(This is Part 2A of a five-part series on produce safety by Roy E. Costa, R.S., M.S., a registered professional sanitarian and founder/owner of Environ Health Associates Inc. Part 1B was posted here on March 18, 2015, Part 1A was posted here on Feb. 25, 2015, and the series introduction was posted here on Feb. 10, 2015.)

The Development of Food Safety Systems in Agriculture

The organized practice of growing fruits (the seed-bearing portion of a plant) and vegetables (the edible portions of plants) for human and domesticated animal consumption emerged at the dawn of recorded history. Evidence of agricultural endeavors date back at least 12,000 years. The altering of communities of fruits and vegetables for man’s own benefit resulted in significant changes in once formerly hunter-gatherer communities, and mankind’s success in agriculture paved the way for the birth of our modern civilized society.

There is nothing more iconic than the image of the farmer plowing his field, and anyone rubbing shoulders with these hard-working individuals enters a world of timeless traditions.

The application of food safety in the growing and harvesting of produce is, however, a new development. Only in the past 20 years or so have experts formulated agricultural food safety principles borrowed mainly from food manufacturing, and these rapidly evolving systems of safety and hygiene rules are impacting farming in many ways. One must thoroughly appreciate the history of agriculture as we impose these new concepts on farming operations and realize that they are mostly foreign to traditional farming methods.

Food safety in any application may seem quite simple, and so it appears to be in agriculture, at least on the surface. If the growing area is free of contamination and workers are in good health, and the environment, water and overall growing conditions do not negatively impact operations, consumption of fresh fruits and vegetables should be considered a low risk for causing foodborne illness.

The evidence, however, points strongly in the other direction. Produce-borne outbreaks caused by bacteria, parasites and viruses are all-too-common events and, in many instances, investigation reveals unsanitary conditions in the growing area as the initial source of the pathogenic agent.

In 2006, spinach produced by Earthbound Farms caused a disastrous E. coli O157:H7 outbreak that seriously affected public health and sent shockwaves through the entire produce industry. The protracted outbreak investigation was confounded by poorly documented supply chain record-keeping, but, eventually, the trail led to a small farm in San Benito, CA, nestled in the foothills of central California’s Sierra Nevada. In the meantime, consumers nationwide stopped purchasing spinach, which, in turn, caused a serious market crash.

This outbreak illustrated several important factors that would play out again and again in future produce-linked outbreaks. Most important, from the point of view of the safety of the growing area, it was found that feral pigs frequented the farming area; fecal specimens from one herd collected close by revealed E. coli O157:H7, but, interestingly, not the outbreak strain.

The source of the spinach only came to light many weeks after the first case of E. coli, and, in the meantime, the fields had been harvested and product shipped to the Earthbound Farms processing plant for processing, packaging and distribution. Investigators obtained environmental samples from the facility that revealed the causative agent, and, in order to eradicate the bacteria from its processing equipment and environment, the facility ultimately had to close temporarily. In total, more than 200 people were sickened and three of them died. Following that outbreak, the company redesigned its food safety practices to become an industry leader in growing safe produce.

The ensuing crisis of consumer confidence at the time created a powerful driver for change, and the years that followed saw wide-scale adoption by farmers of industry-led Good Agricultural Practices (GAP). The application of control measures based on FDA guidance documents with significant enhancements continues until this day.

Challenges in Agricultural Food Safety

The U.S. Food and Drug Administration (FDA) tells us to consider the following pre-harvest risks when growing fruits and vegetables, and this paper will evaluate the relative importance of the most significant ones and further explore current public health concerns:

• Feces contamination of growing and harvesting areas by humans and wild and domestic animals
• Unsafe irrigation water
• Runoff
• Flooding
• Growing area land use
• Adjacent land use (septic systems, leach fields, biosolids, industrial operations, intense livestock operations)
• Infected workers harvesting and handling produce, or poor hygiene
• Improper cleaning and sanitizing of harvest equipment and utensils
• Cross-contamination in recycled irrigation water
• Inadequate pest control
• Contaminated containers
• Contaminated seed and sprouting
• Contaminated soil
• Green, or inadequately composted, manure
• Air (dust)
• Water for other uses (for example, pesticides, foliar treatments, growth hormones)
• Manure and soil amendments

Feces contamination of growing and harvesting areas by humans, and wild and domestic animals:

Wild Animals:

Intrusion by wild animals is a serious issue from a crop-loss standpoint and can have severe economic consequences. Farmers have traditionally attempted to control significant grazing by deer and the uprooting of plants by feral pigs, as well as the damage caused by birds and ground animals, such as rodents, rabbits and raccoons. Efforts to control wild animal populations, however, are only marginally effective, and, in some regions, crop losses of 20-30 percent can be expected from deer, while a large flock of birds can completely destroy a crop in a day or two.

