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Publication #SL375

Salmonella and Pathogenic E. coli in the Crop Production Environment: Potential Sources, Survival, and Management1

Max Teplitski, Andree George, and George Hochmuth2


Over the last two decades, at least a dozen major outbreaks of gastroenteritis caused by non-typhoidal Salmonella or enterovirulent E. coli have been linked to the consumption of sprouts, nuts, and fresh (or minimally processed) fruits and vegetables.1 These outbreaks caught scientists and the public off guard because these pathogens were not previously considered “plant-associated.” This EDIS publication highlights recent discoveries that focus on the ecology of human pathogens in the crop production environment. A better understanding of how pathogens persist outside of animal hosts in agricultural water, soils, and plants will have major impacts on managing produce safety from “farm to fork.”

Most Salmonella and pathogenic E. coli can infect humans, domestic animals, and most wild animals. However, the majority of E. coli strains are non-pathogenic, normally reside in the healthy human intestine, and are required to maintain proper conditions for the function of other beneficial microorganisms of the gut. Nevertheless, virulent strains of E. coli, namely O157:H7, O104, O121 (and a few others) have been associated with outbreaks of foodborne illness. What are the sources of these pathogens in the crop production environment? How prevalent are these pathogens in wild animals and environmental samples? How does this knowledge affect our approach to produce safety? Having answers to these questions will better enable us to protect against foodborne illness caused by Salmonella and E. coli.

Domestic and Wild Animals as Vectors of Human Pathogens

Salmonella and pathogenic E. coli have been commonly isolated from beef and dairy cattle. In three surveys, between 13%–100% of cattle were found to harbor either E. coli O157:H7 or Salmonella.1, 2 In contrast, a recent survey of free-range cattle in the leafy green production areas in California reported only one positive test for the pathogens in >700 samples.3 There is no clear reason for the discrepancy between these studies; however, the husbandry practices associated with free-range cattle may discourage the introduction and spread of E. coli O157:H7 through herds. Regardless of the underlying causes for these differences, these results demonstrate that not all cattle herds will have a similarly high rate of carrying the human pathogen and that risks to produce safety associated with proximity to beef or dairy operations should be established on a case-by-case basis using scientifically valid data.

Between 13%–23.4% of feral swine tested positive for the same pathogens in two surveys, and feral swine have the second highest incidence of carrying pathogenic E. coli.4 White-tailed deer are less of a concern than feral pigs, but they still can carry pathogenic E. coli (0.5%–2.4% of samples taken) and Salmonella (7% of samples), so they could pose a risk when cattle ranges are accessible to deer.1, 5 No clear consensus exists on which wildlife species are consistent carriers of Salmonella. Sparrows, towhee, and crows, as well as feral pigs, coyotes, deer, elk, opossum and skunk, all tested positive for Salmonella in one study, while mice, rabbits, raccoons, squirrels, blackbirds, geese, mallards, and starlings all tested negative.3 Therefore, wild or domestic animals intruding into production fields may increase the risk of produce contamination, but the extent of the increase in risk is hard to quantify.

Improperly Treated Wastes as a Source of Human Pathogens

Animal and human wastes are important reservoirs of pathogens. Farm runoff contaminated with E. coli O157:H7 and other bacteria has been linked to outbreaks of illness. Therefore, developing strategies to reduce or eliminate pathogens in farm wastes is crucial to prevent contamination. When composting animal waste, maintaining the temperature at 160–170°F for 2–3 weeks is effective against E. coli and Salmonella, as is forced aeration or manual turning of compost (which promotes increased alkaline reaction). Regardless of the composting method, wastes and liquid runoff should be contained during the first 2–5 weeks of composting to prevent bacteria from seeping into groundwater, where Salmonella can survive for months. Preventing liquid wastes from running off into surface water reservoirs is especially important, as mounting evidence suggests that Salmonella can easily multiply in surface waters during warm months.

The role of different livestock bedding materials in survival of Salmonella and E. coli is unclear. On-farm studies at the Ohio State University found fewer E. coli bacteria in cattle raised on sand bedding (compared to wood shavings), while a German study reported no difference in Salmonella numbers isolated from broiler poultry raised on wood-shaving bedding or on plastic “trampoline” floors. Other factors, like moisture content of different bedding materials, bedding temperature, processing, aeration, etc., may also complicate how bedding impacts the survival of these pathogens.

