vvEPA
United
Environmental Protection
Agency
Literature Review of
Contaminants in
Livestock and Poultry
Manure and Implications
for Water Quality
July 2013
-------
Office of Water (43041)
EPA 820-R-13-002
July 2013
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EPA-OW Literature Review of livestock and Poultry Manure EPA 820-R-l 3-002
July 2013
Acknowledgements and Disclaimer
This document is designed to provide technical background information for the USEPA's Office of Water
research efforts. This report makes no policy or regulatory recommendations; it does identify information
gaps that may help define research needs for USEPA and its federal, state, and local partners to better
understand these issues. The Lead USEPA Scientist is Octavia Conerly and Co-Lead Lesley Vazquez Coriano,
Health and Ecological Criteria Division, Office of Science and Technology, Office of Water. This document
was prepared under USEPA contract No. GS-10F-0105J, Task Order 1107 with The Cadmus Group, Inc.
This report received technical expert reviews from many scientists within USEPA and from the U.S.
Department of Agriculture, Agricultural Research Service.
This document is not a regulation or guidance. Mention of trade names or commercial products does not
constitute an endorsement or recommendation for use.
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AFO
ARS
AU
AWWA
BMP
BOD
BVDV
CAFO
CDC
CENR
CFR
CIDR
DNA
ECOSAR
EHEC
EQIP
ERS
GAG
HAB
HEV
HUS
MCL
NAHMS
NARMS
NAS
NITG
NPDES
NPS
NRG
NRCS
NRDC
NYSDEC
ODTS
Acronyms and Abbreviations
Animal Feeding Operation
Agricultural Research Service
Animal Unit
American Water Works Association
Best Management Practice
Biochemical Oxygen Demand
Bovine Viral Diarrhea Virus
Concentrated Animal Feeding Operation
Centers for Disease Control
Committee on Environment and Natural Resources
Code of Federal Regulations
Controlled Internal Drug Release
Deoxyribonucleic Acid
Ecological Structure Activity Relationships
Escherichia coli O157:H7
Environmental Quality Incentives Program
Economics Research Service
Granular Activated Carbon
Harmful Algal Bloom
Hepatitis E Virus
Hemolytic-Uremic Syndrome
Maximum Contaminant Level
National Animal Health Monitoring System
National Antimicrobial Resistance Monitoring System
National Academy of Sciences
Nutrient Innovations Task Group
National Pollutant Discharge Elimination System
Nonpoint Source
National Research Council
Natural Resources Conservation Service
Natural Resources Defense Council
New York State Department of Environmental Conservation
Organic Dust Toxic Syndrome
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OST Office of Science and Technology
PAC Powdered Activated Carbon
PCIFAP Pew Commission on Industrial Farm Animal Production
PCR Polymerase Chain Reaction
PHAC Public Health Agency of Canada
RNA Ribonucleic Acid
rBGH Recombinant Bovine Growth Hormone
RO Reverse Osmosis
SPARROW SPAtially Referenced Regressions On Watershed attributes
TMDL Total Maximum Daily Load
USD A United States Department of Agriculture
USEPA United States Environmental Protection Agency
USFDA United States Food and Drug Administration
USGAO United States Government Accountability Office
USGS United States Geological Survey
WBDO Waterborne Disease Outbreak
WBDOSS Waterborne Disease and Outbreak Surveillance System
WHO World Health Organization
WRI World Resources Institute
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Executive Summary
This Literature Review of Contaminants in Livestock and Poultry Manure and Implications for Water Quality was
prepared by the United States Environmental Protection Agency (USEPA) as part of ongoing efforts to
better understand the environmental occurrence and potential effects related to contaminants of emerging
concern. Past reviews of animal manure have focused primarily on nutrient issues. This report focuses on
summarizing technical information on other components, particularly pathogens and contaminants of
emerging concern such as antimicrobials and hormones that may affect water quality. The report makes no
policy or regulatory recommendations; it does identify information gaps that may help define research needs
for USEPA and its federal, state and local partners to better understand these issues.
Over the past 60 years in the United States (U.S.), farm operations have become fewer in number but larger
in size. This has been particularly true in livestock and poultry production. Since the 1950s, the production of
livestock and poultry in the U.S. has more than doubled; however, the number of operations has decreased by
80%. Food animal production has shifted to more concentrated facilities with animals often raised in
confinement. Production has also become more regionally concentrated. This has been done, in part, to meet
the demands for meat and animal products from a growing human population in the U.S. and abroad.
The U.S. Department of Agriculture's (USDA) 2007 Census of Agriculture data are used to estimate beef and
dairy cattle, swine, and poultry production. Using standard USDA methods, an estimated 2.2 billion head of
livestock and poultry generated approximately 1.1 billion tons of manure in 2007. Manure can be a valuable
resource as a natural fertilizer. However, if not managed properly, manure can degrade environmental quality,
particularly surface water and ground water resources. The increasing concentration of animal production can
lead to concentrations of manure that exceed the beneficial needs of the farmland where it was produced. A
2001 report from the USDA's Economic Research Service found that 60%-70% of the manure nitrogen and
phosphorus may not be able to be assimilated by the farmland on which it was generated. As an example of
the increasing concentration of production, from 1997 to 2007, the number of swine produced in the US
increased by 45%, but the number of swine farms decreased by 30%; over 40% of all swine were produced in
just two states, Iowa and North Carolina. Also illustrating the regionalization, Alabama, Arkansas, and
Georgia account for over 30% of U.S. broiler (chicken) production.
Livestock and poultry manure can contain a variety of pathogens. Some are host-adapted and, therefore, not a
health risk for humans. Others can produce infection in humans and are thus termed zoonotic. The more
common zoonotic pathogens in manure include Escherichia coli 0157:H7, Campylobacter, Salmonella,
Crypto sporidium parvum, and Giardia lamblia. Viruses can also be associated with manure, although less is known
about their survival in manure. Survival of microorganisms in manure, soils, and water varies greatly (from
days to as much as a year) depending upon the organism and the environmental conditions. Risks from
manure-associated pathogens can arise when runoff, spills, or infiltration enable microorganisms to reach
surface water or groundwater, or when land-applied manure, or irrigation water impacted by manure, comes
into contact with food crops. The level of risk to humans depends upon a number of factors that dictate how
readily the microorganisms are transported through the environment and how long they remain infectious, as
well as the numbers of microbes and their infectious doses. Most outbreaks of waterborne and foodborne
gastrointestinal illness, even those caused by zoonotic pathogens, are attributable to human fecal
contamination, although agricultural sources have been implicated in a number of cases. With current
surveillance, the degree to which manure-related pathogens may be involved in outbreaks is poorly
understood due to difficulties in identifying etiologic agents and sources of contamination, and also because
many cases of illness go unreported.
It is estimated that most (60%-80%) livestock and poultry routinely receive antimicrobials. Antimicrobials
may be administered to treat and prevent diseases and outbreaks, or at sub-therapeutic levels to promote
animal growth and feed efficiency. The U.S. Food and Drug Administration (USFDA) reported that 28.8
million pounds of antimicrobials were sold for animal use in 2009; some estimates suggest this is four times
greater than what was used for human health protection during that same year. However, available data are
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limited and detailed use estimates vary. The overuse and/or misuse of antimicrobials (in general) can facilitate
the development and proliferation of antimicrobial resistance, an issue of concern for animal and human
health protection. Research indicates that antimicrobial use in livestock and poultry has contributed to the
occurrence of antimicrobial-resistant pathogens found in livestock operations and nearby environments.
USDA surveys reported that 74% of Salmonella and 62% of Campylobacter isolates from swine manure were
resistant to two or more antimicrobials. Most antimicrobial resistance related to human health is likely the
result of overuse and misuse of certain medications in humans. The overlap between livestock and human
antimicrobial use is also recognized as an area of concern for human health because the effectiveness of these
medications in treating human infections may be compromised. The USFDA banned the use of
fluoroquinolones in poultry in 2005 because of human health concerns. The extent to which antimicrobial-
resistant human infections are related to the use of antimicrobials in livestock and poultry, is unclear and
would benefit from further research.
Hormones are naturally produced by, and in some cases artificially administered to, livestock and poultry.
Beef cattle may be treated with hormones to improve meat quality and promote animal growth; dairy cows
may be treated to control reproduction and increase milk production. An estimated 720,000 pounds of
natural and synthetic hormones were excreted by livestock and poultry in 2000. Research indicates that
hormones and their metabolites may be present in environments and surface waters proximal to livestock and
poultry operations. While typically detected at low concentrations in water, hormones are biologically active at
very low levels and are classified as endocrine disrupters. In aquatic ecosystems, hormones may affect the
reproductive biology and fitness of aquatic organisms. Because hormones are excreted by all mammals,
including humans, the majority of research has focused on hormone releases from waste water treatment
plant discharges. Limited recent research suggests that exposure to hormones from livestock operations and
manure may adversely impact the reproductive endocrinology of some fish. More research on the use,
occurrence, fate, and transport of natural and synthetic hormones from production facilities and cropland
treated with manure is necessary to fully understand their potential impact.
Manure discharges to surface waters can be caused by rain events, spills, storage lagoon and equipment
failures, or the improper application of manure, including application to frozen or saturated ground. In some
cases, fish mortalities may be caused by oxygen depletion or ammonia toxicity from large loadings of manure.
In addition, while cases are limited, nutrients from livestock and poultry manure have been indicated as a
cause of harmful algae blooms in surface waters. Harmful algae blooms produce cyanotoxins that may be
harmful to animals and aquatic life, as well as to humans when exposed in recreational waters or from
drinking water supplies. Proper management and maintenance of lagoons, and minimizing winter land
application of manure all help prevent manure discharges to surface waters.
A combination of source water protection, manure management, and water treatment processes can help
reduce surface water pollution and remove contaminants from drinking water. While most research has
focused on pathogen removal during drinking water treatment, a limited base of recent research has provided
some insight into antimicrobial and hormone removal. A stronger understanding of the prevalence and
concentrations of antimicrobials and hormones in drinking water, as well as research on which treatment
processes best remove these compounds, will help in planning strategies to minimize their consumption and
any potential associated health effects.
Good manure management practices, which include the beneficial use of treated manure, linked to sound
nutrient management, can help to minimize many problems related to other contaminants. The USDA and
their state partners provide technical and financial assistance, as well as conservation practice standards for
nutrient and manure management. This report provides a brief introduction to existing programs. The review
is not exhaustive, however it provides links to additional information for individuals working in water quality
programs.
