Table 1

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 Deng

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

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

Isolate	Outbreak		Phylogenetic reference†			Population group	Phylogeny prediction	RF prediction
Isolate	Year	Confirmed vehicle	Isolate	Year	Source	Population group	Phylogeny prediction	RF prediction
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.

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Page created: December 18, 2018

Page updated: December 18, 2018

Page reviewed: December 18, 2018

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