Microbial Safety of Organic Fruits and Vegetables

Project Overview

Project Type: Research and Education
Funds awarded in 2003: $139,650.00
Projected End Date: 12/31/2006
Region: North Central
State: Minnesota
Project Coordinator:
Francisco Diez-Gonzalez
University of Minnesota

Annual Reports


  • Fruits: melons, apples, berries (other), berries (strawberries)
  • Vegetables: broccoli, cabbages, cucurbits, greens (leafy), peppers, tomatoes


  • Crop Production: conservation tillage
  • Education and Training: participatory research
  • Natural Resources/Environment: grass waterways
  • Pest Management: mulching - plastic, trap crops, traps
  • Production Systems: agroecosystems, permaculture
  • Soil Management: earthworms, green manures, organic matter, soil analysis


    Microbiological analyses of fruits and vegetables produced by farms in Minnesota and Wisconsin were conducted to determine coliform and Escherichia coli counts, and the presence of E. coli, Salmonella and E. coli O157:H7. During the 2003 and 2004 harvest seasons, 14 organic (certified by accredited organic agencies), 30 semi-organic (used organic practices but not certified) and 19 conventional farms were sampled to collect and analyze 2,029 pre-harvest produce samples (473 organic, 911 semi-organic, 645 conventional). E. coli prevalence was linked to certain farm management practices, collected through farmers’ surveys at the beginning of each of the two harvest seasons. Effect of the harvest months on E. coli prevalence was determined using generalized estimated equation model of logistic regression. The E. coli isolates were fingerprinted using pulsed filed gel electrophoresis, and the clonal diversity among isolates obtained from the same farm was determined. None of the produce samples had Salmonella or E. coli O157:H7 contamination in the two years of this study. E. coli contamination was detected in 8% of the samples, and leafy greens, lettuces and cabbages had significantly greater E. coli prevalence compared to all the other produce types in both years for the three farm types. Fertilization of produce with animal wastes increased the risk of fecal contamination significantly in both organic and semi-organic produce. Organic farmers who aged their animal manure for less than 6 months had 4-times greater risk of fecal contamination in their produce, compared those that aged for more than 6 months. The risk of contamination from the fecal indicator bacterium was significantly greater in June and July compared to August and September, irrespective of year of sampling, produce types and farm types. A wide diversity was observed among the E. coli isolates from the produce collected from different farms, and also among the isolates obtained from the same farm over the three years. These results have been presented at different scientific meetings and the most relevant results of the investigation have been sent to the participating farmers.


    Fresh fruits and vegetables, including fruit juices are essential components of the regular diet of any human group. Numerous evidence of health and nutritional benefits from the consumption of fresh fruits and vegetables has been documented in the literature (9, 14, 21). According to most agricultural economists, the sales of fresh-cut produce have increased sharply from approximately $3 billion in 1994 to $12.5 billion in 2004 (42). The U. S. Department of Agriculture (USDA) has recently emphasized the need for consumption of fresh produce by recommending at least five daily servings in the diet (6).

    In recent years, the sales of organic foods have increased at an annual average rate of 20% in the U. S., and most estimates suggest that the market expansion for organic foods will continue at the same rate for the next 5 years (8, 33). As much as 42% of the organic food sales are contributed by organic produce and 93% of which is in the form fresh fruits and vegetables (8). The USDA’s Organic Rule implemented in 2002, included the acceptable production practices for foods marketed as “organic” which largely limited the use of fertilizers to animal and plant wastes for vegetable crop production (32).

    In recent years, the number of foodborne outbreaks caused by contaminated fresh fruits and vegetables increased sharply. Produce accounts for 12% of foodborne illnesses and 6% of foodborne outbreaks today in the U. S., compared to 1% and 0.6%, respectively, in the 1970s (5). A report by Sivapalasingam et al. (36) suggested that the majority of produce-related foodborne outbreaks, for which the etiological agent(s) were identified, were caused by pathogenic bacteria. In the last 10 to15 years, Salmonella and Escherichia coli O157:H7 have been the two most common etiological agents responsible for produce-related outbreaks in this country. Published reports have documented outbreaks of Salmonella and E. coli O157:H7 infection from produce consumption in various states in the U. S., including Minnesota (13, 26).

    Because organic growers rely primarily on animal manure for fertilization of their soil, it has been suggested that organically grown foods have a greater risk of pathogenic contamination, compared to their conventional counterparts (38). However, there are very few published reports that have conducted microbial risk assessment studies of organic fruits and vegetables. In our previous study, the prevalence of Escherichia coli in certified organic produce at the pre-harvest stage was greater than their conventional counterpart, but this difference was not statistically significant (29). That study also reported that none of the pre-harvest certified organic and conventional produce tested positive for either Salmonella or E. coli O157:H7 and only two semi-organic samples had Salmonella contamination. Another study found similar levels of E. coli contamination in organic and conventional spring mix, and all samples were negative for Salmonella and Listeria monocytogenes (34). The issue whether organic produce poses a greater risk for foodborne disease, however, remains largely unresolved.

