Manure Pathogens and Microbial Byproducts

Animal Manure Management May 19, 2017 Print Friendly and PDF

livestock and poultry environmental learning center logo with cow, pig, and chicken sillhouettes over a map of the U.S. with three circling arrowsTeam members: John P. Brooks, Ph.D. - link to research; Carl Bolster, Ph.D. - link to research; Kimberly Cook, Ph.D. - link to research; Robert Dungan, Ph.D. - link to research; John Carney - link to research

Links to PEDv (Porcine Epidemic Diarrhea Virus).  

Introduction to Manure Pathogens

The majority of animal manures and municipal biosolids produced in the U.S. are utilized as soil nutrient amendments for forage and crop production (National Research Council, 2002; Burkholder et al., 2007).  In the U.S., approximately 450,000 animal feeding operations (AFOs) or concentrated animal feeding operations (CAFOs), produce approximately 100 million dry Mg of manure per year (Burkholder et al., 2007).  Manures are generally not treated beyond storage which results in quasi-treatment prior to land application, in contrast to municipal biosolids which are always treated to some extent (Kelley et al., 1994; Pell, 1997; Hutchison et al., 2004, 2005a,b; Mannion et al., 2007; Brooks et al., 2009).  Approximately 16,000 municipal wastewater treatment plants operate in the U.S. producing a total of 6.7 million dry tons of biosolids annually (National Research Council, 2002).  A requirement for the utilization of these residual wastes is proper environmental stewardship; however, the presence of enteric microbial pathogens can compromise the land application process, for the occupational- and public-exposed.  Mead et al. (1999) estimated that 76 million cases of foodborne illness occur annually in the United States (U.S.), of which 38 million could be attributed to known etiological agents.  Scallan et al. (2011), recently estimated 9.4 million cases from known etiological agents and 38.4 million from unknown agents.  Among the known pathogens, Campylobacter jejuni, Salmonella spp., Clostridium, and norovirus account for 60 to 70% of all outbreaks (Mead et al., 1999; Scallan et al., 2011).    


Manure Pathogens in Soil, Water, & Air Sources

Animal feces or runoff carrying manure-borne microbial pathogens have been implicated in some of the largest water and food borne outbreaks in recent years (Curriero, et al., 2001; Hrudey et al. 2003).  The Salinas Valley, CA, Milwaukee, WI, and Walkerton, Ontario (Canada) outbreaks documented animal manure-borne food-crop and drinking water outbreaks (Hoxie, et al., 1997; Hrudey et al., 2003; USFDA, 2006).  In all three cases, land applied manure was not necessarily the implicated source; however runoff and feral animals were determined to be infectious vectors.  Both residuals (manure and Class B biosolids) potentially contain a wide range of pathogens, some common to both and others specific to each residual.  Manure, depending on its origin, can be a source of Campylobacter jejuni, Escherichia coli O157:H7, Salmonella spp., Listeria monocytogenes, Cryptosporidium parvum, and Giardia lamblia (Guan and Holley, 2003; Hutchison et al., 2004, 2005a; McLaughlin et al., 2009a).  Municipal Class B biosolids can additionally contain human viruses, depending on municipality and treatment (Straub et al., 1993; Viau and Peccia, 2009; Wong et al., 2010; Pepper et al., 2010).  Viruses of the enterovirus group (enterovirus 68-101, Coxsackievirus, poliovirus, and echovirus), rotavirus, adenovirus, and norovirus can all be present in Class B biosolids.

Table 1: Pathogen levels in manure and class B biosolids (Update coming soon). 

Figure 1: How do I come into contact with a pathogen? (Update coming soon)

Antibiotic Resistant Bacteria (Update coming soon)

Disease outbreaks in the public health and agricultural domains due to antibiotic resistant bacteria, have brought forth more public attention to medical and agricultural antibiotic use.  These infections are of great concern, due to their prolonged course of infection.  Due to this public and political pressure, some industries are beginning to reduce the amount of antibiotics introduced to livestock at sub-therapeutic doses.  In Europe, the complete banishment of antibiotic non-therapeutic use has resulted in increased therapeutic prescriptions, and thus far has not had the large impact on public health that was once anticipated.  Little is understood as to the incidence and persistence of antibiotic resistant bacteria (ARB) in the community and agricultural environments; likewise the impact associated with agricultural sources of antibiotic resistant bacteria such as manure land-application is questioned.

Manure Land Application Strategies to Mitigate Antibiotics and Antibiotic Resistance Genes in the Agricultural Environment

This article discusses the effects of various land application strategies on the fate and transport of manure borne antibiotics and antibiotic resistance genes in soil and runoff. It is broken down into three sections: manure storage; land application methods; and vegetative barrier. Although studies were conducted using swine manure slurry, it is expected that that the general conclusion would also apply to other types of manure. Prior to a detailed description of the findings, it first presents some background information about manure-borne antibiotics and antibiotic resistance genes.

Best Management Practices

Evaluation of BMPs and treatment technologies on impact of fate and transport of pathogens, PACs, and antibiotic resistant bacteria using an integrated research approach.  Ecologically sustainable agriculture depends on effective management of livestock manure, manure amended soils, runoff, and agricultural wastewater.  Traditional and alternative livestock manure, runoff and wastewater control and treatment systems are primarily designed for the control of nutrients.  However, other fecal-derived contaminants such as pathogens, hormones, and PACs can also be present in these waste streams.  The fate of these manure-borne contaminants in these types of treatments systems is unknown. Since manure-borne contaminants pose a risk to human, animal, and environmental health, the reduction of these contaminants needs to be investigated.  This knowledge will lead to the development of management practices that optimize manure-borne contaminant control.

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This work is supported by the USDA National Institute of Food and Agriculture, New Technologies for Ag Extension project.