Helping Small-Scale and Socially Disadvantaged Growers in Improving Microbial Quality of Irrigation Water in Kentucky

Abstract

Water plays a critical role in the growth and management of fresh produce, being a vital resource and a potential vector for pathogens. To address these concerns, guidelines for the microbiological quality of treated wastewater, recreational, irrigation, and drinking water have been established worldwide. With multiple outbreaks linked to Escherichia coli (E. coli) contamination, monitoring and improving water quality standards have become essential, especially for small-scale and limited-resource farmers. The Food Safety and Modernization Act (FSMA, 2014) in the United States was introduced to regulate microbiological safety of produce, focusing on irrigation water. Approximately 77% of farmers in Kentucky are small farmers, of which, 4.2% supply directly to consumers through various avenues, accounting for approximately USD 24 million a year. This study examined the microbial quality of irrigation water used in Kentucky, focusing on the presence and number of coliform bacteria and E. coli. The report covers findings from a year-long program providing free microbial water quality testing to producers (n = 90), analyzing groundwater and surface water samples (n = 296). Results indicate surface water showing a significantly higher risk of exceeding FSMA thresholds. The findings emphasize the need for continued outreach, education, and accessible testing resources to support compliance with evolving Produce Safety Rule regulations, especially among small-scale producers.

1. Introduction

Water is a key ingredient in the healthy and safe growth and management of produce, but it can also be a means for entry and growth of pathogens [1]. The microbial water quality used in irrigation and post-harvest washing, in particular, are sources of importance, as they have been identified as key ways in which various pathogens can potentially contaminate fresh produce [2,3]. In the United States, an outbreak of E. coli O157:H7 occurred in 2018 across multiple states involving romaine lettuce, the source of which was traced to the use of contaminated post-harvest water. In all, 210 people were infected, 96 hospitalized, and 5 deaths were reported [4]. More than 25 other foodborne outbreaks have been reported since 2018. Of those, almost half were connected with the consumption of contaminated produce involving various strains of E. coli [5].

Surface water is substantially used as the source of irrigation water. It can become contaminated with microorganisms that are washed into as runoff from various sources and pathways, such as agricultural waste, domestic and wildlife waste, and manure from storage areas, rangelands, pastures, and feedlots [6]. Groundwater and rainwater have a relatively lower probability of microbial contamination than surface water, but pathogens still have a chance to contaminate the water source through various means, including sewage overflows, polluted stormwater runoff, and agricultural runoff [7,8,9].

Good Agricultural Practices (GAPs) and Good Handling Practices (GHPs) are essential to minimize microbial food safety risks in all the steps involved in producing fresh produce. Sound training and compliance with GAPs and GHPs help mitigate pathogens from entering the produce. However, the application of GAPs alone is not enough to ensure safety, partly due to the open nature of farming in general. Noncompliance with GAPs and GHPs at any stage in production, harvesting, and processing serves as an opportunity for the introduction of potential biological contamination.

Fresh produce belongs to the ‘ready to eat’ category of foods, which require minimal processing. According to the 2022 U.S. Agricultural Census, Kentucky has approximately 69,425 individual farms, averaging 179 acres each. Of those, about 2944 farms supply food sold directly to the consumer, valued at more than USD 24 million in 2022 [10]. Market value monitoring has shown that these agricultural sales have increased 53% from 2002 to 2022 [11]. This increasing direct producer-to-consumer exchange may proportionately increase the risk of contamination, leading to potential illnesses and outbreaks. Medium- and large-scale farms were mandated by earlier versions of the FSMA to comply by requiring a farm safety plan and implementing GAPs, as well as periodical inspections of the operations. Furthermore, produce generated from such operations normally goes through microbial quality checks before it enters the market.

Treated wastewater, recreational, irrigation, and drinking water are all vulnerable to potential microbial contamination. International organizations, such as the World Health Organization (WHO) and European Union (EU), and various independent countries have established guidelines with reference to E. coli count in various sources of water through suitable legislation (

Table 1. Guidelines and legislation for the microbiological quality of treated wastewater, recreational water, irrigation water, and drinking water.

