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Volume 25, Number 1—January 2019
Research

Zoonotic Source Attribution of Salmonella enterica Serotype Typhimurium Using Genomic Surveillance Data, United States

Shaokang Zhang, Shaoting Li, Weidong Gu, Henk den Bakker, Dave Boxrud, Angie Taylor, Chandler Roe, Elizabeth Driebe, David M. Engelthaler, Marc Allard, Eric Brown, Patrick McDermott, Shaohua Zhao, Beau B. Bruce, Eija Trees, Patricia I. Fields, and Xiangyu DengComments to Author 
Author affiliations: University of Georgia Center for Food Safety, Griffin, Georgia, USA (S. Zhang, S. Li, H. den Bakker, X. Deng); Centers for Disease Control and Prevention, Atlanta, Georgia, USA (W. Gu, B.B. Bruce, E. Trees, P.I. Fields); Minnesota Department of Health, St. Paul, Minnesota, USA (D. Boxrud, A. Taylor); Translational Genomics Research Institute, Flagstaff, Arizona, USA (C. Roe, E. Driebe, D.M. Engelthaler); US Food and Drug Administration, College Park, Maryland, USA (M. Allard, E.W. Brown); US Food and Drug Administration, Laurel, Maryland, USA (P. McDermott, S. Zhao)

Main Article

Table 1

Retrospective source attribution of zoonotic outbreaks of Salmonella enterica serotype Typhimurium, United States*

Isolate
 Outbreak
Phylogenetic reference† Population group
 Phylogeny prediction
 RF prediction
Year
 Confirmed vehicle
 Isolate
 Year
 Source
STM2207 2013 Ground beef STM296 2006 Bovine G9 + +
STM2208 2013 Ground beef STM296 2006 Bovine G9 + +
STM2209 2007 Pot pie turkey STM093 2005 Poultry G7 + +
STM2210 2007 Pot pie turkey STM093 2005 Poultry G7 + +
STM2211 2007 Pot pie turkey STM093 2005 Poultry G7 + +
STM2212 2007 Pot pie turkey STM093 2005 Poultry G7 + +
STM2213 2013 Live poultry STM2114 2016 Bovine G7 – +
STM2214 2013 Live poultry STM2114 2016 Bovine G7 – +
STM2215 2011 Ground beef STM1563 2011 Bovine G6 + +
STM2216 2011 Ground beef STM1563 2011 Bovine G6 + +
STM2217 2015 Pork STM2116 2016 Swine G2a + +
STM1016 2010 Cattle contact STM328 2008 Bovine G9 + +
STM1075 2010 Cattle contact STM978 2010 Bovine G2a + +
STM995 2010 Cattle contact STM978 2010 Bovine G2a + –
STM996 2010 Cattle contact STM978 2010 Bovine G2a + –
STM1065 1998 Raw milk STM034 2004 Bovine G9 + +
STM988 2009 Chicken STM1975 2015 Bovine G9 – +

*RF, Random Forest; +, correct prediction; –, incorrect prediction.
†The livestock genome that had the most recent common ancestor with an outbreak query genome.

Main Article

Page created: December 18, 2018
Page updated: December 18, 2018
Page reviewed: December 18, 2018
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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