Barriers, such as fences, are only effective for larger herbivores, such as deer or pigs (and very sturdy fences are required), but there is virtually no completely effective barrier for birds or small ground animals (short of enclosure in a greenhouse).

Bird control has taken several forms, such as gas cannons and other acoustical repellents, visual repellents, physical exclusion and biochemical repellents, but the persistence of birds is remarkable, especially Canadian geese and certain migratory birds (cedar waxwing), starlings, sparrows and crows. Virtually all birds can be vectors for Salmonella and Campylobacter, as well as parasites, such as Cryptosporidium and Cyclospora cayetanensis, while Salmonella and E. coli are the major concerns with herbivores.

Wild animals and agriculture have existed side by side for millennia, so it is not reasonable that we can solve the animal intrusion problem in just a few years. Furthermore, there is a competing side of the argument that says such wild populations of animals should be nourished rather than exterminated!

Striking a balance between allowing some natural populations of animals in farming areas and restricting or eliminating them is not easily accomplished. Probably the best defense against contamination by animals is diligence by farmers and especially immediately before harvest. Knowing when and where such intrusion and potential contamination is occurring is critical to any type of mitigation. Areas favored by animals may include the portions of crops nearest to natural cover and riparian areas; birds especially like to drink water when feeding. Often the marginal areas set back away from roads or human activity will be the most impacted by deer, although raccoons and pigs can range widely in a field. Most of the deer and wild pig activity occurs during nocturnal hours, early morning and at dusk, while bird activity may reflect migratory patterns, with the availability of roosting and nesting locations favoring feeding sites.

Animals may favor the growing area depending on the level of maturity of the crop; the closer to harvest, often the more attractive the crop becomes. Therefore, the period just before harvesting is likely the best time to intervene. Interventions include scouting areas at night, lights and netting (in berry crops and grapes) and trapping, but probably the best intervention is for the producer to recognize where animal intrusion has taken place and not harvesting those zones with the contamination. Adverse findings include feces, tracks, gnawing and pecking, as well as rooting by pigs. Harvesters need a degree of experience to recognize the signs of animals and a thorough scouting of the blocks before harvesting must take place. When evidence is found, the affected areas require marking, flagging, or otherwise cordoning off. This must be coupled with supervision to ensure that these zones are not harvested. Such crops can be “placed on hold” and tested before harvest, but it is best not to harvest the crop and to plow it under. Traps may be useful to control pigs and raccoons, but, once caught, disposal or relocation of the animal is a problem, and trapping usually requires a licensed entity and can be costly and time-consuming.

Domestic Animals:

Domestic animal production coexists with produce farming, and the produce farmer may also rear cattle or other domestic animals. Growers benefit in this arrangement by having a means to dispose of silage, and, at the same time, benefit from the use of manure for crop nutrition. Domestic animal production produces wastes, which can easily find their way to produce fields with equipment, people, wind, dust and rain. While field fencing is usually adequate to control small herds of cattle, fences must be kept repaired and in the proper place. The setbacks between domestic animals and crops are poorly defined in the third-party standards, and there is controversy and a lack of reliable scientific data to guide the farmer as to how far to separate operations. The many variables, such as topography, soils, drainage and the type of crop, all affect the ability of pathogens in adjacent animal waste to contaminate a crop. Animal wastes may also affect irrigation water sources, especially surface water sources, although poorly constructed or shallow wells may also be impacted. These setbacks are best determined on a case-by-case basis through a risk assessment that studies the topography, slope of the land, drainage and water-holding characteristics of soils, and takes into consideration the magnitude of the adjacent animal population.

FDA’s Food Safety Modernization Act (FSMA) is expected to address the setback issue, but, as with everything in this Act, only time will tell if a final rule will actually be enforced.

Human Waste:

Human contamination of growing areas is still a potential problem in spite of the advances made in the availability of portable toilets and hand-washing facilities in produce operations. A farm needs at least one portable toilet for every 20 workers, and separate facilities are required when women are present. Constant oversight and maintenance is required to ensure there is always a sufficient amount of water, soap, and hand-drying devices. But compliance with personal hygiene requirements, as basic as they are, is often problematic, with cultural, language issues and time constraints all impeding effectiveness.