Country/Region	Criteria (CFU/100 mL) a	Document Type	Reference(s)
Treated Wastewater
WHO (unrestricted) b		Guideline	[12]
Root crops c	≤103 E. coli
Leaf crops d	≤104 E. coli
Drip irrigation, high-growing crops e	≤105 E. coli
Drip irrigation, low-growing crops f	≤103 E. coli
Italy	<10 E. coli and absence of Salmonella	Regulation	[3,13]
Spain	<100 E. coli	Regulation	[3,14]
Recreational Waters (coastal and fresh waters)
WHO	<500 enterococci	Guideline	[15]
EU g	Inland waters: <330 enterococci or <900 E. coli Coastal and transitional waters: <185 enterococci or <500 E. coli	Guideline	[16]
United States	<35 enterococci or <126 E. coli	Guideline	[17]
Irrigation water (for all water types)
Canada	<100 fecal coliforms	Guideline	[3,18]
Canada (British Columbia)	200 fecal coliforms	Guideline	[3,18]
EU	Between 100 and 10,000 E. coli	Guideline	[19]
Drinking Water
WHO	<1 E. coli	Guideline	[20]
EU	0 E. coli	Directive	[21]
The Netherlands	0 E. coli	Decree	[22]
United States	0 E. coli	Regulation	[23]

^a Unless stated other; ^b the use of treated wastewater to grow crops usually eaten raw; ^c that may be eaten uncooked; ^d nonrooted salad crops, including vegetables eaten uncooked, e.g., lettuce, cabbage; ^e crops that are grown above ground that generally do not touch the soil, e.g., fruit trees, olives; ^f nonrooted crops grown low or near the soil surface; ^g EU, European Union.

).

In the US, the Food Safety and Modernization Act (FSMA) of 2014 mandated monitoring of the microbiological quality of irrigation water for individuals and organizations involved in all fresh produce production. The FSMA set forth provisions that allowed small farms that average USD 25,000 or less per year for three years in fresh produce sales to be exempt from maintaining farm safety certification. In general, these farms make up a large portion of the producers who sell directly to consumers, specifically in smaller states such as Kentucky [24].

In 2016, as part of the FSMA, the Produce Safety Rule (PSR) was enacted. In its original version, the PSR mandated scientifically based regulations regarding the microbial and sanitary quality of agricultural water [25]. Agricultural water is defined as “water that is intended to or is likely to contact the harvestable portion of covered produce or food-contact surfaces” [24]. This includes water used in production during the growth and care of the produce and post-harvest water used during or after harvest. Before the introduction of this version of the PSR, the produce industry was held to a more voluntary monitoring system provided by the Food and Drug Administration (FDA) [25].

In 2015, the population of Kentucky consumed 4.3 billion gallons of water daily. Approximately 95% of this water usage was from surface water such as from streams, rivers, lakes, ponds, and cisterns. The remaining 5% of groundwater sources include wells or aquifers [26]. Of the total daily water usage, approximately 85 million gallons were used for agricultural purposes, including 2.84 million gallons per day of groundwater for irrigation and 36.7 million gallons per day of surface water for irrigation [26]. This high usage of surface water sources can potentially lead to a greater risk of bacterial contamination, including but not limited to pathogenic strains of Escherichia coli (E. coli) on produce.

The Centers for Disease Control and Prevention (CDC) report that an estimated 48 million individuals become sick, some 128,000 hospitalized, and about 3000 individuals die from foodborne-related illnesses each year in the U.S. [27]. Fresh produce has long been and remains the leading cause of these foodborne-related outbreaks and illnesses, with a significant number of outbreaks involving coliform bacteria in general and Escherichia coli O157:H7 in specific [27]. Coliform bacteria are not specifically a taxonomic group, but a working definition used to describe a group of Gram-negative, facultatively anaerobic, rod-shaped bacteria that ferment lactose to produce acid and form gas within 48 hr at 35 °C [28]. Within the group of coliform bacteria is E. coli, commonly found in the lower intestines of warm-blooded organisms [28]. While most strains of E. coli are harmless, some may prove to be serious and pathogenic, such as the Shiga toxin-producing E. coli (STEC) [27]. STEC outbreaks make up up to 5% of the country’s outbreaks and 6% of the foodborne-related illnesses and tend to be present in raw or undercooked meat products, raw milk, or fresh produce grown with contaminated water broadcast through irrigation or improper washing [27].

A majority of Kentucky producers earn less than USD 25,000 annually from selling fresh produce. Per the original FSMA PSR (2014), small and limited-resource farmers were exempt from the requirement for irrigation water certification [10], thereby making it voluntary. However, given the scale of produce generated and introduced into the market, and to stay compliant with the then-PSR concerning the microbial quality of irrigation water, it offered an opportunity for introducing intentional and targeted education programming and creating new resources for water quality testing for small, limited-resource, and socially disadvantaged farmers in the Commonwealth of Kentucky.

