
AU - Musser, Kimberlee A.
AU - Shudt, Matthew
AU - Strain, Errol
AU - Wiedmann, Martin
AU - Wolfgang, William J.
PY - 2014
Y1 - 2014
N2 - 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.
AB - 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.
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U2 - 10.3201/eid2008.131399
DO - 10.3201/eid2008.131399
M3 - Article
C2 - 25062035
AN - SCOPUS:84905223467
SN - 1080-6040
VL - 20
SP - 1306
EP - 1314
JO - Emerging infectious diseases
JF - Emerging infectious diseases
IS - 8
ER -