Currently, most third-party standards call for a sufficient number of portable toilets to be within 5 minutes walking distance, or a quarter-mile of workers at all times. This requires numerous freestanding portable toilets in specific locations throughout the farm, or for the units to be on wheels. Even then, suitable places to locate the units may be difficult to find. A half-mile walk through rugged terrain in 90-degree heat may encourage workers to take shortcuts, and a diligent inspector all too often uncovers human fecal remains and signs of toilet waste in, or immediately adjacent, to growing areas. Furthermore, the portable toilets themselves are potential sources of contamination, with each containing a holding tank of at least 10 gallons of raw sewage that must be pumped out safely at least two to three times a week when at capacity. Servicing and otherwise maintaining these units is an ongoing, labor-intensive and expensive undertaking, and violations of rules regarding the accessibility, care and upkeep of these facilities is still quite common in spite of the industry’s newfound emphasis on personal hygiene. Some very sensitive operations, such as in tomato harvesting, find it necessary to dedicate a “monitor” for the portable toilets. The sole function of this employee is to make sure employees use the facilities properly and that they wash their hands afterward.

The sinks provided with these portable toilets are barely adequate, producing a small amount of unheated water. The efficacy of hand-washing under these conditions is debatable.

Unsafe Irrigation Water:

Although some farmers do not irrigate crops (“dryland” farming techniques), the norm is to utilize available sources of water to supplement rainfall. In some areas, the availability of water sources (“water rights”) has become a volatile political issue, and experts warn of impending water shortages. Most states have water authorities that manage the use of water, placing restrictions on the amount of water allowed. Due to these pressures, farmers are often forced to use water with marginal qualities, use treated municipal wastewater, and to recycle irrigation water.

Water sources may include groundwater, with wells tapping both shallow and deep aquifers, and surface water, e.g., ponds, lakes, rivers and streams, as well as canals and ditches. All of these sources are subject to varying degrees of potential contamination, but surface water sources are very vulnerable. Rivers, streams, canals and ditches are open, flowing bodies of water, and contaminants that may be found in the watershed are easily distributed to downstream locations. Sources of pollution include point sources, such as industrial operations that may release heavy metals and toxic discharges, sewage treatment plants, storm water drains and myriad non-point sources found in developed areas. Cattle and Concentrated Animal Feeding Operations (CAFOS) are significant risks and have been suspected as a source of pathogens in rural environments. The lack of land use planning often brings produce areas in close proximity to cattle, pigs, and poultry houses.

The problems of land use are at the root of many of the contamination issues in farming, but there is just so much available land and remedies are difficult to find. Political considerations prevail, rather than a planned approach to decisions as to where to locate competing industries.

Ground water sources, while somewhat safer, are also subject to contamination depending on their depth, construction, and characteristics of the water table. One of the missing links in our safety programs is the lack of standards for the construction of irrigation wells. While the EPA Safe Drinking Water Act proscribes the construction of potable water wells and distribution systems, most regulatory authorities have exempted agricultural wells from their rules.

Irrigation systems can use methods, such as overhead irrigation using what are known as pivots, sub-irrigation methods such as seepage, and micro-drip irrigation. While direct foliar application of water probably carries the highest risk, all methods can contaminate crops and soil.

The development of standards for pre-harvest application of irrigation water continues to be controversial, and FSMA rules are much anticipated. The key microbiological standard in use now is based on the level of generic E. coli. When an operation has only one sample result, the total bacterial count cannot exceed 125 CFU (colony forming units). As the sample data pool increases over time, a 5 sample rolling mean can be calculated; in this scenario, the average colony count cannot exceed 235 CFU in a 100mL sample. While these limits appear to be protective, scientific validity for these limits is somewhat lacking, and the standards themselves have been derived from EPA’s Recreational Bathing Rule. In places such as Florida, which is blessed with an exceptionally pure, deep aquifer (the Floridan Aquifer), ground water rarely, if ever, fails to meet the requirements, while in intensively farmed areas, such as the San Joaquin Valley in California, it is likely to find excessive concentrations of E. coli.

For many with impaired water quality, growers must treat the water with an antimicrobial to bring it into compliance, mostly using chlorine either as hypochlorite or gaseous chlorine.

But treatment and regular testing is not enough; farmers must have a validated sampling plan that is based on a risk assessment. This requires studying the characteristics of the irrigation system, mapping, selecting representative sample points, a systematic approach, effective sampling methods, and the accurate interpretation of results. If undesirable results of irrigation testing are obtained, procedures must be in place to verify the safety of the products under production since the last water test and to confirm findings with a second test. Mitigation of contamination in well casings may be accomplished through the super-chlorination or shocking of the well; however, in worst-case scenarios, undesirable water sources must be abandoned and secondary sources utilized.

While farmers are very knowledgeable about the physical operations of wells, they may lack the basic understanding of microbiological standards and tests and how to interpret results, and they may also lack expert knowledge about the safe and effective use of antimicrobial agents.