Microbial Safety of Organic Fruits and Vegetables

2005 Annual Report for LNC03-231

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

Microbial Safety of Organic Fruits and Vegetables


A comparative microbial risk assessment of fresh produce grown by organic and conventional farms in the Upper Midwest was conducted based on data analysis of the detection of generic Escherichia coli in fresh produce collected during the previous two years. Additional statistical analysis has indicated that the prevalence of this indicator microorganism per produce variety was not different between organic and conventional produce. Among produce varieties, leafy greens, lettuces and cabbages had significantly greater E. coli prevalence compared to all other produce types in both years for the different farm types.

Objectives/Performance Targets

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.


Objective 1)
The activities leading to this objective have been completed and for the most part this objective was accomplished as proposed. During the harvest seasons 2003 and 2004, a total of 64 farmers participated in this project by allowing us to collect samples of lettuce, tomatoes, cabbage, leafy greens, strawberries, raspberries, broccoli, cucumbers, squash, apples, zucchini and other produce from their fields, and by answering farm management practices surveys. From that total, 14 farmers reported using organic practices that were certified by an accredited agency (organic farmers), 24 growers indicated using organic practices but they were not certified (semi-organic), and 26 farmers accounted the use of conventional agricultural practices (conventional farmers).

During the harvest seasons from May to September each farmer was visited from 1 to 4 times depending on the availability of crops, and three individual samples of each produce variety were collected. The number of samples from certified organic, semi-organic, and conventional farmers were for 2003: 178, 372 and 297, respectively; for 2004: 289, 539 and 348, respectively. The total number of samples was 2,029. The produce varieties that accounted for most of the samples were: leafy greens (other than lettuce), 14.5%; peppers (green, yellow, bell), 13.8%; tomatoes, 11.7%; cabbage, 9.8%; cucumber, 8.9%; zucchini, 7.6%; and lettuce, 7.4%.

The results of the microbiological analyses of these samples were as follows:

A. Coliform determination

Coliform bacteria were detected in approximately 70% of the semi-organic fruits and vegetables in each of the two years of sampling. Among organic produce, 84% in 2003 and 80% in 2004 were coliform-positive samples. For conventional produce, 75% in 2003 and 64% in 2004 were positive for the presence of coliforms. In the two years of this study, the average coliform counts for any of the types of farm ranged from 1.5 to 2.3 log MPN/g. Conventional produce had significantly less coliform levels than organic and semi-organic produce in 2003, but in 2004 this difference was only significant for semi-organic samples. From a subset of 826 samples positive for coliforms, Enterobacter spp. was detected in 58% and Klebsiella spp. was identified in 28%. Ent. cloacae and K. oxytoca were the two predominant coliform species.

B. Escherichia coli prevalence

The majority of the produce samples did not have detectable levels of Escherichia coli contamination. In the two years of sampling, 68 (8%) of semi-organic samples and 34 (7%) of organic fruits and vegetables had detectable levels of E. coli contamination at farms. For conventional produce, as many as 13 (2%) samples tested positive for this fecal indicator bacteria. Among the 24 participating semi-organic farms, 11 farms in 2003 and 14 in 2004 had at least one E. coli contaminated produce samples. Four of the 14 organic farms in 2003 and 7 of the 8 organic farms in 2004 had at least one E. coli contaminated sample. Among the conventional growers, 3 out of 19 in 2003 and 5 of the 14 in 2004 had at least one E. coli-positive produce sample.

The prevalence of E. coli in those farms, which had at least one contaminated produce sample, ranged from 3.7 to 50% in 18 of the 57 participating farms in 2003, and from 1.4 to 50% in 26 of the 46 participating farms in 2004. In the year 2003, the E. coli prevalence in semi-organic farms varied from 4.8% to 50%, while the prevalence in organic farms was within a narrower range of 11% to 33%. The prevalence of the fecal indicator in conventional farms was never greater than 7% in 2003. In 2004, E. coli prevalence in semi-organic farms ranged from 2 to 50%, while the prevalence in organic farms varied from 1 to 24%. The prevalence in conventional farms in 2004 varied within a wider range of 3 to 38%, compared to the prevalence range among this farm type in 2003.

