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Volume 20, Number 8—August 2014
Research

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

Henk C. den Bakker, Marc W. Allard, Dianna Bopp, Eric W. Brown, John Fontana, Zamin Iqbal, Aristea Kinney, Ronald Limberger, Kimberlee A. Musser, Matthew Shudt, Errol Strain, Martin Wiedmann, and William J. WolfgangComments to Author 
Author affiliations: Cornell University, Ithaca, New York, USA (H. den Bakker, M. Wiedmann); US Food and Drug Administration, College Park, Maryland, USA (M.W. Allard, E.W. Brown, E. Strain); New York State Department of Health/Wadsworth Center, Albany, New York, USA (D. Bopp, R. Limberger, M. Shudt, K.A. Musser, W.J. Wolfgang); Connecticut Department of Public Health, Rocky Hill, Connecticut, USA (J. Fontana, A. Kinney); Wellcome Trust Centre for Human Genetics, Oxford, UK (Z. Iqbal)

Main Article

Table

Retrospective cohort of Salmonella enterica serovar Enteritidis isolates analyzed by whole-genome cluster analysis *

ID no. Collection date State PFGE-MLVA combined† Cluster detected by epidemiology‡ Cluster detected by WGCA‡
10_28670 2010 Aug 8 NY JEGX01.0004-B – –
10_29153 2010 Aug 10 NY JEGX01.0004-W – –
10_29949 2010 Aug 16 NY JEGX01.0004-B – –
10_30147 2010 Aug 22 NY JEGX01.0004-W – Cluster B
10_31528 2010 Aug 26 NY JEGX01.0004-W – –
10_33213 2010 Sep 10 NY JEGX01.0004-W – LTCF
10_33369 2010 Sep 10 NY JEGX01.0004-W – LTCF
10_33371 2010 Sep 11 NY JEGX01.0004-W – LTCF
10_35179 2010 Sep 12 CT JEGX01.0004-W LTCF LTCF
10_35180 2010 Sep 12 NY JEGX01.0004-W LTCF LTCF
10_35182 2010 Sep 12 NY JEGX01.0004-W LTCF LTCF
10_35178 2010 Sep 13 NY JEGX01.0004-W LTCF LTCF
10_35181 2010 Sep 13 NY JEGX01.0004-W LTCF LTCF
10_34601 2010 Sep 13 NY JEGX01.0004-W – LTCF
10_34213 2010 Sep 13 NY JEGX01.0004-B – –
10_33603 2010 Sep 14 NY JEGX01.0004-B – –
10_34599 2010 Sep 15 NY JEGX01.0004-W – Cluster A
10_35183 2010 Sep 16 CT JEGX01.0004-W LTCF LTCF
10_35184 2010 Sep 16 NY JEGX01.0004-AE – –
10_36119 2010 Sep 17 NY JEGX01.0004-W LTCF LTCF
10_34587 2010 Sep 20 NY JEGX01.0004-W – LTCF
10_35417 2010 Sep 22 NY JEGX01.0004-W – LTCF
10_36319 2010 Sep 28 NY JEGX01.0004-W – LTCF
10_37723 2010 Oct 4 NY JEGX01.0004-B – –
10_36979 2010 Oct 8 NY JEGX01.0004-W – LTCF
10_39087 2010 Oct 27 NY JEGX01.0004-B – –
10_38792 2010 Oct 29 NY JEGX01.0004-W – LTCF
11_03844 2011 Feb 1 NY JEGX01.0004-W – Cluster B
11_06235 2011 Feb 21 NY JEGX01.0004-W – Cluster A
11_21079 2011 Jul 13 NY JEGX01.0004-W – Cluster A
11_22186 2011 Jul 22 NY JEGX01.0004-W – Cluster B
11_27690 2011 Sep 6 NY JEGX01.0004-W – Cluster B
11_31312 2011 Oct 5 NY JEGX01.0004-W – Cluster B
11_30508 2011 Oct 9 NY JEGX01.0004-W – Cluster B
11_32014 2011 Oct 22 NY JEGX01.0004-W – Cluster B

*ID, identification; PFGE, pulsed-field gel electrophoresis; MLVA, multilocus variable-number tandem-repeat analysis; WGCA, whole-genome cluster analysis; NY, New York; –, sporadic outbreaks; LTCF, isolates assigned to long-term care facility outbreak; CT, Connecticut.
†The letter designating the New York MLVA type follows PulseNet PFGE pattern designation.
‡Cluster designations are indicated by boxes in Figure 1.

Main Article

Page created: July 18, 2014
Page updated: July 18, 2014
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The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.
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