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Table of Contents
Acknowledgements and Disclaimer i
Acronyms and Abbreviations iii
Executive Summary v
1. Introduction 1
2. Distribution of Livestock, and Manure Generation and Management 5
2.1. Background 5
2.2. Cattle, Poultry and Swine 5
2.3. Aquaculture 10
2.4. Summary and Discussion 11
3. Pathogens in Manure 13
3.1. Types of Pathogens Found in Livestock 13
3.2. Pathogens by Livestock Type 18
3.3. Occurrence of Pathogens in Water Resources 19
3.4. Survival of Pathogens in the Environment 20
3.5. Transport of Pathogens in the Environment 22
3.6. Summary and Discussion 25
4. Antimicrobials in Manure 27
4.1. Introduction 27
4.2. Estimates of Antimicrobial Use 28
4.3. Antimicrobial Excretion Estimates 35
4.4. Antimicrobial Stability and Transport in the Environment 35
4.5. Antimicrobial Occurrence in the Environment 36
4.6. Summary and Discussion 37
5. Hormones in Manure 39
5.1. Introduction 39
5.2. Estimates of Exogenous Hormone Use 40
5.3. Hormone Excretion Estimates 41
5.4. Hormone Stability and Transport in the Environment 42
5.5. Hormone Occurrence in the Environment 44
5.6. Summary and Discussion 45
6. Potential Manure-Related Impacts 47
6.1. Harmful Algal Blooms and Cyanotoxin Production 47
6.2. Fish Kills 49
6.3. Antimicrobial Resistance 49
6.4. Endocrine Disruption 56
6.5. Waterborne Disease Outbreaks 58
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6.6. Potential Manure-Related Impacts Summary and Discussion 63
7. Drinking Water Treatment Techniques for Agricultural Manure Contaminants 65
7.1. Source Water Protection 65
7.2. Drinking Water Treatment Techniques 66
7.3. Summary and Discussion 69
8. Managing Manure to Control Emerging Contaminants 71
8.1. Land Application of Manure 71
8.2. Manure Storage 72
8.3. Treating Manure 73
8.4. Financial and Technical Assistance Programs 76
8.5. CAFO Regulations 76
8.6. Additional Technical Resources 77
References 79
Appendix 1. Livestock Animal Unit and Manure Production Calculations 109
Appendix 2. Animal Life Stages 121
Appendix 3. Additional Technical Resources for Manure Management 123
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List of Figures
Figure 6-1. Potential pathways for the spread of antimicrobial-resistance from animals to humans 51
List of Tables
Table 1-1. Key pollutants from livestock operations and animal manure 2
Table 2-1. Top ten states with the highest beef cattle production and associated manure
generation in 2007 6
Table 2-2. Top ten states with the highest total swine (market and breeder hogs) production and
associated manure generation in 2007 7
Table 2-3. Top ten states with the highest broiler chicken production and associated manure
generation in 2007 8
Table 2-4. Top ten livestock and poultry manure producing states in 2007 9
Table 2-5. Top ten states with the highest manure generation in 2007 on a farmland area basis 9
Table 2-6. Top ten aquaculture states in 2005 11
Table 3-1. Occurrence, infective doses, and diseases caused by some of the pathogens present in
manure and manure slurries from cattle, poultry, and swine 14
Table 4-1. Select antimicrobials that are approved for use by the U.S. Food and Drug
Administration for use in humans, livestock, and poultry 28
Table 4-2. Estimates of antimicrobial use or sales for livestock in the U.S 29
Table 4-3. Commonly used antimicrobials administered to beef cattle 30
Table 4-4. Commonly used antimicrobials administered to dairy cows 31
Table 4-5. Commonly used antimicrobials administered to swine 32
Table 4-6. Commonly used antimicrobials administered to poultry 33
Table 4-7. Commonly used antimicrobials and parasiticides in aquaculture 34
Table 5-1. Natural hormones and select metabolites 39
as well as the functional purpose of the hormone 39
Table 5-2. Synthetic hormones that may be administered to and excreted by beef cattle and/or
dairy cows 40
Table 5-3. Estimated livestock and poultry endogenous hormone excretion in the U.S. in 2000 41
Table 5-4. Half-lives of natural and synthetic hormones in the environment 43
Table 6-1. Types of harmful or nuisance inland algae, toxin production, and potential adverse
impacts 48
Table 6-2. Occurrence of antimicrobial-resistant isolates in livestock and poultry manure from
conventional livestock operations 52
Table 6-3. Manure-related waterborne and foodborne disease outbreaks 58
Table 8-1. Key USDA-NRCS programs that may provide financial assistance to producers 76
Table A-l. The number of animal units (AU) and associated manure generation per animal type as
defined by USDA's NRCS 109
Table A-2. Total animal units and estimated tons of manure produced for beef and dairy cattle in
2007 Ill
Table A-3. Total animal units and estimated tons of manure produced for cattle other than beef
and dairy cattle and for all cattle combined in 2007 112
Table A-4. Total animal units and estimated tons of manure produced for breeder and market
hogs in 2007 113
Table A-5. Total animal units and estimated tons of manure produced for swine (breeder and
market hogs combined) in 2007 114
Table A-6. Total animal units and estimated tons of manure produced for broiler and layer
chickens in 2007 115
Table A-7. Total animal units and estimated tons of manure produced for turkeys, as well as all
poultry (broilers, layers, and turkeys combined) in 2007 116
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Table A-8. Livestock (cattle, swine, and poultry) animal units as a total and per acre of farmland in
2007 117
Table A-9. Total estimated livestock and poultry (cattle, swine, and poultry) manure and estimated
tons of manure per acre of farmland in 2007 118
Table A-10. Freshwater and saltwater aquaculture farms in the U.S. during 2005 119
Table A-ll. Aquaculture in the U.S. presented as total acres and sales 120
Table A-12. Livestock animal type and life stages definitions 121
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1. Introduction
This literature Review of Contaminants in Livestock and Poultry Manure and Implications for Water Quality was
prepared as part of the United States Environmental Protection Agency's (USEPA) ongoing efforts to better
understand the environmental occurrence and potential effects related to contaminants of emerging concern.
The report makes no policy or regulatory recommendations; it does identify information gaps that may help
define research needs for USEPA and its federal, state and local partners to better understand these issues.
Over the past 60 years the structure of American agriculture has significantly changed. Across all agricultural
sectors, farm operations have expanded — farms have gotten larger and fewer in number. The shift from the
"family farm" is perhaps most pronounced in the production of livestock and poultry. Since the 1950s, the
production of livestock and poultry in the United States (U.S.) has more than doubled, however the number
of operations has decreased by 80% (Graham and Nachman 2010). Food animal production has evolved
from largely grazing animals and on-farm feed production to fewer and larger operations and increasingly
more to concentrated facilities, often with animals raised in confinement (Ribaudo and Gollehon 2006,
MacDonald and McBride 2009). This has been done, in part, to meet the demands for meat and animal
products from a growing human population in the U.S. and abroad.
The increase in concentration of livestock and poultry also leads to increased concentration of animal manure
that must be managed. As production has shifted to much larger, more concentrated operations, livestock
and poultry operations have become separated from the land base that produces their feed (Gollehon et al.
2001). Historically, manure was used as fertilizer on the farm to provide nutrients for plant growth on the
cropland, pasture or rangeland that, in turn, partly provided the feed for the animals raised on the farm.
Manure can also improve soil quality, when managed appropriately as a fertilizer, where the producer
considers the right rate, timing, source, and method of application (NRC 1993). However, while livestock
manure can be a resource, it can also degrade environmental quality, particularly surface and ground water if
not managed appropriately (Kumar et al. 2005). The geographic concentration of livestock and poultry can
lead to concentrations of manure that may exceed the needs of the plants and the farmland where it was
produced. A report from the U.S. Department of Agriculture's Economic Research Service (USDA ERS)
found that more than 60% of manure nitrogen and 70% of manure phosphorus cannot be assimilated by the
farmland on which it is generated (Gollehon et al. 2001). Runoff related to manure is considered a primary
contributor to widespread nutrient water quality pollution in the U.S., as described in the 2009 "An Urgent
Call to Action" report generated by the Nutrient Innovations Task Group (see also Gollehon et al. 2001,
Ruddy et al. 2006, Dubrovsky et al. 2010).
While manure's contributions to nutrient water quality impairment is perhaps its most widely recognized
impact, manure and livestock management practices may now also be a source of other contaminants (see
Table 1-1). Manure often contains pathogens (many of which can be infectious to humans), heavy metals,
antimicrobials, and hormones that can enter surface water and ground water through runoff and infiltration
potentially impacting aquatic life, recreational waters, and drinking water systems (Gullick et al. 2007, Rogers
2011). The shift towards concentrated livestock production has led to other practices that can contribute
contaminants other than nutrients to the environment. To improve animal production efficiency and
counteract the greater potential susceptibility of disease in concentrated and confined living conditions,
livestock and poultry may be treated with antimicrobials to treat or prevent diseases and infections or treated
sub-therapeutically to promote animal growth (McEwen and Fedorka-Cray 2002). Some livestock and poultry
also receive steroid hormones to promote animal growth and/or control reproductive cycles (Lee et al. 2007).
Pesticides are used to control insect and fungal infestations and parasites as well as other pests. Heavy metals,
such as zinc, arsenic, and copper are sometimes added as micronutrients to promote growth.
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Table 1-1. Key pollutants from livestock operations and animal manure.
Pollutant
Nitrogen
Phosphorus
Potassium
Organic
Compounds
Solids
Salts
Trace
Elements
Volatile
Compounds
Including
Greenhouse
Gases
Pathogens
Antimicrobials
Hormones
Other
Pollutants
Description of Pollutant
Organic forms (e.g., urea) and inorganic
forms (e.g., ammonium and nitrate) in
manure may be assimilated by plants
and algae.
As manure ages, phosphorus
mineralizes to inorganic phosphate
compounds that may be assimilated by
plants.
Most potassium in manure is in an
inorganic form available for plant
assimilation; it can also be stored in soil
for future plant uptake.
Carbon-based compounds decomposed
by micro-organisms. Creates
biochemical oxygen demand because
decomposition consumes dissolved
oxygen in the water.
Includes manure, feed, bedding, hair,
feathers, and dead livestock.
Includes cations (sodium, potassium,
calcium, magnesium) and anions
(chloride, sulfate, bicarbonate,
carbonate, nitrate).
Includes feed additives (arsenic,
copper, selenium, zinc, cadmium), trace
metals (molybdenum, nickel, lead, iron,
manganese, aluminum), and pesticide
ingredients (boron).
Includes carbon dioxide, methane,
nitrous oxide, hydrogen sulfide, and
ammonia gases generated during
manure decomposition.
Includes a range of disease-causing
organisms, including bacteria, viruses,
protozoa, fungi, prions and helminths.
Includes antibiotics and vaccines used
for therapeutic and growth promotion
purposes.
Includes natural and synthetic
hormones used to promote animal
growth and control reproductive cycles.
Includes pesticides, soaps, and
disinfectants.
Pathways to the
Environment
• Overland discharge
• Leachate into ground
water
• Atmospheric deposition
as ammonia
• Overland discharge
• Leachate into ground
water (water soluble forms)
• Overland discharge
• Leachate into ground
water
• Overland discharge
• Overland discharge
• Atmospheric deposition
• Overland discharge
• Leachate into ground
water
• Overland discharge
• Leachate into ground
water
• Inhalation
• Atmospheric deposition
of ammonia
• Overland discharge
• Potential growth in
receiving waters
• Overland discharge
• Leachate into ground
water
• Atmospheric deposition
• Overland discharge
• Leachate into ground
water
• Overland discharge
• Leachate into ground
water
Potential Impacts
• Eutrophication and harmful algal
blooms (HABs)
• Ammonia toxicity to aquatic life
• Nitrate linked to
methemoglobinemia
• Eutrophication and HABs
• Increased salinity in surface
water and ground water
• Eutrophication and HABs
• Dissolved oxygen depletion, and
potentially anoxia
• Decreased aquatic biodiversity
• Turbidity
• Siltation
• Reduction in aquatic life
• Increased soil salinity
• Increased drinking water
treatment costs
• Aquatic toxicity at elevated
concentrations
• Eutrophication
• Human health effects
• Climate change
• Animal, human health effects
• Facilitates the growth of
antimicrobial-resistance
• Unknown human health and
aquatic life effects
• Endocrine disruption in fish
• Unknown human health effects
• Unknown human health and
ecological effects
• Potential endocrine disruption in
aquatic organisms
Adapted from USEPA (2002a) Exhibit 2-2.
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Livestock and poultry operations and related manure management practices account for 18% of all human-
caused greenhouse gas emissions (Steinfeld et al. 2006); ruminant livestock and liquid manure handling
facilities account for nearly 30% of methane emissions from anthropogenic activities (USEPA 201 la). Besides
greenhouse gas emissions, air quality degradation, particularly from concentrated livestock and poultry
operations, has been documented, related to releases of toxic as well as odorous substances, particulates, and
bioaerosols containing microorganisms and human pathogens (Merchant et al. 2005). Air quality degradation
has been related to human health concerns for workers in confined operations and also for neighbors to large
facilities (Donham et al. 1995 and 2007, Merchant et al. 2005, Mirabelli et al. 2006).
Recognizing the potential for human and ecological health effects associated with the other contaminants in
manure, this report focuses on the growing scientific information related to contaminants of emerging
concern - particularly pathogens, antimicrobials, and hormones in manure - and reviews the potential and
documented human health and ecological effects associated with these manure contaminants. Many other
groups and initiatives are focusing on nutrient water quality issues (i.e., Nutrient Innovation Task Group
(NITG) 2009, Dubrovsky et al. 2010), including the relative contributions of animal manure. This report
briefly discusses the magnitude of manure generation (which is often highly localized) for perspective on the
relationship to these emerging contaminants and their prevalence in the environment, for major livestock
types - beef and dairy cattle, swine, poultry and aquaculture. Sections that follow summarize information on
pathogens, antimicrobials, and hormones, followed by a review of known or associated impacts related to
manure. These sections are followed by a brief review of drinking water treatment methods that can help to
deal with contaminants that may be related to manure (and other sources). And the last section of the report
provides some direction to other resources and information on manure management. Following good manure
management practices which include alternative uses of manure that are both economically and
environmentally sustainable, linked to sound nutrient management, can help to minimize many problems
related to other contaminants. The USDA NRCS provides technical and financial assistance as well as
conservation practice standards for nutrient and manure management.
