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

被引：119

作者：

den Bakker, Henk C. ^{[1
]}

Allard, Marc W. ^{[2
]}

Bopp, Dianna ^{[3
]}

Brown, Eric W. ^{[2
]}

Fontana, John ^{[4
]}

Iqbal, Zamin ^{[5
]}

Kinney, Aristea ^{[4
]}

Limberger, Ronald ^{[3
]}

Musser, Kimberlee A. ^{[3
]}

Shudt, Matthew ^{[3
]}

Strain, Errol ^{[2
]}

Wiedmann, Martin ^{[1
]}

Wolfgang, William J. ^{[3
]}

机构：

[1] Cornell Univ, Ithaca, NY USA

[2] US FDA, College Pk, MD USA

[3] New York State Dept Hlth, Wadsworth Ctr, Albany, NY USA

[4] Connecticut Dept Publ Hlth, Rocky Hill, CT USA

[5] Wellcome Trust Ctr Human Genet, Oxford, England

来源：

EMERGING INFECTIOUS DISEASES | 2014年 / 20卷 / 08期

关键词：

FIELD GEL-ELECTROPHORESIS; TANDEM REPEAT ANALYSIS;

D O I：

10.3201/eid2008.131399

中图分类号：

R392 [医学免疫学]; Q939.91 [免疫学];

学科分类号：

071005 [微生物学]; 100108 [医学免疫学];

摘要：

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.

引用

页码：1306 / 1314

页数：9

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