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Volume 25, Number 1—January 2019

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 2

Selected key genetic features for zoonotic source prediction of Salmonella enterica serotype Typhimurium using a Random Forest classifier

Feature rank* Affected gene Feature type Gene function (reference)
1 fliC Single-nucleotide polymorphism Motility, serotype diversity, intestinal colonization (16)
5 traA Accessory gene Pilin precursor. intestinal colonization (16)
6 spvB Accessory gene Virulence (17), intestinal colonization (16)
9 1930† Accessory gene Intestinal colonization (16)
11 1874† Indel Intestinal colonization (16)
13–15, 28 cusCFBA Accessory gene Putative copper efflux system (18)
16 silP Accessory gene Silver efflux pump (17)
21 yafA Accessory gene Intestinal colonization (16)
24 sspH2 Accessory gene Virulence and potential host range factor (19)
27 0286A† Accessory gene Intestinal colonization (16)
31 pipB2 Accessory gene Virulence (20)
32 proQ Accessory gene Global posttranscription regulation (21), intestinal colonization (16)
34 spvD Accessory gene Virulence (22)
37 Trap Accessory gene Intestinal colonization (16)
39 yhfL Indel Intestinal colonization (16)
41 0835† Accessory gene Intestinal colonization (16)
43 traJ Accessory gene Intestinal colonization (16)
45 yceA Accessory gene Intestinal colonization (16)
46 exc Accessory gene Intestinal colonization (16)

*Features are ranked by the mean decrease of prediction accuracy through randomly permuting values of the feature. The larger the mean decrease, the higher the rank. Only features that are located in genes that have reported involvement in intestinal colonization, virulence, and other functions related to livestock environment adaptation are listed. The full list of analyzed features, including the top 50 for zoonotic source prediction, is provided in Appendix 1 Table 6. Indel, insertion/deletion.
†Locus identification of the reference genome SL1344.

Main Article

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