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. Wolfgang
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.
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