This report is focused on manure and does not address other waste management issues related to livestock
and poultry operations (e.g., disposal of dead animals, spoiled feed). The purpose of this report is to
summarize publicly available literature for those involved with watershed protection and management and the
linked efforts for source water protection and planning for drinking water systems. As noted in the report,
there are very different levels of information available on many of these topics associated with manure.
Hence, the report can also help to identify information gaps and guide research needs for the U.S.
Environmental Protection Agency (USEPA) and other partners to better understand these issues.
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2. Distribution of Livestock, and Manure Generation and Management
2.1. Background
Livestock and poultry production in the U.S. has changed significantly since the 1960's, transitioning towards
larger operations separated from the land base that produces their feed (Graham and Nachman 2010). Also,
large operations now typically specialize in production of one animal type, often at one stage of its lifecycle
(MacDonald and McBride 2009). For example, in swine production, hogs may be transferred from a farrow-
to-feeder farm during the initial life stages, to a feeder-to-finish farm and finally to a slaughter plant, rather
than being raised at one facility (MacDonald and McBride 2009). The majority of animals are also now raised
in confinement where feed is brought to the animal rather than the animals seeking feed in a pasture or on
the range (Ribaudo and Gollehon 2006).
Because of the shift in farming practices towards
larger animal feeding operations, livestock and
poultry production has become more
regionalized, and large volumes of manure are
oftentimes generated relative to smaller land areas
for application (Gollehon et al. 2001). In some
areas, the large quantity of manure generated by
large operations relative to the small area
available for land application magnifies the
potential environmental and human health
impacts associated with manure runoff and
discharges to surface water and ground water.
The mass of manure generated is related to the
mass, or size of the animals involved. For
example, an average 160-pound human produces
approximately two liters of waste per day (feces
and urine), whereas an average 1,350-pound
lactating dairy cow generates 50 liters of manure
(including urine) per day (Rogers 2011). Most
animal manure is applied to cropland or grasslands without treatment. Nutrients may be assimilated by the
growing plants on cropland and grassland (Graham and Nachman 2010). Through manure storage, handling,
and land application, the contaminants associated with manure (i.e., pathogens, antimicrobials, hormones,
etc.; see Table 1-1) have the potential to enter the environment (Kumar et al. 2005, Lee et al. 2007, PCIFAP
2008).
» In 2007, 2.2 billion livestock generated an
estimated 1.1 billion tons of manure (as excreted).
^ In 1998, USEPA estimated that the livestock
manure produced was 13 times greater than all the
human sewage produced in the U.S.
v From 1997 to 2007, the number of swine produced
in the U.S. increased by 45%, but the number of swine
farms decreased by over 30%, resulting in more
concentrated manure generation. Over 40% of all
swine were produced in just two states: Iowa and
North Carolina.
* Cattle (beef, dairy, and other) produce about 80%
of all livestock manure in the U.S. - the top 10
producing states produce about 56% of the total.
2.2. Cattle, Poultry and Swine
This report uses USDA's 2007 Census of Agriculture livestock and poultry inventory counts to illustrate the
distribution of the major animal types (beef and dairy cattle, swine, and poultry) in the U.S. and related
manure generation. These tables presented below (and in Appendix 1), summarizing this information by state,
are simply to provide perspective on the differences that are apparent around the U.S., and to provide insight
on the magnitude of the issues at the state and regional level. These comparisons are made using standard
conversion factors developed by the USDA's Natural Resources Conservation Service (NRCS); livestock and
poultry counts were converted to animal units (AU), which are a unit of measure based on animal weight
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(1 AU — 1,000 pounds live animal weight) (see for example Kellogg et al. 2000, Gollehon et al. 2001). For
example, one beef cow or steer equals one AU, whereas it takes 250 layer chickens to equal one AU. The
amount of manure generated is directly related to animal weight. Therefore, converting animal counts to AUs
allows for the estimation of livestock manure generation and is also a method for standardizing farm
operation size across livestock types (Gollehon et al. 2001). (For further information on AU and manure
generation calculations, refer to Appendix 1). Several USDA and United States Geological Survey (USGS)
reports (i.e., Kellogg et al. 2000, Gollehon et al. 2001, Ruddy et al. 2006) have calculated livestock manure
generation using the 1997 USDA Census of Agriculture data. Their estimates, and those presented in this
report, are very similar in number, scope, and perspective. (These reports, and this current report, all use the
same basic conversion factors noted, but the USDA reports also incorporate more detailed livestock
marketing data). The USDA and USGS reports present results at a more detailed scale (i.e., county,
watershed, or farm-level manure production), and have been focused on nutrients and nutrient management.
Livestock and poultry distribution and manure generation are summarized below (more complete and
detailed state-by-state livestock inventories and estimates of manure generation are tabulated in Appendix 1).
In 2007, approximately 2.2 billion cattle, swine, and poultry were produced in the U.S. (USDA 2009a),
generating an estimated 1.1 billion tons of manure (manure estimates used here are as excreted, wet-weight).
Cattle include beef cattle, dairy cattle, and other cattle and calves (such as breeding stock). Swine include
market hogs, which are sent to slaughter after reaching market weight, and breeder hogs, which are used for
breeding purposes. Poultry includes chickens as broilers (raised for meat), and as layers (produce eggs), and
turkeys. Note that the Census of Agriculture numbers do not account for all the marketing of animals that
takes place during a year, and end-of-year 2007 counts were used for analyses. Different than cattle, poultry
have a high turnover rate throughout the year. For example, broiler chickens are typically sent to slaughter
after five to nine weeks (MacDonald and McBride 2009).
Table 2-1. Top ten states with the highest beef cattle production
and associated manure generation in 2007.
National
Rank
1
2
3
4
5
6
7
8
9
10
State
TEXAS
MISSOURI
OKLAHOMA
NEBRASKA
SOUTH DAKOTA
MONTANA
KANSAS
TENNESSEE
KENTUCKY
ARKANSAS
Top Ten Subtotal
U.S. TOTAL
Total Beef
Cattle AUs
5,259,843
2,089,181
2,063,613
1,889,842
1,649,492
1,522,187
1,516,374
1,179,102
1,166,385
947,765
19,283,784
32,834,801
Percent of
Total Beef
Cattle AUs*
16.0%
6.4%
6.3%
5.8%
5.0%
4.6%
4.6%
3.6%
3.6%
2.9%
59%
Total
Estimated
Tons
Manure
60,488,195
24,025,582
23,731,550
21,733,183
18,969,158
17,505,151
17,438,301
13,559,673
13,413,428
10,899,298
221,763,516
377,600,212
* Animal units (AUs) represent 1,000 pounds of live
cattle per AU (see Kellogg et al. 2000, Gollehon et al.
for complete listing of all states. Reference: Inventory
animal weight, or one beef
2001). See Appendix 1
from USDA 2009a.
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The changes in livestock and poultry production — the shift towards fewer, larger, more concentrated
production facilities - has resulted in regional and local differences in the distribution of the 2.2 billion
animals raised in the U.S. These differences will in turn relate to differences in the issues involved in manure
management and the potential for environmental impacts of various contaminants. For example, beef cattle
are produced predominantly in the Great Plains and Midwest. According to USDA's 2007 Census of
Agriculture, Texas alone accounts for 16% of U.S. beef cattle production with an estimated 60.5 million tons
of manure generated - two and a half times greater than the amount generated by the second largest beef
cattle producing state (Table 2-1). In contrast, swine are largely produced in Iowa and North Carolina,
accounting for 27% and 16%, respectively, of total U.S. production (Table 2-2). Broiler production is
predominantly based in the southern and eastern U.S., with Georgia, Arkansas, and Alabama accounting for
nearly 30% of U.S. production. An estimated 20.3 million tons of manure from broiler chickens was
generated in those three states in 2007 (Table 2-3).
Table 2-2. Top ten states with the highest total swine (market
and breeder hogs) production and associated manure
generation in 2007.
National
Rank
1
2
3
4
5
6
7
8
9
10
State
IOWA
NORTH
CAROLINA
MINNESOTA
ILLINOIS
INDIANA
NEBRASKA
MISSOURI
OKLAHOMA
KANSAS
OHIO
Top Ten Subtotal
U.S. TOTAL
Total
Swine AUs
2,409,994
1,382,252
999,762
607,844
486,599
462,548
435,930
367,821
256,349
243,700
7,652,800
8,910,943
Percent of
Total Swine
AUs*
27.0%
15.5%
11.2%
6.8%
5.5%
5.2%
4.9%
4.1%
2.9%
2.7%
86%
Total
Estimated
Tons
Manure
31,912,337
17,056,820
12,767,962
7,289,960
6,140,286
5,543,892
5,252,950
4,140,186
3,171,100
3,066,558
96,342,053
111,256,177
* Animal units (AUs) represent 1,000 pounds of live animal weight (see Kellogg
et al. 2000, Gollehon et al. 2001). See Appendix 1 for complete listing of all
states. Reference: Inventory data from USD A 2009 a.
Manure management is inherently a local issue, related to the number and type of animals, the land base for
application of the manure, the type of operations (i.e., confined feeding operations), and many management
factors. Detailed information on all these factors is more difficult to come by, and such estimates are not the
purpose or within the scope of this report. (The USDA's Census of Agriculture also does not provide this
information (Gollehon et al. 2001)). However, in 2002, a comprehensive review of state livestock production
programs was conducted on behalf of USEPA to provide estimates of the number of Animal Feeding
Operations (AFOs) and Concentrated Animal Feeding Operations (CAFOs) in each state (Tetra Tech, Inc.
2002). According to that study, the states that had the most AFOs with more than 1,000 AUs were Iowa,
North Carolina, Georgia, and California.
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Table 2-3. Top ten states with the highest broiler chicken
production and associated manure generation in 2007.
National
Rank
1
2
3
4
5
6
7
8
9
10
State
GEORGIA
ARKANSAS
ALABAMA
MISSISSIPPI
NORTH CAROLINA
TEXAS
MARYLAND
DELAWARE
KENTUCKY
MISSOURI
Top Ten Subtotal
U.S. TOTAL
Total
Broiler
AUs
517,363
444,830
391,953
330,982
329,498
260,686
143,964
112,291
109,399
102,537
2,743,505
3,522,083
Percent of
Total Broiler
AUs*
14.7%
12.6%
11.1%
9.4%
9.4%
7.4%
4.1%
3.2%
3.1%
2.9%
78%
Total
Estimated
Tons
Manure
7,744,926
6,659,104
5,867,541
4,954,799
4,932,592
3,902,473
2,155,138
1,680,999
1,637,707
1,534,984
41,070,264
52,725,576
* Animal units (AUs) represent 1,000 pounds of live animal weight, or 455
broilers per AU (see Kellogg et al. 2000, Gollehon et al. 2001). See Appendix
1 for complete listing of all states. Reference: Inventory data from USD A 2009 a.
While manure use and management is a local issue, the state data can also provide some illustrations and
valuable perspectives. Table 2-4 summarizes the top ten states related to manure production (this is the sum
of the AUs for all livestock, swine, and poultry, and the estimated manure production, as excreted; see
Appendix 1). As might be expected, the list is comprised of the major agricultural states, including Texas,
Iowa, and California. Texas accounts for about 12% of the AUs and manure produced in the U.S. Total AUs
and manure are dominated by beef and dairy numbers because of their body size. Nationally, cattle were
responsible for nearly 83% of total livestock manure generation in 2007, followed by swine (10%) and poultry
(7%). Refer to Appendix 1 for complete livestock and poultry production and manure generation tables.