The objective of the project was to provide water quality testing to determine the presence and quantification of coliform bacteria and Escherichia coli (E. coli) in irrigation water and offer consultations, educational support, and resources to producers on microbial water test results and to provide mitigation strategies.

2. Materials and Methods

The services provided by the irrigation water quality program offered producers a chance to test the microbial quality of the water used in the production process, especially for the presence and quantification of coliforms and E. coli. This service has been offered free of charge to all producers in Kentucky. The PSR in effect between 2014 and 2024 required the completion of a microbial water quality profile (MWQP) at specific increments, depending on the nature of water used for irrigation, such as ground- and surface water. For groundwater, four samples were required to be tested initially over the first year/growing season, followed by one sample each year [29]. For surface water, 20 samples were required to be tested throughout two to four years/growing seasons, followed by five samples yearly after the initial period [29]. Municipal water used for irrigation was exempt from this requirement. The MWQP comprised a four-year rolling data set of the water testing results. Within this data set are two central values: the geometric mean (GM) and the statistical threshold (STV) of generic E. coli, measured in colony-forming units (CFUs) [29]. The allowable limits set forth by the then-FSMA PSR were a GM of 126 or less CFUs of generic E. coli per 100 mL of water and an STV of 410 or less CFU generic E. coli per 100 mL of water [29].

To facilitate service to Kentucky’s limited-resourced and socially disadvantaged farmers, four testing sites were created: one in Frankfort (Central KY), Whitesburg (Eastern KY), Hodgenville (South Central KY), and Bowling Green (Western KY). These sites offered testing to producers around the state.

Between May 2023 and October 2024, small and limited-resource farmers (90) signed up and received water quality testing service free of charge. During that time, water samples were collected and tested (n = 296), groundwater (n = 185) and surface water (n = 111). Samples were collected by the producers and taken to a laboratory site. Samples were kept on ice when more than 4 h was needed from collection to testing.

The microbial quality testing of the irrigation water was performed utilizing an IDEXX Colilert Quanti-Tray/2000 system. This system requires collecting a sample of 100 mL of water, using aseptic conditions. In the lab, to the 100 mL of water, the Colilert reagent from IDEXX is added [30]. The water with reagent is then added to a sealable tray, which is then passed through the sealer, which evenly distributes the 100 mL of sample water evenly to all the available wells (large and small) in the tray [30]. The test is based on a defined substrate technology (DST) that facilitates detection of coliforms and, more specifically, E. coli [30]. The test’s medium contains two nutrient indicators, O-nitrophenyl-beta-D-galactopyranoside (ONPG) and 4-methylumbelliferyl-β-D-glucuronide (MUG), which are metabolized by the coliforms and E. coli, respectively, resulting in color differentiations [30]. Coliforms use β-galactosidase to metabolize ONPG, which changes the medium from colorless to yellow. E. coli uses β-glucuronidase to metabolize MUG and create fluorescence under UV light, as shown in Figure 1. The sample is then incubated at 37 °C for 24 h, after which the testing tray is visualized under UV light (IDEXX UV Viewing Cabinet) [31]. Large and small wells that show changes in color (yellow) and fluorescence (blue) were counted, and data were interpreted using the MPN table supplied by IDEXX. This test has been approved by the FDA 21 CFR 112 [25]. Results, with interpretations, were provided to the producers with educational support and resource connection.

3. Results and Discussion

The test system has a range of detecting of 0 to 1011.2 CFU/100 mL. The results obtained from the samples collected from June 2023 to October 2024 showed a broad range of coliform and E. coli counts (

Table 2. (a) Test Results Relating to 126 CFU/100 mL Threshold. (b) Test Results Relating to >126 CFU/100 mL Threshold.

