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Volume 31, Number 4—April 2025
Research

Attribution of Salmonella enterica to Food Sources by Using Whole-Genome Sequencing Data

Erica Billig Rose1, Molly K. Steele1Comments to Author , Beth Tolar, James Pettengill, Michael Batz, Michael Bazaco, Berhanu Tameru, Zhaohui Cui, Rebecca L. Lindsey, Mustafa Simmons, Jess Chen, Drew Posny, Heather Carleton, and Beau B. Bruce
Author affiliation: Centers for Disease Control and Prevention Atlanta, Georgia, USA (E.B. Rose, M.K. Steele, B. Tolar, Z. Cui, R.L. Lindsey, J. Chen, H. Carleton, B.B. Bruce); US Food and Drug Administration, College Park, Maryland, USA (J. Pettengill, M. Batz, M. Bazaco); US Department of Agriculture, Washington, DC, USA (B. Tameru, M. Simmons, D. Posny)

Main Article

Table 1

Number of Salmonella isolates used to train a random forest model by food commodity, location of collection (domestic vs. international sampling) and, if domestic, entity that collected the isolate, 2003–2018*†

Category Domestic sampling‡
 International§ Missing location Total
FSIS NARMS FDA/CFSAN Other Total
Chicken 1,477 1,010 3,075 31 5,593 168 72 5,833 (31)
Vegetables NA NA 1,284 42 1,326 1,055 9 2,390 (13)
Turkey 121 486 1,630 33 2,270 6 12 2,288 (12)
Pork 362 1,226 238 67 1,893 121 12 2,026 (11)
Beef 344 597 628 34 1,603 77 3 1,683 (9)
Fish 13 NA 47 1 61 984 2 1,047 (6)
Nuts/seeds NA NA 415 4 419 516 12 947 (5)
Fruit NA NA 151 9 160 532 6 698 (4)
Shellfish NA NA 20 NA 20 527 10 557 (3)
Egg 266 NA 60 15 341 32 11 384 (2)
Other poultry 52 NA 43 13 108 94 3 205 (1)
Other meat NA NA 80 2 82 112 2 196 (1)
Grains/beans NA NA 124 NA 124 40 6 170 (1)
Dairy NA NA 74 7 81 71 7 159 (1)
Game
 NA
 NA
 63
 NA
 63
 15
 NA
 78 (<1)
Total 2,635 (14) 3,319 (18) 7,932 (43) 258 (1) 14,144 4,350 (23) 167 (<1) 18,661

*Values are no. or no. (%). CDC, Centers for Disease Control and Prevention; CFSAN, Center for Food Safety and Applied Nutrition; FDA, Food and Drug Administration; FSIS, Food Safety Inspection Service; HACCP, Hazard Analysis and Critical Control Point; NA, not available; NARMS, National Antimicrobial Resistance Monitoring System; USDA–ARS, US Department of Agriculture’s Agricultural Research Service. †Includes 603 isolates collected prior to 2003. ‡Domestic sampling by various agencies and programs: FSIS (HACCP, baselines, exploratory), NARMS (FSIS and FDA), FDA CFSAN (including GenomeTrakr Network), and other (CDC PulseNet, USDA–ARS, university laboratories, and state laboratories). §International includes isolates from nondomestic GenomeTrakr laboratories.

Main Article

1These first authors contributed equally to this article.

Page created: March 02, 2025
Page updated: March 24, 2025
Page reviewed: March 24, 2025
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