As discussed, many of the concerns for environmental impacts of manure generation relate to settings where
there is a large mass of manure but a relatively small land base for application of the manure. Even at the
state level, these differences can be illustrated. The top livestock states, such as Texas, California, and Iowa
(Table 2-4) also have large areas of farm land. Presenting total manure generation on a farmland area basis
paints a different picture. Table 2-5 shows the state level estimate for tons of manure generated per farmland
acre. Smaller states along the eastern seaboard rise to the top of the list; these states are key poultry and swine
producing states but have far more limited farmland than the major farm states. (This tabulation divides the
total estimated manure for livestock and poultry by the acreage for "land in farms" from the 2007 Census of
Agriculture (USDA 2009a). "Land in farms" is defined by the USDA (2009a) as primarily agricultural land
used for grazing, pasture, or crops, but it may also include woodland and wasteland that is not under
cultivation or used for grazing or pasture, provided it is on the farm operator's operation. This is an
oversimplification at the state level: land in farms is an overestimate of the actual land likely available for
application of manure; manure as excreted is likely an overestimate of the mass of manure to be handled,
dependent on the management practice. However, it illustrates the differences that are inherent in the
distribution of the different types of livestock and poultry settings around the U.S.
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Table 2-4. Top ten livestock and poultry manure producing
states in 2007.
National Rank
1
2
3
4
5
6
7
8
9
10
State
TEXAS
CALIFORNIA
IOWA
NEBRASKA
KANSAS
OKLAHOMA
MISSOURI
WISCONSIN
MINNESOTA
SOUTH DAKOTA
U.S. TOTAL
Total AUs
11,109,770
5,235,439
5,586,515
5,235,899
4,932,902
4,571,012
4,178,962
3,213,092
3,268,570
3,179,772
92,969,509
Percent of
Total U.S.
Manure
11.5%
6.2%
6.1%
5.3%
5.0%
4.7%
4.3%
3.8%
3.6%
3.3%
Total
Estimated
Tons Manure
128,048,896
68,496,143
68,360,493
59,100,556
55,792,510
52,036,892
48,070,611
42,531,594
39,816,914
36,358,712
1,113,232,385
* Data estimated from USDA's 2007 Census of Agriculture livestock counts
converted to animal units, folkwing USDA 's NRCS methodology. Reference:
USDA 2009a.
Table 2-5. Top ten states with the highest manure generation in
2007 on a farmland area basis.
National Rank
1
2
3
4
5
6
7
8
9
10
State
NORTH CAROLINA
DELAWARE
VERMONT
PENNSYLVANIA
WISCONSIN
CALIFORNIA
NEW YORK
MARYLAND
VIRGINIA
IOWA
Estimated Tons
Manure/Acre
Farmland*
3.85
3.81
3.05
2.99
2.80
2.70
2.66
2.23
2.22
2.22
* Refer to Appendix 1 for further description on
livestock manure generation calculations. Reference:
USDA 2009a.
The way in which livestock and poultry are raised differs by animal type as well as the size of the production
facility. Chapter 8 provides further information on manure management programs and strategies. Beef cattle
tend to be raised outdoors in pens or corrals, where the manure accumulates and is scraped up along with any
bedding materials and soil (in pens), stored in a facility, or stockpiled until it can be land applied on or off-site
(USEPA 2009a). In larger, concentrated operations, drainage ditches may flow through beef cattle operations,
discharging stormwater, manure, animal feed, bedding materials, and other waste to a nearby collection pond
or lagoon (Gullick et al. 2007). Dairy cows may be housed in tie stall barns, free stall barns, or outdoor open
lots (USEPA 2009b). Dairy cow manure may be scraped from indoor barns and temporarily stored in a solid
stack in steel or concrete tanks, or flushed from barn surfaces and discharged to lagoons (Zhao et al. 2008).
Swine are typically housed over slatted floors, allowing manure to be washed down and routinely flushed out
of the housing facility (Gullick et al. 2007). Swine manure may be flushed to an underground pit (57% of
operations), a lagoon (23% of operations), or another storage area, like a manure pile (20% of operations)
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(USDA 2002a). Poultry, including broilers, layers, and turkeys, are almost always raised indoors with manure
accumulating and mixing with bedding material (Zhao et al. 2008). Most layers are housed in elevated cages,
allowing manure to accumulate below or drop onto a conveyer belt that removes the manure from the
building (Gullick et al. 2007). Manure from layers is typically washed from the housing facility to a storage pit
(Zhao etal. 2008).
Swine and dairy cow production, in particular, have become increasingly concentrated. Between 1997 and
2007, there was a 33% decrease in the number of swine farms yet a 45% increase in the number of swine
processed (USDA 2009a). As shown in Table 2-2, 86% of all U.S. swine production in 2007 occurred in the
top ten swine producing states, and the top five states alone account for over two-thirds of U.S. production.
From 1997 to 2007 there was a 44% decrease in the number of dairy farms in the U.S., yet the number of
dairy cows has remained relatively level, increasing by 1% during that time period (USDA 2009a).
2.3. Aquaculture
Aquaculture is a unique component of commercial animal production, very directly related to water
resources, and it is also discussed in this report where information is available. The aquaculture sector of U.S.
agriculture has been steadily increasing, with a rise in demand for seafood coinciding with declining wild fish
and shellfish populations; in providing controlled conditions it may offer production advantages of selective
breeding as well as improved disease control (Cole et al. 2009). The USDA's 2005 Census of Aquaculture
reported over 4,300 aquaculture farms in the U.S., covering nearly 700,000 acres (USDA 2006). Aquaculture
operations may be either freshwater or saltwater, producing an array of aquatic organisms. Aquaculture
products include food fish (e.g., catfish, salmon, carp), sport fish (e.g., bass, crappie, walleye), ornamental fish
(e.g., goldfish, koi), baitfish (e.g., crawfish, fathead minnows), crustaceans (e.g., crawfish, lobsters, shrimp),
mollusks (e.g., mussels, oysters), aquatic plants, and other animals (e.g., alligators, snails, turtles) (USDA
2006). According to the USDA's Aquaculture Census, production in 2005 was situated predominantly in the
southern U.S., with Louisiana having the highest total number of freshwater and saltwater operations, as well
as the most acres used for aquaculture (USDA 2006). Related to regionalized production and larger but fewer
farms, in 2005, the top ten states alone accounted for 95% of the total U.S. aquaculture acreage (see Table
2-6), but less than 50% of the nation's aquaculture farms (refer to Appendix 1 for a complete table).
Catfish production was the dominant commodity in U.S. aquaculture in 2005, with nearly one-third of
production occurring in Mississippi (USDA 2006). Trout were the second largest commodity - the majority
of which were produced in Idaho (USDA 2006). Catfish are typically raised in ponds, while trout are often
reared in flow-through raceways. As defined by the USDA's 2005 Aquaculture Census, flow-through
raceways are long, narrow, confined structures in which the water flows into one end and exits the other
(USDA 2006). Raceways can be closed systems, in which water flows through a series of ponds prior to
discharging into a headwater pond that flows back into the system, or they can be directly linked with a river
or stream, using the natural flow to flush water through the system and back into a stream.
Waste produced in aquaculture consists of feces, excess feed, dead fish and other aquatic organisms,
nutrients, antibiotics, hormones, pesticides, anesthetics, minerals, vitamins, and pigments (Gullick et al. 2007,
Cole et al. 2009). As reviewed by Amirkolaie (2011), up to 15% of feed may be uneaten or spilled, and
between 60% and 80% of dietary dry matter may be excreted in intensive aquaculture operations. Aquaculture
waste may be managed by removing solids from the water via a settling basin or filtration system, after which
the solids may be composted or applied to cropland as fertilizer (Gullick et al. 2007).
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Table 2-6. Top ten aquaculture states in 2005.
National
Rank
1
2
3
4
5
6
7
8
9
10
Top Ten
Subtotal
U.S.
TOTAL
State
LOUISIANA
MISSISSIPPI
FLORIDA
ALABAMA
ARKANSAS
WASHINGTON
NORTH
CAROLINA
MASSACHUSETTS
VIRGINIA
CALIFORNIA
--
--
Total # of
Farms
873
403
359
215
211
194
186
157
147
118
2,863
4,309
State
LOUISIANA
MISSISSIPPI
CONNECTICUT
ARKANSAS
MINNESOTA
ALABAMA
WASHINGTON
VIRGINIA
CALIFORNIA
TEXAS
--
--
Total Farm
Acres
320,415
102,898
62,959
61,135
41,023
25,351
13,478
12,555
9,340
7,083
656,237
690,543
* See Appendix 1 for complete
Reference: USD A 2006.
listing of all states and total aqu
'aculture acreage.
2.4. Summary and Discussion
Livestock production in the U.S. is a major industry, representing $154 billion in sales in 2007 — nearly a 55%
increase since 1997 (USDA 1999, USDA 2009a). In 2007, 77.6 million cattle AUs (beef and dairy), 8.9 million
swine AUs, and 6.4 million poultry AUs generated over 1.1 billion tons of manure (see Appendix 1; inventory
data from USDA 2009a). Throughout the various stages of livestock production, considerable amounts of
manure and associated contaminants can enter the environment, potentially impacting surface water and
ground water, through runoff and discharges. According to the USDA, the shift towards large animal feeding
operations and confined operations has resulted in the concentration of wastes and other changing
production practices (MacDonald and McBride 2009). Livestock and poultry production has become more
concentrated, and larger volumes of manure are generated relative to local land areas where it may be applied;
with limited farmland available for manure application, the potential for environmental impacts is of
increased concern (Gollehon et al. 2001). For example, despite the fact that dairy cow production remained
relatively level between 1997 and 2007, the total number of dairy farms in the U.S. decreased by nearly half
during that same ten year time period (USDA 2009a), indicative of the shift towards larger livestock
production operations.
The remaining chapters of this report focus on livestock excretion of some key contaminants (e.g., pathogens,
antimicrobials, hormones), and their stability in the environment. Livestock manure is a source of pathogens
that have the potential to cause infections in humans. Widespread livestock antimicrobial use has been shown
to facilitate the growth of antimicrobial-resistant bacteria (WHO 2000), and there is evidence of a linkage
between antimicrobial-resistant human infections and foodborne pathogens from animals (Swartz 2002).
Hormones excreted by livestock also may contribute to risks to aquatic life, potentially impacting fish
reproductive fitness and behavior (Lee et al. 2007, Zhao et al. 2008). Chapter 6 of this report provides a
review and analysis of the potential human health and ecological impacts of these emerging contaminants
associated with manure.
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3. Pathogens in Manure
Manure from livestock and poultry contains a variety of pathogens; some are highly host-adapted and not
pathogenic to humans, while others can produce infections in humans (USEPA 2002b). Pathogens that are of
animal origin but that can be transmitted to humans are termed "zoonotic" and include prions, viruses,
bacteria, protozoa, and helminths (Rogers and Haines 2005). Some may infect one type of livestock, while
others may infect several types of animals in addition to humans (Cotruvo et al. 2004). Zoonotic pathogens
can have serious public health consequences and garner public attention when major outbreaks occur. Animal
agriculture has been implicated as a possible source of contamination in a number of significant outbreaks of
human illness (see Section 6.5).
Zoonotic pathogens can be difficult to eradicate from livestock and poultry production facilities because
some are endemic to the animal (Rogers and Haines 2005, Sobsey 2006). Furthermore, zoonotic pathogens
may have a resistant stage in their life cycle (e.g., a cyst or spore) that enhances their survival in the
environment and facilitates transmission to other animals or humans through ingestion of fecal-contaminated
water or food. Zoonotic pathogens have the potential for transport to ground water and surface water and
may be subsequently ingested through recreation or drinking water (see Section 3.4), with potential
implications for human and animal health. They may also contaminate food crops through fecally-
contaminated runoff or irrigation water or by contact with soil to which manure has been applied (e.g.,
Pachepsky et al. 2012, Pachepsky et al. 2011, Rogers and Haines 2005) (see Section 6.5).
This chapter will evaluate manure-associated pathogens that may cause human illness and the various factors
contributing to human exposure. Sections 3.1 and 3.2 cover pathogen characteristics, infectious doses, and
prevalence by livestock type for important select examples. Section 3.3 briefly discusses the occurrence of
pathogens in surface water, ground water, and sediments. Survival of pathogens in various environmental
media (manure, soil, sediment, and water) is discussed in Section 3.4, and transport in the environment is
discussed in Section 3.5.