    Numerous reports have documented that animals such as cattle, sheep, pig and chicken are major reservoirs of foodborne pathogens such as E. coli O157:H7 and Salmonella (12, 24, 40). When farmers use manure from these animals for fertilization of produce plants, these pathogens might get transmitted to fruits and vegetables harvested from those plants (3). Such transmission was reported in lettuce when manure, inoculated with laboratory cultures of E. coli O157:H7, was used for fertilization of (37). Composting is an exothermic microbiological process, which generates high temperatures like 55 to 65C under proper conditions of aeration, moisture, particle size and carbon-to-nitrogen ratio for long enough duration that inactivates these foodborne pathogens (10). Published reports have documented the effectiveness of composting in destroying E. coli O157:H7 and Salmonella in cow manure (23). The USDA has specified composting techniques that organic growers are required to follow to minimize the risk of contamination from manure-based fertilizers (32). The USDA has also specified fertilization-to-harvest intervals that would reduce the chances of pathogen survival in non-composted manure. A few reports evaluated the effectiveness of such duration in minimizing risk of contamination in vegetables (16).

    A few surveys focusing on microbial quality of organic produce have also been reported in the literature. All these surveys focused on retail and post-harvest samples of organic vegetables, and none of these studies reported the presence of pathogenic bacteria such as Salmonella and E. coli O157:H7 in organic produce (22, 25, 35). Outbreaks of infection from foodborne pathogens in contaminated organic produce have not been documented in the U. S. to date. The generation of data on comparative microbiological quality and safety of organic and conventional produce at farms would greatly enhance our understanding of factors that contribute to contamination of fresh fruits and vegetables. The reports available in the literature have documented the survival of contaminating bacteria in manure and in manure-amended soil (7, 15). Other laboratory and garden-scale studies have evaluated the effects of manure treatment and application to soil on the survival of pathogenic and fecal indicator bacteria in agricultural soil and vegetables grown in such soils (17).

    In the United States, the number of foodborne outbreaks from produce consumption reaches the maximum during the summer months, while in the winter, such outbreaks occur less frequently (31). In Minnesota, a consistent seasonality pattern in the number of outbreaks of foodborne Escherichia coli O157:H7 infection has been reported (2). Published reports on microbiological quality of fresh fruits and vegetables have not focused on variation in contamination during different months of the year. In a study on organic leaf lettuce in Norway, the samples were collected in July, August, September and October, 2001 (22). They reported counts of thermo tolerant coliform and E. coli, and E. coli prevalence in the samples collected during those months, but it was a study with one year of sampling, and did not report variation in the counts and prevalence across the four months of the study. In another report, microbiological quality of organic and conventional spring mixes were compared (34). Sampling was done in one year, during the four months of April to August. Like the previous report, that study also did not focus on variation in microbiological counts during the four months. A larger study involved 398 samples of leafy greens, herbs and cantaloupes collected from farm during a longer period of November 2000 to May 2002 (20). Although this report involved samples collected during a period more than a year, they did not report the variation in bacteria; counts and prevalence during these months of the study.

    Recently, Ishii et al. (18) and Byappanahalli et al. (4) reported the survival and subsequent naturalization of Escherichia coli in temperate soils of watersheds of various lakes. Both of these reports determined that E. coli can persist in these environmental niches for months, and even for a year, and eventually become a natural habitat of the environment. The persistence of E. coli in an environment such as farms producing fruits and vegetables has not been studied.

    Project objectives:

    A. Project Objectives
    The specific objectives of this proposal are to:
    1) Determine the presence of fecal indicator organisms (coliforms, Escherichia coli) and pathogens (E. coli O157:H7, Salmonella) in organic and conventional fruits and vegetables produced by farmers in Minnesota and Wisconsin at the preharvest stage.
    2) Conduct trace-back investigations in participating organic farms by comparisons of bacterial strains isolated from environmental samples and those isolated from produce
    3) Identify potentially high-risk management practices and provide recommendations for improvement
    4) Disseminate results and findings among the agricultural community.

    B. Project Outcomes
    1) A quantitative and comparative microbial risk assessment of fresh fruits and vegetables produced by organic farms.
    2) A series of improvements in management practices such as modifications in manure type, proper use of composting and time of application of organic fertilizers that will eventually reduce the risk of microbial contamination and produce safer fruits and vegetables.
    3) Enhanced farmers’ awareness regarding application of manure fertilizer, irrigation water and the rationale for composting requirements.
    4) Increased confidence of those farmers already using practices linked to low microbial loads and better safety of their produce.
    5) Strengthen organic agriculture by providing the basis for enhanced consumer confidence that might lead to increased demand.
    6) Help solving the long-standing debate on the microbial safety of the organic fruits and vegetables for the scientific community and the society in general.

    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 U.S. Department of Agriculture or SARE.