Surveys of Microbiological Water Quality

Contaminated water has the potential to contaminate fresh produce at various points in the production cycle. Therefore, microbiological water quality must be ensured at all points in the production cycle. Surveys of water quality in major vegetable production regions suggest that well/irrigation water is free of human pathogens.4 Surface waters, however, can have a significantly higher rate of pathogen isolation. In California, ~3% of surface water samples tested positive for pathogenic E. coli, and over 7% tested positive for Salmonella.3 In the southeastern United States (North Carolina, Georgia, and Florida), incidence of Salmonella in surface water samples is nearly an order of magnitude greater than in California.6 Depending on the production region, using untreated surface waters for crop irrigation or produce washes poses a significant food safety risk.


Fruit and vegetable fields normally harbor microorganisms, and in less than 1% of the samples, these produce-associated microbial communities may contain human pathogens, like Salmonella and pathogenic E. coli. Promoting microbiological safety of produce is an important goal. Understanding how human pathogens are introduced into the vegetable production environment can help identify critical points where loads of pathogens could be significantly reduced. Intrusions of wild and domestic animals can contaminate produce in the field, but the risk is not uniform. No animal can be singled out as the most common vector of the pathogens. Depending on the crop production region, untreated surface waters (but not well/irrigation water) may pose a risk of contaminating produce. Therefore, rigorous water testing and disinfection protocols must be in place.


1 R. Mandrell, "Enteric Human Pathogens Associated with Fresh Produce: Sources, Transport, and Ecology," in Microbial Safety of Fresh Produce, ed. X. Fan (Ames, Iowa: Blackwell Publishing, 2009).

2 T.P. Stephens, G.H. Loneragan, T.W. Thompson, A. Sridrara, L.A. Branham, S. Pitchiah, and M.M. Brashears, "Distribution of Escherichia coli O157 and Salmonella on Hide Surfaces, the Oral Cavity, and in Feces of Feedlot Cattle," Journal of Food Protection 70, no. 6 (2007):1346-49.

3 L. Gorski, C.T. Parker, A. Liang, M.B. Cooley, M.T. Jay-Russell, A.G. Gordus, E.R. Atwill, and R.E. Mandrell, "Prevalence, Distribution, and Diversity of Salmonella enterica in a Major Produce Region of California," Appl Environ Microbiol 77, no. 8 (2011):2734-48.

4 M.T. Jay, M. Cooley, D. Carychao, G.W. Wiscomb, R.A. Sweitzer, L. Crawford-Miksza, J.A. Farrar, D.K. Lau, J. O'Connell, and A. Millington, "Escherichia coli O157:H7 in Feral Swine near Spinach Fields and Cattle, Central California Coast," Emerging Infectious Diseases 13, no. 12 (2007):1908-11.

5 J.M. Sargeant, D.J. Hafer, J.R. Gillespie, R.D. Oberst, and S.J. Flood, "Prevalence of Escherichia coli O157:H7 in White-tailed Deer Sharing Rangeland with Cattle," Journal of the American Veterinary Medical Association 215, no. 6 (1999):792-94.

6 M. Rajabi, M. Jones, M. Hubbard, G. Rodrick, and A.C. Wright, "Distribution and Genetic Diversity of Salmonella enterica in the Upper Suwannee River." International Journal of Microbiology (2011):461321.


This material is based on Project 23 (“A Safe Harvest”) supported by the Florida Department of Agriculture and Consumer Services, under Specialty Crop Block Grant Funding, contract #16858. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the Florida Department of Agriculture and Consumer Services.



This document is SL375, one of a series of the Soil and Water Science Department, UF/IFAS Extension. Original publication date October 2012. Reviewed August 2015. Visit the EDIS website at


Max Teplitski, associate professor; Andree George, PhD student and McKnight Fellow; and George Hochmuth, professor, Soil and Water Science Department; UF/IFAS Extension, Gainesville, FL 32611.

The Institute of Food and Agricultural Sciences (IFAS) is an Equal Opportunity Institution authorized to provide research, educational information and other services only to individuals and institutions that function with non-discrimination with respect to race, creed, color, religion, age, disability, sex, sexual orientation, marital status, national origin, political opinions or affiliations. For more information on obtaining other UF/IFAS Extension publications, contact your county's UF/IFAS Extension office.

U.S. Department of Agriculture, UF/IFAS Extension Service, University of Florida, IFAS, Florida A & M University Cooperative Extension Program, and Boards of County Commissioners Cooperating. Nick T. Place, dean for UF/IFAS Extension.