3.1. Types of Pathogens Found in Livestock
A number of pathogens are associated with fecal matter from livestock and poultry, but only a few pose a
known or potential threat to humans, including (USEPA 2004a, Rogers and Haines 2005, Sobsey et al. 2006,
Pappas et al. 2008, Bowman 2009):
Bacteria: Escherichia mli (E. coli) O157:H7 and other shiga-toxin producing strains, Salmonella spp.,
Campylobacterjejuni, Yersinia enterocolitica, Shigella sp., Eisteria monocjtogenes, Eeptospira spp., Aeromonas
hydrophila, Clostridiumperfringens, bacillus anthraxis (in endemic area) in mortality carcasses
Parasites: Giardia lamblia, Cryptosporidiumparvum, ¥>alantidium coli, Toxoplasmagondii, Ascaris suum and
A. lumbricoides, Trichttris trichuria
Viruses: Rotavirus, hepatitis E virus, influenza A (avian influenza virus), enteroviruses, adenoviruses,
caliciviruses (e.g., norovirus)
In addition to pathogens (and often in lieu of pathogens), environmental samples can be tested for microbial
indicator organisms, which indicate the possibility of fecal contamination (and thus, the possibility of
pathogens). Commonly used indicator organisms include fecal coliforms, E. coli, and enterococci (Perdek et
al. 2003). Clostridium perfringens and coliphages also show promise as indicators because they are present in
manure from all animals (e.g., Perdek et al. 2003) (C. perfringens is a spore-forming bacterium that is common
on raw meat and poultry and is a common cause of foodborne illness (CDC 201 la)). Testing for indicator
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organisms is more efficient and less expensive than testing for a suite of pathogens associated with livestock
and poultry runoff. Indicator organisms have been detected in manure and slurry as well as in runoff (e.g.,
Thurston-Enriquez et al. 2005, Wilkes et al. 2009). Indicators can, however, have different survival and
transport capabilities than pathogens and do not always correlate well with illness or with the pathogens
themselves (Perdek et al. 2003). As rapid molecular genetic methods of pathogen detection and enumeration
gain wider use, reliance on microbial indicators will lessen. In addition, research is ongoing to better
understand the relationships between indicators, pathogens, and other environmental variables such as
hydrological conditions and persistence in soils environments (e.g., Wilkes et al. 2009; Rogers et al. 2011).
Table 3-1. Occurrence, infective doses, and diseases caused by some of the pathogens present in
manure and manure slurries from cattle, poultry, and swine.
Pathogen
Occurrence (% of positive manure
samples)*
Cattle
Poultry
Swine
Infective
Doses
Human Diseases and Symptoms
Baetarta
Salmonella spp.
£ co// 0157:H7
Campylobacter
spp.
Yersinia
enterocolitica
Listeria spp.
0.5- 18
3.3-28
5-38
-
0-100
0-95
0
57-69
-
8**
7.2 - 100
0.1 - 70
14-98
0-65
5.9-20
100-
1,000 cells
5 -10 cells
< 500 cells
10,000,00
0 cells
<10,000
cells
Salmonella enteritis, Typhoid Fever, Paratyphoid
fever (diarrhea, dysentery, systemic infections that
spread from the intestinal tract to other parts of
the body, abdominal pain, vomiting, dehydration,
septicemia arthritis and other rheumatological
syndromes)
Enteric colibacillosis (diarrhea with or without
bleeding), abdominal pain, fever, dysentery, renal
failure, hemolytic-uremic syndrome , arthritis and
other rheumatological syndromes
Campylobacter enteritis (diarrhea, dysentery,
abdominal pain, malaise, fever, nausea, vomiting,
septicemia, meningitis,, Guillain-Barre syndrome
(neuromuscular paralysis), arthritis and other
rheumatological syndromes
Yersiniosis (Intestinal infection mimicking
appendicitis, diarrhea, fever, headache, anorexia,
vomiting, pharyngitis, arthritis and other
rheumatological syndromes)
Listeriosis (diarrhea, systemic infections,
meningitis headache, stiff neck, confusion, loss of
balance convulsions miscarriage or stillbirth)
Brsrtoiea
Cryptosporidium
spp.
Giardia
0.6-23
0.2 - 46
6-27
-
0-45
3.3- 18
10 -1,000
oocysts
10-25
cysts
Cryptosporidiosis (infection that can be
asymptomatic, cause acute but short-lived
diarrheal illness, cause chronic diarrheal illness, or
be quite severe and cholera-like, with cramping,
abdominal pain, weight loss, nausea, vomiting,
fever, pneumonia, biliary system obstruction and
pain)
Giardiasis (diarrhea, abdominal cramps, bloating,
fatigue, hypothyroidism, lactose intolerance,
chronic joint pain)
References: Rogers and Raines 2005, Pachepsky et al. 2006, Bowman 2009, USEPA 2010a, Ziemer et al. 2010, and
USD A 2007a, 2007b, 2009'b, and 2010 a., Ho et al. 2007, Weber et al. 1995, Mohammed et al. 2009.
* Percentage of manure samples testing positive for the pathogen. Range of minimum and maximum percentage as reported in the
literature. ** Eased on a single study.
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Information on the prevalence, illnesses (primarily gastrointestinal), and infectious doses (numbers of
organisms required to cause infection) associated with some of the bacterial and protozoan agents are
provided in Table 3-1. Occurrence indicates the percentage of manure samples in which the pathogen was
detected. The subsections below provide brief descriptions of selected bacterial, protozoan, and viral
pathogens as well as summaries of the pathogens associated with each animal type.
3.1.1. Bacteria
Below are brief summaries of five zoonotic pathogenic bacteria that can cause serious waterborne or
foodborne illness and that are associated with animal manure: Salmonella, E. cob O157:H7, Camfylobacter,
Yersinia entemcolitica, and Usteria monocytogems. This list is not comprehensive, but includes some of the
organisms that figure prominently in illness and mortality.
3.1.1.1. Salmonella
Nontyphoidal Salmonellae, the type of Salmonella typically associated with the human infection salmonellosis,
are found in the gastrointestinal tracts of cattle, poultry, and swine. (The typhoid agents Salmonella typhii and
paratyphi are specific to humans and are therefore not zoonotic). A higher prevalence of Salmonella has been
detected in larger chicken, dairy cow, and swine animal feeding operations related to increased herd density
and size as well as increased shedding of Salmonella (Bowman 2009, USEPA 2010a). Salmonella prevalence also
varies with animal age and type (Seller et al. 2010). The infectious dose for Salmonella is estimated to range
from 100 to 1,000 cells (Ziemer et al. 2010), and in 2009, nearly 50,000 cases of salmonellosis were reported
in the U.S. (CDC 2011b), although that number does not distinguish between foodborne and waterborne
cases.
3.1.1.2. E. co/i O157-.H7
Most strains of E. coli bacteria are harmless and live in the intestines of healthy humans and other animals
(Rosen 2000). E. coli O157:H7, however, is a pathogenic strain of the group enterohemorrhagic E. coli
(EHEC). This strain is an emerging cause of waterborne and foodborne illness and has been implicated in a
number of outbreaks (Table 6-3) (Gerba and Smith 2005). E .coli O157:H7 is especially dangerous to young
children and the elderly. Similarly to Salmonella, a higher prevalence of E. coli O157:H7 has been detected in
larger dairy cow and swine production operations (Bowman 2009). E. coli O157:H7 has been found to be
more prevalent in the gastrointestinal system and manure of young calves, lambs, and piglets (Hutchinson
2004, Seller et al. 2010) and appears to colonize cattle for one to two months (Rosen 2000). Prevalence tends
to vary by season, increasing during warmer, summer months (Hutchison 2004) and decreasing in colder,
winter months (Muirhead et al. 2006). In contrast to Salmonella, the infectious dose of E. coli O157:H7 is quite
low, with estimates of 5 to 10 cells (Ziemer et al. 2010).
3.1.1.3. Campylobacter
ii bacteria are commonly transmitted to humans via contaminated water and food (Perdek et
al. 2003) and may co-occur with E. coli (AWWA 1999). Campylobacter prevalence appears to vary depending on
the age of the animal, though conflicting results among reports suggest that other environmental (i.e., animal
feeding operation size) and animal-specific factors likely influence prevalence. For example, Hutchison (2004)
reported higher prevalence of Campylobacter in wastes generated by livestock containing young animals (calves,
lambs, or piglets), whereas Seller et al. (2010) and USEPA (2010a) reported increased prevalence in older
animals. Estimates for infectious dose in humans are generally < 500 organisms (Table 3-1) (Rosen 2000,
Pachepsky et al. 2006, Bowman 2009).
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3.1.1.4. Yersinia enterocolitica
litica causes gastroenteritis and is generally known as a foodborne pathogen (Perdek et al. 2003),
although Yersinia species are also found in water as well as wild and domestic animals (Rosen 2000). Yersinia
enterocolitica\\?& been detected in swine feces (Olson 2001). In particular, Yersinia enterocolitica O:3 is pathogenic
to humans and has been found in the tonsils, oral cavities, intestines, and feces of up to 83% of pigs (Olson
2001); pigs are thus considered a primary reservoir for this pathogen (Rosen 2000). The infectious dose may
be in the range of millions of bacteria (Rogers and Haines 2005). Y. enterocolitica and other Y. enterocolitica-\&&
organisms have been isolated from feces of pigs, cattle, and other animals (Brewer and Corbel 1983).
3.1.1.5. Listeria monocytogenes
Usteria monocytogenes causes severe illness, including diarrhea and meningitis. This bacterium is resistant to
adverse environmental conditions (i.e., heating, freezing, and drying). Pathogenic strains are found in
ruminants in which they can cause disease (Bowman, 2009). Usteria monocytogenes is also found in poultry
(Chemaly et al. 2008) as well as sheep, pigs, and other animals (Weber et al. 1995). Levels of Usteria spp. can
vary by season; Hutchinson (2004) reports that it is more likely to be isolated during March to June
(Hutchinson 2004). Husu et al. (2010) reported that prevalence in fecal samples is higher during the indoor
season than when the animals are at pasture. According to the USFDA (2012a), the infectious dose for
humans may vary widely and depends upon a number of factors, including the strain, susceptibility of the
host, and the matrix in which it is ingested. It has been reported to be <10,000 (Table 3-1), but USFDA
(2012a) notes that for susceptible individuals consuming raw or inadequately pasteurized milk, it may be as
low as 1,000 cells.
3.1.2. Parasites
Three selected types of illness-causing parasites that may be present in manure, Cryptosporidiumparvum, Giardia
lamblia, and helminthes (worms) are briefly discussed below. Cryptosporidium and Giardia cause gastrointestinal
illness; infection with helminthes can cause problems that include pneumonia, cysts, or intestinal infections.
3.1.2.1. Cryptosporidium
Cryptosporidium parvum is a protozoan parasite that can cause cryptosporidiosis, or gastric and diarrhea! illness,
in humans (Table 3-1) (Rose 1997). Cryptosporidiosis can be contracted through ingestion of small, hardy
oocysts from fecally contaminated drinking water supplies, food, recreational waters, pools, and direct contact
with animals (Perdek et al. 2003). There is currently no treatment for Cryptosporidiosis, and it can lead to
fatality in vulnerable populations such as the immunocompromised. Cryptosporidium parvum is shed primarily
by relatively young animals (Rosen 2000, Bowman 2009), and upper age estimates for shedding range from 30
days (Rosen 2000) to six months (Atwill 1995). Prevalence is greater during the summer months (Garber et al.
1994, Scott et al. 1994). Cattle can shed substantial quantities of oocysts; estimates include 10 million (Rosen
2000) to more than one billion oocysts per gram of manure (USEPA 2004a), which is orders of magnitude
higher than the infectious dose (Table 3-1) (Bradford and Schijven 2002, Pachepsky et al. 2006).
3.1.2.2. Giardia
Giardia lamblia is the most common cause of protozoan infection in humans (Perdek et al. 2003), causing a
gastrointestinal illness known as Giardiasis. Giardiasis can be treated with drugs, and it is not considered a
fatal illness. Giardia lamblia forms a durable egg-like cell called a cyst through which infection is transmitted,
typically via ingestion of fecal-contaminated water (Ziemer et al. 2010). Giardia may be present in cattle as
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young as five days old, up to adults, although prevalence peaks when the calves are young. Prevalence has
been reported to range from less than 14% to 100% in calves less than six months old (Rosen 2000, Seller et
al. 2010). As with Crypto sporidium, the infectious dose for Giardia is low (10 to 25 cysts) (Pachepsky et al.,
2006), and Giardia cysts can be shed in large numbers. According to one study, concentrations of Giardia cysts
can be over 1,000 cysts/g in swine lagoon wastewater (Ziemer et al. 2010).