(a)
≤126 CFU/100 mL
	Source
E. coli results	Ground	Surface
<1	159	4
1.0	6	5
2.0	2	-
3.1	2	-
5.2	-	1
6.3	1	2
7.3	-	2
7.5	1	1
8.1	-	1
8.6	2	-
10.9	-	1
12.2	-	1
13.4	1	-
16.1	1	1
16.6	-	1
17.5	-	1
22.8	-	1
25.0	-	1
25.6	1	-
26.9	-	1
30.1	1	-
30.9	1	-
32.4	-	1
33.1	-	1
36.4	1	-
38.9	1	-
39.3	1	-
43.5	-	3
47.3	-	1
48.0	-	1
55.6	-	1
58.4	-	2
65.0	2	-
67.0	-	1
68.9	-	1
71.7	-	2
79.4	-	1
80.1	-	1
91.0	-	1
95.9	-	1
96.0	-	2
98.3	-	1
105.0	-	2
105.8	-	2
106.3	-	1
108.1	-	1
115.3	-	1
121.1	-	1
TOTAL	183	53
(b)
>126 CFU/100 mL
	Source
E. coli results	Ground	Surface
142.1	1	1
142.3	-	1
165.8	1	-
166.4	-	1
172.2	-	2
172.3	-	1
185.0	-	1
186.0	-	1
198.9	-	2
201.4	-	1
218.7	-	2
260.3	-	1
280.9	-	2
298.7	-	2
328.2	-	1
344.1	-	2
360.9	-	1
378.4	-	1
456.9	-	1
478.6	-	1
524.7	-	1
549.3	-	1
648.6	-	1
686.7	-	1
689.3	-	2
791.5	-	1
829.7	-	2
870.4	-	1
913.9	-	6
960.6	-	5
1011.2	-	12
TOTAL	2	58

, Figure 2). Groundwater samples ranged from 0 to 165.8 CFU/100 mL, with most of the samples returning a value of 0 CFU/100 mL. Surface water samples, however, ranged the entirety of the test’s possibility, 0 to 1011.2 CFU/100 mL. Those water samples that consistently gave higher-than-acceptable baseline values for E.coli were offered information, resources, and strategies on mitigating the issue on their farms. Furthermore, based on the current findings, we plan to offer focus groups and workshops to farmers focusing on best practices to keep the baseline value of E. coli counts in the acceptable range.

The water testing program offered small, limited-resourced, and socially disadvantaged farmers in Kentucky access to free-of-charge water testing. It enabled them to take a proactive approach to safe production practices that the then-FSMA PSR required, as producer sales increased. As the project started to grow, an announcement by the FDA changed the PSR’s requirements for harvest and post-harvest agricultural water for covered produce other than sprouts. The new PSR rules were published in July 2022 and were to go into effect for large farms on 26 January 2023, and stagger yearly for other farms based on small and very small size. Further changes to the pre-harvest agricultural water rules were made with an effective date of July 2024, with the largest farms being affected first, starting April 2025, and other farms to follow by size, yearly [25].

The changes to the PSR pertained to covered farms, along with changes to water assessments, hazard identification, and risk management. Covered farms still use agricultural water for pre-harvest activities for covered produce. The water assessment changes are important to this project, as they differ from when it was first initialized. Covered farms are now required to assess agricultural water used in pre-harvest activities once annually and whenever a significant change occurs. Those changes may pertain to increases in the possible introduction of hazards into or onto produce or food contact surfaces [24]. Farms are then to evaluate the possible factors that may be impacting the produce safety: location and nature of the water source, type of water distribution system, the degree to which the system is protected, type of application, the time interval between the last direct application, etc. [24]. Covered farms are to determine if corrective actions or mitigation may be appropriate. Charts on the FDA website cover the assessment and corrective actions in more detail [24].

4. Conclusions

Certain limitations to the study include factors such as the number of participating famers, length of the study, and changes to the PSR. The sample size of the study was limited by the ability to find and recruit willing participants, mostly due to the expressed concerns regarding privacy of the data. The initial focus was to help farmers to establish an MWQP for their respective sources of irrigation water. However, the abrupt changes in the FSMA’s PSR changed the overall dynamics, as the focus shifted from these being ‘required’ to ‘optional’.

Along with the resources, educating producers on current regulations and overall GAPs is critical to the program. Since the program is voluntary, producer participation has been a limiting factor related to the program’s visibility within the producer communities. Further outreach to local farmers’ markets, collaboration with local extension agencies, and further participation in producer-oriented conferences could help gain more exposure. Another challenge encountered was the producers’ perceptions of the program and the motives for the service. Some producers were concerned with privacy issues and the intentions of the program’s creator, questioning the data utilization and access.

The issues addressed specifically within this project highlight the need for economic opportunities and income for producers and farmers through job creation. This project aimed to support and promote domestic direct producer-to-consumer marketing of produce for farmers’ markets, roadside stands, agritourism activities, community-supported agriculture programs, and online sales.

This project will help develop tools for improved water quality to meet FSMA regulations and thereby increase greater production among participating farmers, especially small and socially disadvantaged farmers. The tools developed through this project will provide techniques and practices that growers can rapidly adopt at local agriculture markets, including those that provide direct financial support to a network of markets or other relevant organizations.