Background

The majority of all animal manure in the U.S. is spread, sprayed or otherwise applied to agricultural land. The volumes of animal waste produced often exceed local demand for use as fertilizer, yet transportation costs prohibit widespread distribution of manure. Consequently, most manure is land-applied within about 10 miles of beef cattle feedlots, dairy barns, poultry houses or swine facilities. If improperly managed, this manure can significantly degrade environmental quality and impact human and animal health. Utilization of contaminated irrigation water or manures containing pathogenic or parasitic agents are considered to be important factors in the occurrence and epidemiology of water- and food-borne diseases. Investigative data from some outbreaks have shown that manure was the source of the causal agent. As agronomic areas are more compressed and the proximity of animal production units comes closer to areas used to grow crops receiving little processing, such as fresh produce, the potential for contamination of irrigation water or soils and subsequent cross contamination of food crops increases.

Recycling of manure to the land without adequate pathogen reduction directly increases the risks of human illness via water- or food-borne contamination, as well as cycling pathogens back to animals on the farm. This is true for pathogens associated with foods of animal origin as well as produce that may have been contaminated during production. Techniques, such as composting or deep stacking, to reduce pathogen levels in manure are often not used by producers because they require extra time, attention, special equipment or structures, and impose additional costs.

Generally, soil that has not recently received raw manure (liquid, slurry, partially dried, or improperly composted) or inadequately treated sewage has not been found to harbor indigenous populations of enteric pathogens and parasites. Manure, however, is not the only on-farm source of pathogens and parasites. Other farm sources include: dust, aerosols, irrigation and runoff water, farm workers, plant residues, and the soil. For example, Bacillus cereus, Clostridium spp, and Listeria monocytogenes, can be readily found in many soils in association with plant material, vegetables, and decaying leaves and other plant parts. In addition, coliforms such as Enterobacter spp. and Klebsiella spp. are common inhabitants of soil and plant material, even in the absence of fecal material. This limits the use of traditional fecal coliform methods as indicators of fecal contamination, and reinforces the need for standardization of methods for assessment of fecal contamination of produce.

It is well established that pathogen spread in the environment results from improper treatment and land application of sewage, slaughter offal, sludge, biosolids, slurry and manure, as well as from wild and domesticated animals. This may lead, by way of contamination of surface waters and colonization of birds, rodents and insects, to the contamination of animal feeds or directly contribute to the re-colonization of farm animals. Despite what is known about potential vectors of pathogen contamination, many critical questions remain to be answered. The lack of knowledge about pathogen survival in manure and improperly treated biosolids and about the adequacy of various manure management techniques to reduce the levels of these pathogens clearly points to the need for research on these issues. The fate of pathogens in the environment (e.g., transport and survival) after manure and other byproducts have been land applied or otherwise disposed is not adequately known. In addition, better estimates of human and animal exposure are required for risk assessment to adequately assess the benefit of manure and byproduct treatment strategies.

Although many pathogens threaten the safety of our food and water, certain foodborne and waterborne microorganisms are of particular public health concern. The following pathogens have been targeted for immediate attention by the Federal Food Safety Initiative Consortium: Salmonella species, Campylobacter jejuni/coli, Escherichia coli O157:H7 and other related strains; the parasite Cryptosporidium parvum; and enteroviruses. In addition, the recurring incidence of foodborne illness outbreaks caused by Listeria monocytogenes and the potential for more extensive involvement of Mycobacterium paratuberculosis and Yersinia enterocolitica indicate the need for additional research on the involvement of these microorganisms in the farm-to-table pathway of disease agent spread.

The microbial pathogens listed above may give rise to diseases that are far more serious than the uncomfortable but relatively temporary inconvenience of diarrhea and vomiting, which are the most common symptoms of so-called 'food poisoning.' Infections can result in very serious immediate consequences, such as spontaneous abortion, as well as long-lasting conditions such as reactive arthritis, Guillain-Barré syndrome (the most common cause of acute paralysis in adults and children), and hemolytic uremic syndrome (HUS), which can lead to kidney failure and death, particularly in young children.

Many of the pathogens that have emerged over the past 10 years cannot be easily detected and quantified in complex environmental samples such as manure, compost, soil, and foods. Application of current standard methods to the variety of matrices involved in determining the exposure at the farm end of the farm-to-table continuum will require adaptation and possibly development of new methods for detection and quantification of viable microorganisms.

Methods need to be developed, validated, and implemented for rapid testing of very low levels of Campylobacter, Salmonella, Toxoplasma, Vibrio, E. coli O157:H7, Cyclospora, Cryptosporidium parvum, and viruses in manure, soils, composts, biosolids, aquaculture byproducts, and freshly harvested fruits and vegetables. Research will be coordinated with EPA's efforts to develop better test methods for Cryptosporidium and other contaminants in drinking water.

Pathogenic microorganisms in livestock and poultry can become resistant to antimicrobial agents and conditions that have been traditionally relied on to eliminate or prevent their growth on certain commodities. Various strategies for dealing with this have been proposed. None, however, have addressed the potential for shedding of antibiotic resistant strains in manure and their dissemination beyond the animal production facility to locations where manure is land applied or where runoff from such applications ultimately contacts. Manure may contain antibiotic resistant strains that establish or disseminate through the environment unless manure is disinfected prior to beneficial land use. Treatments to reduce microbes and especially pathogens in manure prior to land use is one strategy for reducing dissemination of such strains. The extent of persistence of such strains needs to be established so that effects of manure treatments on reducing their persistence can be determined.

Control of manure and byproduct pathogens to protect human and animal health

Develop management practices and treatment technologies to effectively handle, store and apply animal manure and byproducts in agricultural production systems while preventing contamination of food and water by pathogens.