3.1.2.3. Helminthes
Helminthes are worms that may be parasitic in plants and animals or may be free-living (NRCS/USDA,
2012). Parasitic worms of concern include Platyhelminthes (flatworms) and Nematoda (roundworms). Some
(e.g., most flatworms) have complex lifecycles that require several hosts (Rogers and Haines 2005). The most
common parasite in humans is Ascaris lumbricoides, a large parasitic roundworm for which humans are the
definitive host (NRCS/USDA/2012, Ziemer et al. 2010). Important helmmthes that infect livestock include
Ascaris suum and Trichuris suis (cattle and pigs) (Bowman 2009). Ascaris suum is associated with swine in
particular (Ziemer et al. 2010); its eggs are hardy and can survive in soil and feces for years (Olsen 2001).
Illnesses caused by Ascaris sp. include pneumonia when the worms invade the lungs or intestinal infection
(NRCS/USDA 2012). Infection of humans with zoonotic helminthes generally occurs via consumption of
raw or undercooked meat rather than through exposure to feces (Ziemer et al. 2010); these organisms are not
discussed further in this chapter.
3.1.3. Viruses
A number of viruses, including prevalent enteric viruses that cause gastroenteritis, are present in livestock and
poultry and have zoonotic potential. Below are brief descriptions of three common viruses: rotavirus,
norovirus, and hepatitis E virus.
3.1.3.1. Rotavirus
Rotavirus is an enteric virus that causes millions of cases of diarrhea in the U.S., primarily in infants and
children less than two years of age (Perdek et al. 2003). It has been found in swine, cattle, lambs, and other
animals (Cook et al. 2004). There is evidence for zoonotic transmission in that serotypes and genotypes of
animal strains have been found in humans, and there is evidence for reassortment (mixing) of genetic material
between human and animal rotaviruses (Laird et al. 2003, Cook et al. 2004, Ziemer et al. 2010). The estimated
infectious dose for rotavirus is low (10 to 100 virus particles) (Grieg and Todd 2010).
3.1.3.2. Norovirus
Noroviruses are enteric viruses that cause diarrhea in humans as well as livestock in swine and cattle. They are
a leading cause of non-bacterial gastroenteritis, estimated to cause more than 90% of outbreaks worldwide
(Wang et al. 2006). Swine are believed to serve as an important reservoir for human norovirus, which is
closely related to porcine norovirus. Also, there may be reassortment between human and porcine strains
(Mattison et al. 2007). A study by Wang et al. (2006) found that noroviruses are found only in finisher hogs,
(those ready for slaughter), with a prevalence of 20%. The infectious dose is estimated at 10 to 100 virus
particles (Moe et al. 1999).
3.1.3.3. Hepatitis E
Hepatitis E virus (HEV) causes liver inflammation. Humans are the primary reservoir, but swine are also an
important reservoir (Perdek et al. 2003, Kasorndorkbua et al. 2005). According to one study, up to 100% of
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swine tested seropositive for HEV in commercial herds in the Midwestern U.S. (Meng et al. 1997). Another
study identified HEV ribonucleic acid (RNA) in about 23% of hogs (Fernandez-Barredo et al. 2006). Swine
shed the virus for three to four weeks, primarily weaners (hogs being weaned from nursing) and hogs in their
first month of feeding (Kasorndorkbua et al. 2005). Swine and human HEV are closely related (Meng et al.
1997). Researchers have noted cross-species infections of human and swine HEV (e.g., Ziemer et al. 2010).
The infectious dose is not known (PHAC 2010), nor is its survival in manure known (Ziemer et al. 2010).
3.2. Pathogens by Livestock Type
Several of the major zoonotic pathogens, including those described in the previous section, are associated
with more than one type of livestock, although the health risks that they pose may vary depending upon the
species and prevalence. The following subsections briefly summarize which pathogens associated with cattle,
swine, and poultry may cause illness in humans.
3.2.1. Cattle
Beef and dairy cattle are carriers of several zoonotic
pathogens including E. cob O157:H7, Cryptosporidium
parvum, Giardia lamblia, Campjlobacter, Leptospira, various
enteroviruses, norovirus, Usteria monocjtogenes, and
Salmonella (Cotruvo et al. 2004, Bowman 2009) (Table 3-1).
The prevalence of some pathogens has been found to be
greater in larger herds (e.g., Bowman 2009, USEPA 2010a;
subsections 3.1.1 and 3.2.1). Cattle are an important
reservoir of E. coli O157:H7, and any herd may contain
asymptomatic animals. Estimates of E. coli O157:H7
prevalence vary widely. According to a study published for
the World Health Organization (WHO), an estimated 30%
to 80% of cattle carry E. coli O157:H7 (Cotruvo et al.
2004). In contrast, a study of cattle in 13 U.S. states
showed that less than 2% of cattle tested positive for the
organism (Dargatz 1996). Other estimates range from
about 3% to 28% (Table 3-1; see text box). Cattle are also considered to be a significant source of potential
human infection with Giardia lamblia (Bowman 2009) and Crjptosporidiumparvum (Table 3-1).
E. Co//O157:H7 in Cattle
E. coli is found frequently among cattle
operations. A 1997 survey of 100 feedlots
in the U.S. found E. cob O157:H7 in 63%
of the feedlots tested. However, only 1.8%
of manure samples tested positive at these
feedlots. Another study found that as
many as 28% of beef cattle were shedding
E. coli. O157:H7, and more than 43% of
carcasses tested positive for the bacterium
(References: Hancock et al. 1997, Bowman
2009).
3.2.2. Swine
Swine are hosts to a large number of pathogens including Campjlobacter, Yersinia enterocolitica, Giardia, Salmonella,
Crjptosporidium, E. coli O157:H7, Leptospira, Ealantidium coli, Listeria, and viruses (rotavirus, norovirus, HEV)
(Perdek et al. 2003, Rogers and Haines 2005, Mattison et al. 2007, Ziemer et al. 2010, USEPA 2010a). A U.S.
survey found that about 80% of pigs older than three months test positive for HEV (Bowman 2009). Swine
urine is a potentially important source of L£ptospira, which has been implicated in waterborne infections
(Bowman 2009). Swine Cryptosporidia present a lower risk to humans because the species they carry are
specifically adapted to swine as a host (USEPA 2010a). These pathogens may be transmitted to humans either
through direct contact with swine waste (e.g., workers at an animal feeding operation) or indirectly through
the environment (e.g., swimming in manure-contaminated water or consuming contaminated drinking water).
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3.2.3. Poultry
and Camfylobacterjejuni are highly prevalent among poultry in the U.S. (USEPA 2010a), and the
serotypes are similar to those implicated in human infections (Ziemer et al. 2010; Rogers and Haines 2005).
Campylobacter but^leri, now Arcobacter but^leri, has also been isolated in poultry (Houf et al. 2003). Chickens do
not pose a risk for humans with respect to Cryptosporidium and Giardia; the Cryptosporidium species that infect
chickens are a low risk to humans, and chickens do not appear to carry Giardia (USEPA 2010a).
Campylobacter in Poultry
bocter is found in the intestines of both wild and domestic animals, especially poultry. Flocks may
approach 100% infection rates in poultry facilities. Campylobacter is commonly (>50%) found in chicken
manure and is also associated with swine and, to a lesser degree, cattle manure. The pathogen is typically
transmitted via contaminated water and food. Campylobacter may co-occur with E. coli. (References:
AWWA 1999, Cox et al. 2002, Perdek et al. 2003, USEPA 2010a).
3.3. Occurrence of Pathogens in Water Resources
In the USEPA's 2004 National Water Quality Inventory (USEPA 2009c), microbial contamination was a
leading cause of impairment in rivers and streams, with agriculture identified as an important contamination
source. Microbial constituents may reach surface water bodies via wet weather flows from animal feeding
operations or areas where manure has been land applied or when lagoons are breached. A number of studies
have specifically documented effects from pathogens and indicator organisms (see Section 3.1). For example,
fecal coliforms and Streptococcus, both indicators, have been found in agricultural runoff (Simon and
Makarewicz 2009), through which these microorganisms may reach surface water bodies, sometimes
contributing to exceedances of water quality standards and possibly to exceedances of permit limits (Baxter-
Potter and Gilliland 1988, USEPA 2002b). Work by Kemp et al. (2005) documented Campylobacter'vn. surface
water due to runoff from dairy farming. In grazing areas, free access of cattle to streams allows manure to
reach the water and has been associated with elevated stream bacterial concentrations, with up to 36-fold
increases in E. coli reported in stream water samples compared to upstream levels (Schumacher 2003, Vidon
et al. 2008, Wilkes et al. 2009). Among the protozoa, Cryptosporidium oocysts may be carried in runoff,
especially after rain events, and Giardia cysts have been detected in surface waters as well as ground water
(Cotruvo et al. 2004). A study of Giardia and Cryptosporidium in 66 surface water drinking water sources
revealed Giardia cysts in 81% of raw water samples and Cryptosporidium oocysts in 87% of raw water samples
(LeChevallier et al. 1991). Although in general, contamination of water bodies from viruses in manure is less
well understood, some authors (e.g., Payment 1989, Rosen 2000, Ziemer et al. 2010) have noted that runoff
or waste from lagoons can supply viruses to water bodies (Payment 1989, Rosen 2000, Ziemer et al. 2010).
Microbial populations are also found in bottom sediments. They can be present in higher concentrations than
in the overlying water column because of the tendency of microbes to associate with particles that settle and
because of their improved survival in sediments (see subsection 3.4.2 on factors influencing pathogen
survival) (van Donsel and Geldreich 1971, Davies-Colley et al. 2004). E. «?/« and fecal coliform concentrations
in sediments have been reported as high as 105 colony forming units per 100 mL (Crabill et al. 1999). When
resuspension occurs due to rainstorms or dredging, microorganisms can be released from sediments to the
water column (Kim et al. 2010). Spikes in waterborne fecal indicator bacteria have been observed after rainfall
(Choetal. 2010).
Although soil cover and the unsaturated zone provide protection to ground water with respect to pathogen
contamination (see subsection 3.5.2), microorganisms can reach ground water. When they do, they may travel
downgradient, with the rate of travel depending upon the geologic and hydrogeologic properties of the
aquifer. Enteric viruses have been observed to be transported via ground water (Rogers and Haines 2005),
and a nationwide survey of drinking water wells revealed enteroviruses in 15% of samples (Abbaszadegan et
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al. 2003). Bacteria and Cryptosporidium oocysts are also believed to have the potential to be transported in
ground water; one study documented E. coli contamination of ground water downgradient from an unlined
cattle manure lagoon (Withers et al. 1998). Ground water in karst areas is particularly vulnerable to
contamination because of the channelized nature of the rock, which allows rapid flow and may transport
pathogens greater distances. While shallow unconfmed aquifers are most vulnerable to contamination, deep,
confined aquifers may also be vulnerable to pathogen contamination where there are fractures in the
confining layer or from transport along poorly cemented wells (Borchardt et al. 2007).
Table 3-2. Survival of selected bacterial and parasitic
pathogens found in manure, soil, and water.
Pathogen
Survival (days)*
Soil
Water
Manure
[Jaijterff
Salmonella spp.
£ coli 0157:H7
Campylobacter sp.
Yersinia
enterocolitica
Listeria sp.
16 - 196
2 to >300
7 to 56
10 to >365
<120
35 to XL86
35 to >300
2 to >60
6 to 448
7 to >60
20 to 250
50 to >300
Ito56
10 to >365
>240
/fsQlo/oa
Cryptosporidium
spp.
Giardia
28to>365
< 1 to 28
70 to >450
< 1 to 77
28 to >400
< 1 to 77
*The range shorn the shortest and the longest survival time the
organisms can survive at different temperatures for all types of manure
(cattle, swine and poultry) and water (surface, ground, and drinking
water). References: Rogers and Haines 2005, and Bowman 2009.
3.4. Survival of Pathogens in the Environment
The potential adverse impacts on humans from zoonotic pathogens is directly related to the organisms'
survival in various environmental media such as manure, soil, sediments, surface water, and ground water
(Cotruvo et al. 2004). Survival of zoonotic pathogens in animal manure and in the environment can range
from days to years (Ziemer et al. 2010) depending upon the characteristics of the pathogen and the
environmental conditions (Rogers and Haines 2005). The survival capabilities of Cryptosporidium oocysts
deserve particular mention because of their long survival times in the environment (Ziemer et al. 2010), their
resistance to conventional drinking water disinfection processes (chlorine and chlorine dioxide; see Chapter 7)
(Edzwald 2010), and the lack of any treatment for human infection. Cryptosporidium oocysts can remain viable
in a range of environmental settings and can persist in damp conditions for months (Brookes et al. 2004,
Ziemer et al. 2010).