The prevalence of E. coli in leafy green samples from semi-organic and conventional farms was as much as 3-fold greater than that in organic samples. However, only the difference between the prevalence in semi-organic leafy greens in 2003 was significantly greater than that in the organic ones. When the prevalence for leafy greens was compared among the three farm types for both years combined, the E. coli prevalence in semi-organic (18%) and conventional (24%) leafy greens had significantly greater than the organic (8%) counterparts (P < 0.05). The E. coli prevalence in lettuce ranged from 0% in conventional samples in 2003 to 25% in the same type of farms for 2004 (Table 6). The prevalence in semi-organic cabbages was approximately 2 to 4-times the prevalence in conventional cabbages, for both years. However, these differences were not statistically significant. Organic cucumbers had 8 to 12% E. coli prevalence, which was approximately 2 to 4-times the prevalence in semi-organic cucumbers. This difference in prevalence was not statistically significant. None of the semi-organic, organic and conventional tomatoes had E. coli contamination, in either 2003 or 2004. C. Salmonella and Escherichia coli O157:H7
None of the produce samples analyzed in this project tested positive for any of these bacteria.

Objective 2)
In the spring and fall seasons, samples of soil, manure, compost and water were collected in selected farms that had vegetables positive for E. coli, and were subjected to microbiological analysis. From a total of 80 samples, 8 were positive for this bacterium. Using DNA fingerprinting analysis, we ware able to determine that none of these environmental isolates were related to any of the strains obtained from produce. A similar analysis has identified the same strain isolated from the same farm from two different samples, but has suggested that each isolate was unique per sampling date and farm.

Objective 3)
Since there were no samples positive for the pathogenic bacteria, this objective will be focused on identify management practices linked to E. coli prevalence as an indicator of fecal contamination. In addition to the E. coli prevalence data, we have gathered information about the management practices from most of the farmers for each of the seasons. This information was obtained by mailing a detailed questionnaire that asked about: years in production, crops grown (rotation used), markets, certification agency, specific requirements for fertilization and handling, type of fertilizers, manure sources, composting practices (materials, method, duration, amount applied, timing of applications), harvesting method, and handling practices.

The data is being clustered according the management practices and potential links between them and E. coli prevalence will be identified using statistical analysis. The graduate student working in this project has completed most of his training in advanced statistical analysis tools and we will be conducting this analysis. Because of the complexity of the data, it is critical to employ the most suitable statistics.

Because there were more certified organic and non-certified farmers that used manure or composted manure (90 and 60%, respectively), as compared to conventional farmers (40%), it appeared that the greater prevalence of E. coli was linked to the increased used of animal compost or manure as fertilizer. However, the influence of the larger numbers of produce needs to be factored into the analysis to determine if manure use is indeed responsible for the greater E. coli-positive samples.

Objective 4)
We have communicated directly with each of the participating farmers reporting their individual results and the overall season results after each season. Disseminating the results to the agricultural community will not be done until the risk assessment of management practices is completed. Unfortunately, we have not been very successful in attracting the participating farmers to a meeting. Once we have the risk assessment study based on the statistical comparisons we plan to have a gathering with farmers.

To the scientific community, we presented partial results of season 2003 at the World Congress of Organic Foods, at the Global Good Agricultural Practices Conference in early 2005 and at the International Association for Food Protection Annual meeting in August of last year. We expect to complete the project website early in 2006.
After a previous study similar to this project was published in 2004, our work received considerable attention from the media, and specially form organic and sustainable agriculture websites. We expect that once the results of this project are made public, there will be great interest from the agricultural, scientific and consumer communities.

Project Outcomes
All of the outcomes depend on the completion of objectives 3 and 4 above. In the meantime we have sent for publication to the Journal of Food Protection the first manuscript of this project:
Mukherjee, A., D. Speh, A. T. Jones, K. M.Buesing,1 L. T. L. Xiong,1 and F. Diez-Gonzalez. 2006. (submitted on 1/16/06). Longitudinal microbiological survey of fresh produce grown by farmers in the Upper Midwest. J. Food Prot.

Impacts and Contributions/Outcomes

Because of the limited dissemination of results described above the impact of this particular project has only been felt by the farmers who have participated in the study.
Several of them have benefited by the increased confidence of knowing that their products have consistently tested free from any pathogenic and even fecal indicator bacteria. The level of awareness on food safety among those farmers has also been a positive outcome of this project. We expect that once the final analyses are completed we will be able to reach to a broader audience.


Pauline Nickel

Southwest Research and Outreach Center
23669 130th St.
P. O. Box 428
Lamberton, MN 56152
Dorinda Speh

Research Plot Technician
Southwest Research and Outreach Center
23669 130th St.
P. O. Box 428
St. Paul, MN 56152
Avik Mukherjee

Graduate Research Assistant
University of Minnesota
Department of Food Science and Nutrition
1334 Eckles Avenue
St. Paul, MN 55108