Organic agricultural production benefits from the use of animal manure to improve soil quality and health. Despite its proven benefits, using manure poses some risk to food safety as it may contain pathogenic microorganisms that can contaminate produce and lead to foodborne human illnesses. To investigate risk factors associated with generic E. coli presence in fresh produce grown in manured soil, a two-year study was conducted in USDA National Organic Program-certified organic farms in California, Maine, Minnesota, and Maryland. Farm management, water, environmental, and soil−related factors were ranked using random forest and then assessed in a generalized linear mixed model to evaluate the associations with generic E. coli presence in produce. Factors that significantly increased the odds of generic E. coli presence included increased precipitation over the past 7 days of produce sampling (Odds Ratio (OR) = 1.32, CI 95 = 1.14–1.52), and previous nonagricultural use of crop fields (OR = 48.16, CI 95 = 15.19– 152.67). Leafy greens (OR = 12.82, CI95 = 4.90–33.54) and root vegetables (OR = 19.56, CI95 = 6.11–62.61) had significantly higher odds of generic E. coli presence compared to fruits. Length of time (in days) between manure application and produce sampling also significantly influenced generic E. coli presence odds on Day 60 after manure amendment (OR = 0.04, CI 95 = 0.01–0.17). Higher odds ratio of generic E. coli presence was significantly associated with exclusive manure application in summer (OR = 38.98, CI 95 = 10.05–151.18), fall (OR = 5.89, CI 95 = 1.32–26.14), or winter(OR = 24.95, CI 95 = 2.85–219.08) compared to multiseason application. These findings provide evidence to inform manure application practices and food safety management strategies in organic fresh produce production.
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