The persistence of pathogens in environmental media depends on environmental conditions and the survival
characteristics of the microbes present. The factors influencing pathogen survival include temperature,
ultraviolet (UV) radiation, moisture, pH, nutrient availability, ammonia concentration in the medium,
predation, and competition for nutrients (Rogers and Haines 2005). The sections below include a brief
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overview of the factors that affect the survival of pathogens in manure, soil, sediments, and water, providing
examples relevant to bacteria, protozoa, and viruses.
3.4.1. Manure
Manure can provide a favorable environment for pathogen survival and even re-growth due to the availability
of nutrients as well as protection from UV radiation, desiccation, and temperature extremes (Rogers and
Haines 2005). Conversely, several factors promote die-off in manure, including predation, competition, and
the concentration of inorganic ammonia (Rogers and Haines 2005). Temperature in particular is a critical
factor in pathogen survival, with cooler temperatures generally enabling longer survival times. Bacterial
pathogens such as Salmonella and E. coli O157:H7 can survive for several months in manure when
environmental conditions are favorable (low temperatures, good moisture level) (Rogers and Haines 2005).
Increased temperatures, on the other hand, hasten die-off. The extent of this effect varies by organism, but
survival in manure generally drops markedly at temperatures exceeding 20 to 30°C compared with survival at
cool temperatures (1 to 9°C) (Rogers and Haines 2005). This dependence of survival times on temperature
results in seasonal trends; for example, a study of Salmonella typhimurium in swine slurry showed survival times
of 26 days during summer and 85 days during winter (Venglovsky et al. 2009). As described further in
Chapter 8, microorganisms can be inactivated when using certain manure management practices, such as
composting, which produces elevated temperature (Olson 2001, Schumacher et al. 2003).
The effects of freezing on pathogen survival vary by organism. Viruses can maintain infectiousness after
freezing (Ziemer et al. 2010). Cryptosporidium oocysts have been shown to survive freezing in manure and soil
for more than three months to one year, but Giardia cysts are inactivated (Olson 2001, Rogers and Haines
2005). Salmonella is also not inactivated by freezing (Olson 2001). However, the stress of repeated freeze-thaw
cycles does generally reduce microbial survival (Rosen 2000).
Compared to bacteria and protozoa, less research has been conducted on the survival of viruses in manure.
The available literature, however, suggests that viruses may survive longer than bacteria (Rogers and Haines
2005). For example, extended manure storage (two years) may be required to achieve a 4-log (10,000 fold)
reduction in the concentrations of some viruses such as rotavirus (Pesaro et al. 1995). More research is
needed on virus survival in manure given the potential for viruses to enter into soil when manure is spread on
land and there is a possibility of transport to water and drinking water sources via runoff.
3.4.2. Soils
In soils, pathogen survival is influenced by temperature, moisture content, pH, predation, nutrient availability,
competition with native soil microorganisms, and organic matter content (Rosen 2000, Unc and Goss 2004).
Aside from temperature, moisture exerts an important control, with increased moisture promoting survival
(Reddy et al. 1981, Unc and Goss 2003, Venglovsky et al. 2009). Fecal coliform bacteria survive longer in
organic soils than in mineral soils, possibly due to the greater capacity of organic soils to hold water (Unc and
Goss 2003). Desiccation decreases the survival of Crypto sporidium, Giardia, fecal bacteria such as Campylobacter
(Olson 2001, Rogers and Haines, 2005, Bowman 2009), and viruses (Bosch et al. 2006). Predation by native
soil organisms can contribute to pathogen removal and has been identified as one of several biological factors
in pathogen inactivation that merit further study (Bosch et al. 2006, Rogers and Haines 2005). For viruses,
survival in soils has been found to be increased by adsorption to soil as well as decreased soil pH; the pH
effect is likely due to greater adsorption of viruses to particles at lower pH (Hurst et al. 1980). For bacteria,
however, low pH reduces survival (Unc and Goss 2004).
Exposure to UV light from direct sunlight, such as during land application, can contribute to microbial die-
off and is discussed further below. In manure and in soil, microorganisms will associate with particulates,
where they are protected from sunlight within the soil profile (e.g., Thurston-Enriquez 2005), especially if
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manure is worked into soil during application. At the soil surface, however, microbes will be vulnerable to
inactivation due to sunlight as well as desiccation (Tyrrel and Quinton 2003).
3.4.3. Sediments
Bottom sediments in manure lagoons or natural waters can serve as a very effective reservoir for pathogens
because the sediment environment provides moisture, soluble organic matter, and nutrients as well as
protection from UV light, desiccation, and predation by protozoa (Rogers and Haines 2005, Cho et al. 2010,
Kim et al. 2010). Microorganisms can survive in this environment for long periods of time; fecal bacteria have
been shown to survive in sediments from weeks to months (Schumacher et al. 2003, Cho et al. 2010).
3.4.4. Water Resources
Pathogen survival in water depends upon a variety of factors including water quality (e.g., turbidity, dissolved
oxygen, pH, organic matter content) and environmental conditions (i.e., temperature, predation by
zooplankton). Survival times for Giardia and Cryptosporidium can be quite long (Ziemer et al. 2010);
Cryptosporidium oocysts can survive from months to more than a year in cold water (5°C) (Ziemer et al. 2010;
Olson 2001, Cotruvo et al. 2004, Rogers and Haines 2005). Giardia cysts survive less than 14 days at 25°C but
could survive up to 77 days at 4 to 8°C (Ziemer 2010). Enteric viruses, such as the hepatitis E virus and
hepatitis A virus tend to be stable in water, especially in colder temperatures (Cotruvo et al. 2004).
Some bacteria (e.g., Campylobacter and E. colt) can enter a viable but non-culturable state, in which the
bacteria's metabolism slows and it cannot be grown in culture media, but it retains infectiousness (Perdek et
al. 2003). The viable but non-culturable state can be brought about by low temperatures and stress from
starvation, but the cells will reactivate under favorable conditions (e.g., increased temperature). This state has
implications for monitoring and may cause contamination to be missed during sampling if culture methods
are used for analysis.
As with pathogen survival in manure and soil, exposure to UV light is a key factor in bacterial, viral, and
protozoan die-off in surface waters (Rosen 2000, Cotruvo et al. 2004, Fong and Lipp 2005). For example, UV
light can cause a reduction of up to four orders of magnitude in the viability of Cryptosporidium (Bowman
2009). Ultraviolet light has also been demonstrated to be effective against human enteric viruses and
bacteriophages (Kapuscinski and Mitchell 1983, Fujioka and Yoneyam 2002, Battigelli et al. 1993). Greater
turbidity of the water, however, affords microorganisms some protection from UV light, and an aquifer
environment also protects pathogens against UV exposure and facilitates their survival in ground water.
3.5. Transport of Pathogens in the Environment
Pathogens and indicator organisms associated with manure can be transported to surface water and ground
water through runoff, discharges, infiltration, and atmospheric deposition (Jawson et al. 1982, USEPA 2002b,
Soupir and Mostaghimi 2011). Lagoon spills and flooding of constructed treatment wetlands during severe
rainstorms or lagoon leaks and equipment failures during dry weather may also release waste and associated
pathogens into the environment (Marks 2001, USEPA 2002b, Rogers and Haines 2005). Tile drainage may
also provide a route for microbes in ground water to reach surface waters (Rogers and Haines 2005). The
sections below briefly discuss considerations related to transport in runoff, soil infiltration, and transport in
ground water.
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3.5.1. Runoff and Transport to Surface Water
A key mechanism of pathogen transport to surface waters is via runoff (overland flow from rain or snowmelt,
or releases from manure pond leaks/overflows). During a rain event, for example, the partitioning of flow
between surface runoff and infiltration through the soil depends upon a number of factors. Storm intensity
and duration, soil hydraulic characteristics (e.g., permeability, antecedent moisture and temperature), land
slope, and soil cover have all been shown to influence runoff and therefore pathogen transport (Rosen 2000,
USEPA 2002b). If rainfall intensity exceeds the capacity of the soil to infiltrate water, overland flow occurs,
and microorganisms can be carried rapidly in surface runoff (Tyrrel and Quinton 2003, Unc and Goss 2003).
Clay-rich soils also tend to promote surface runoff due to their low permeability. Additionally, bare soil with
heavy animal traffic can contribute substantial pathogen loads to runoff through erosion of pathogen-laden
soil particles (Rosen 2000).
To be available for transport in runoff, pathogens are released from the manure. Most pathogens do remain
associated with the fecal deposit during rain events (NRCS/USDA 2012). The amount of pathogens that are
released from manure depends upon a number of factors related to the manure itself and the method of
application. Important factors include the loading of pathogens in the manure, the pathogen types and
survival characteristics, and the age and source of the manure. Aging can greatly reduce the amount of
microorganisms that leach out of the manure, due at least in part to declines in the fecal loads in the manure
with time and environmental exposure (NRCS/USDA 2012).
The form of manure (solid versus liquid) may affect how easily pathogens reach waterways (e.g., Thurston-
Enriquez et al. 2005), with liquid application permitting ready transport via runoff. Also, the amount applied
and the style and timing of application will have effects. If manure is applied to frozen ground or immediately
before or after a rain event, there will be a greater chance for pathogen transport in runoff. There is
uncertainty and limited information, however, regarding whether the method of application (surface
application vs. injection) affects runoff quality. Injection may limit runoff from the surface, but UV radiation,
heat, and desiccation on the surface would promote die-off. Tyrrel and Quinton (2003) note that some
studies have shown no difference in water quality but that their own unpublished data for small scale rain
simulation events showed greater (10-fold) fecal coliform transport if waste is surface-applied.
Once pathogens and indicator organisms reach rivers and streams, their transport will be governed by a
number of factors including channel morphology, streambed composition, and turbulence and flow regimes
(NRCS/USDA 2012). Transport of up to 21 kilometers has been reported for bacteria that were
experimentally added to a stream. Microorganisms can be transported either as free organisms (Soupir and
Mostaghimi 2011) or associated with soil or manure particles (USEPA 2002b, Pachepsky et al. 2006, Bowman
2009), with free cells in suspension having the potential to travel farther because their small size minimizes
settling (Tyrrel and Quinton 2003). Free-living organisms may be added to the streambed sediments when
water infiltrates into the streambed (NRCS/USDA 2012).
The amounts of pathogens that become associated with particulates in runoff and surface waters will vary by
organism, source, and the particulates available. Studies of stormwater as well as stream and estuarine settings
have reported 15% to 35% of bacteria to be associated with particles (Characklis et al. 2005, Cizek et al. 2008,
Suter et al. 2011). Also, large fractions of Giardia and Cryptosporidium (60% and 40%, respectively) have been
found to be bound to sediment in streams (Cizek et al. 2008). Microorganisms attached to larger soil particles
may settle, especially in quiescent waters, contributing to pathogen loads in bottoms sediments (Rogers and
Haines 2005). Microorganisms associated with colloids (very small particles that do not settle) will continue to
be transported downstream.
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3.5.2. Transport through Soil to Ground Water
Transport through the soil profile and in ground water involves an extremely complex interplay of physical
and chemical processes that depend upon the size and surface properties of the microorganism; the
composition, mineral surface properties, and texture of the soil or aquifer material; the composition of the
aqueous medium; and the hydraulic conditions (e.g., saturated vs. unsaturated flow). The following
subsections briefly describe some of the features controlling microbial transport and retention.
3.5.2.1. Physical Processes (Filtration and Flow through Soil)
Soil generally provides some degree of protection to ground water resources from pathogens by retaining
them through physical processes (straining/filtering) and/or through adsorption, particularly in the upper
layers of the soil (see subsection 3.5.2.2) (Bicudo and Goval 2003). Fine-grained soils, such as those with
greater silt and clay, are most effective at filtering larger bacteria and protozoa (Rosen 2000, Jamieson et al.
2002). Because of their small size, viruses are less likely to be retained in the soil by filtration than bacteria or
protozoa (Rosen 2000, USEPA 2004a), although they may be removed by adsorption (see subsection 3.5.2.2).
Their small size also renders viruses relatively mobile in ground water (USEPA 2004a).
During heavy rainfall, transport through the soil may be rapid if there is enough water to fill the pore spaces,
and microbes may reach the water table more quickly than during lighter rainfall (Unc and Goss 2003, Rosen
2000, USEPA 2004a). Preferential transport may occur through macropores, wormholes, and root channels
(Jamieson et al. 2002, USEPA 2004a), bypassing the filtering effect of the soil matrix (Rosen 2000).
Wormholes and root channels can be reduced by conventional tillage, but they are not disturbed by
conservation tillage or in pasturelands (Bowman 2009). Conditions especially conducive to microbial
contamination of ground water include a combination of recent manure application on land with coarse,
sandy soil or soil with macropores and a shallow water table (USEPA 2004a, Bowman 2009). Once in ground
water, pathogen transport may be particularly rapid in fractured rocks or karst areas because of large channels
in the rock.
3.5.2.2. Retention by Adsorption in Soil and Aquifers
Adsorption/desorption interactions are extremely important in governing the mobility of microbes. For
example, viruses may be removed by adsorption in the first few inches of soil during infiltration, although
rainfall can later cause desorption of viruses from the soil, allowing for continued transport and continued
contamination (Landry et al. 1979, Goyal and Gerba 1979). Parasites may also be retained. In an experimental
study with intact soil cores, Cryptosporidium parvum oocysts were mostly retained in the soil within the upper
0.75 inch of soil (Mawdsley et al. 1996), although the authors note that the study was done using purified
oocysts, which may not be representative of oocysts in the environment. A number of studies have focused
on understanding bacterial sorption to soils and aquifer sediments, with soil and ground water chemistry both
playing important roles (e.g. Hendricks et al. 1979, Scholl and Harvey 1992, Banks et al. 2003).
The soil and aquifer characteristics that promote microbial adsorption are: a high clay content, high iron
oxyhydroxide and aluminum oxide content, high organic matter, and pH below 7 (e.g., Goyal and Gerba
1979, Rosen 2000). Bacteria tend to adsorb well to ferric oxyhydroxide coatings on clay minerals or quartz
through electrostatic attraction (Mills et al. 1994). Organic carbon in the soil contributes to retention of
viruses and bacteria due to hydrophobic partitioning (e.g., Rogers and Haines 2005). Furthermore, manure
application changes soil pH and adds salts as well as soluble and insoluble organic compounds, altering
properties of both the soil and microbes and potentially affecting retention of microbes by the soil (Unc and
Goss 2004).
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Soil water or ground water characteristics that affect adsorption include pH, ionic strength, divalent cation
concentrations, and dissolved organic carbon. Adsorption of viruses to soil particles is enhanced by low pH
or increased ionic strength of the water (Rogers and Haines 2005). For bacteria, an increase in ionic strength,
particularly due to high divalent cation concentrations, has been shown to increase retention in a sandy
medium (e.g., Mills et al. 1994). Dissolved organic matter, on the other hand, has been found to hinder virus
adsorption (e.g., Goyal and Gerba 1979, Lance and Gerba 1984). If application of liquid manure or leaching
of solid manure by rainfall changes the ionic strength and/or organic carbon content of the soil water or
ground water, the capability of the soil or aquifer system to retain microorganisms may change.
Pathogen
E. coli O157:H7
Salmonella spp.
Campylobacter
spp.
Yersinia
entercolitica
Listeria spp.
Cryptosporidium
parvum
Giardia lamblia
Rotavirus
Norovirus
Hepatitis E virus
Cattle
X
X
X
X
X
X
X
Poultry
X
X
Swine
X
X
X
X
X
X
X
X
X
Selected Key Pathogens Associated with Livestock
3.6. Summary and Discussion
Livestock and poultry manure can carry an array of
zoonotic pathogens, which can be transported to
recreational and drinking water resources. The most
common pathogens of concern are E. colt 0157:H7,
Campy lob acter, Salmonella, Crypto sporidium parvum, and
Giardia lamblia. Other zoonotic organisms include
Usteria and Yersinia, and several viruses may have
zoonotic potential (see text box). Infectious doses
vary widely among pathogens, and some doses are
very low, especially those for E. coli O157:H7 (5 to
10 cells) and the protozoa Cryptosporidiumparvum and
Giardia lamblia (as low as 10 cysts or oocysts; Table
3-1).
Minimizing the potential for human illness from pathogens in manure requires understanding the survival
characteristics of the various pathogens. Survival times in manure and in the environment can range from
days to years depending on the pathogen, the medium, and environmental conditions. Among the common
zoonotic pathogens, however, Cryptosporidium is noteworthy because of its persistence, resistance to
disinfection, and the lack of treatment for the illness it causes. It has been the causative agent of several large
outbreaks for which manure has been identified as a possible source. Less is known about virus survival, and
continued research is needed on virus occurrence, survival, and transport in environmental media.
Because of the different survival capabilities of the various pathogens, different manure management
methods may be needed depending upon the pathogens anticipated; this is an area where further research is
warranted. Composting of manure, especially when properly aerated, is an effective management practice that
can generate the heat needed to inactivate a number of pathogens, including Salmonella, Campylobacter, E. coli,
and protozoa. Ultraviolet light promotes die-off, and spreading manure on the surface during land application
can promote greater die off through exposure to UV light and desiccation, although the manure is more
susceptible to mobilization via runoff. Additional discussion of management methods is provided in
Chapter 8.
Transport of pathogens may occur via runoff, air deposition, or infiltration into soils. The likelihood of
significant transport of pathogens in runoff is increased where soils have low permeability or moderate to
high antecedent moisture conditions, temperatures are below freezing, there is tile drainage, the slope of the
land is steep, and rainfall is intense. Timing of manure land application is an important factor in minimizing
pathogen transport via runoff. For example, avoiding application on frozen or snow-covered ground, during
early spring runoff, when the land is saturated, or when the forecast calls for sufficient precipitation to
produce runoff will help minimize pathogen loadings to surface water (Olson 2001). Transport of
microorganisms in runoff is more likely if excess manure is applied or if manure is misapplied (USEPA
2002a). Once runoff reaches surface water bodies, microbes may become associated with bottom sediments if
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they are adsorbed to particles large enough to settle. Pathogens can, however, be reintroduced to the water
column by resuspension after heavy rain events or human activities such as dredging.
During infiltration through soil, the upper layers of soil generally provide some removal of microbes through
adsorption. The possibility of removal during transport through soil depends upon hydraulic conditions, soil
texture and structure, soil composition, soil water composition, and microbial size and properties. Ground
water is most vulnerable to contamination when manure is applied before a heavy rainstorm in an area with
coarse, sandy soil and a shallow water table. Clayey soils may also promote transport to ground water if they
have macropores and root channels.
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4. Antimicrobials in Manure
Livestock and poultry are often given antimicrobials (i.e., antibiotics and vaccines) to treat and prevent
diseases, as well as to promote animal growth and feed efficiency. Many of the antimicrobials administered to
livestock and poultry are also used in human clinical medicine. Research indicates that sub-therapeutic use of
antimicrobials can select for antibiotic resistance in bacteria. The purpose of this chapter is to provide
estimates of the quantity and types of antimicrobials administered to livestock and poultry, and on
aquaculture operations. Section 6.3 is a follow-up to this chapter, providing information on the extent of, and
potential risks associated with, antimicrobial resistance related to livestock antimicrobial use.
4.1. Introduction
Antimicrobials have been administered to livestock and poultry for over 60 years (Libby and Schaible 1955).
At therapeutic doses, antimicrobials help treat and prevent diseases and outbreaks. Administering
antimicrobials at sub-therapeutic levels can enhance nutrient
adsorption and limits the growth of microorganisms that
may compete for nutrients, allowing the animal to grow to
market weight more quickly, with less feed (MacDonald and
McBnde 2009).
Approximately 60% to 80% of livestock and poultry
routinely receive antimicrobials through feed or water,
injections, or external application (NRG 1999, Carmosini
and Lee 2008). The majority of the antimicrobial use is
estimated to be used for animal growth rather than for
medicinal reasons, and many of these medications are also
used in human clinical medicines (Mellon et al. 2001).
Estimates suggest that as many as 55% of antimicrobial
compounds administered to livestock and poultry are also
used to treat human infections (Table 4-1) (Benbrook 2001,
Kumar et al. 2005, Lee et al. 2007). The sub-therapeutic use
of antimicrobials in livestock and poultry can facilitate the
development and proliferation of antimicrobial resistance
(Sapkota et al. 2007). Additionally, according to Boxall
(2008) and Zounkova et al. (2011), antimicrobials and their
biologically active degradates may be discharged to the
environment from livestock and poultry manure or, in the
case of aquaculture, discharged directly to surface waters,
potentially impacting aquatic life. The overlap between
livestock and human antimicrobial use has been noted by the WHO and others as an area of concern for
human health, because the effectiveness of these medications in treating human infections may be
compromised (WHO 2000, Levy and Marshall 2004, Sapkota et al. 2007).
» Over 29 million pounds of
antimicrobials were sold for livestock
use in 2010 in the US - an estimated 3
to 4 times more than the amount used
by humans.
^ 60% to 80% of livestock routinely
receive antimicrobials, the majority of
which are estimated to be used for
animal growth, rather than for medicinal
purposes.
•S The WHO has noted that sub-
therapeutic antimicrobial use by
livestock and poultry is an area of
concern because of the selection for
antimicrobial resistance.
» Antimicrobials generally do not
biodegrade easily and may be more
mobile in aquatic environments.
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Table 4-1. Select antimicrobials that are approved for use by the U.S. Food and Drug
Administration for use in humans, livestock, and poultry.
Class/Group
Aminocyclitol
Aminoglycoside
(3-lactam
Lincosamide
Macrolide
Polypeptide
Polyene
Sulfonamide
Tetracycline
Antimicrobial
Spectinomycin
Apramycin
Gentamicin
Neomycin
Streptomycin
Amoxicillin
Ampicillin
Cloxacillin
Penicillin
Lincomycin
Erythromycin
Bacitracin
Nystatin
Sulfadimethoxine
Oxytetracycline
Tetracycline
Humans
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
Beef
Cattle
X
X
X
X
X
X
X
X
X
X
X
X
X
Dairy
Cows
X
X
X
X
X
X
X
X
X
X
Swine
X
X
X
X
X
X
X
X
X
X
X
X
X
Poultry
X
X
X
X
X
X
X
X
X
X
X
X
Aquaculture
X
X
X
*TMs table is not meant to be all-inclusive, and not all antimicrobials included in this table are listed in the
individual livestock tables thatfottoiv. For a complete listing of antimicrobials approved for human and livestock
use, visit the USFDA 's website.
4.2. Estimates of Antimicrobial Use
Quantifying livestock antimicrobial use is challenging and estimates vary widely because there are no publicly-
available, reliable antimicrobial use data for food-producing animals (USGAO 201 la). Pharmaceutical
companies are also not required to disclose veterinary drug sales information (Shore et al. 2009), and the types
used at operations may be deemed proprietary information (Sapkota et al. 2007). Furthermore, use estimates
based on dose rates can be complicated. While recommended antimicrobial doses for individual livestock and
poultry range from 0.05 to 3.5 ounces per 1,000 pounds of feed (depending on the animal type and life stage),
it is not uncommon for feed to contain more than the recommended dose (McEwen and Fedorka-Cray 2002,
Kumar et al. 2005). For example, Dewey et al. (1997) reported that 25% of over 3,000 swine facilities studied
in the U.S. supplied antimicrobials at concentrations greater than the recommended dose.
Estimating livestock and poultry antimicrobial use is also challenging because of the varying degrees of usage
on different farms. For therapeutic applications, animals may be treated individually or as groups. Group
application can be related to increased disease susceptibility in larger operations where livestock and poultry
live in close confinement, facilitating infection and disease transfer (McEwen and Fedorka-Cray 2002, Kumar
2005, Becker 2010). In large livestock and poultry operations, antimicrobials may be administered to animals
continuously or for extended periods of time at sub-therapeutic doses (e.g., in feed and water), because this
approach is more efficient and sometimes the only feasible method of production (McEwen and Fedorka-
Cray 2002). According to the USD A, 20% of swine feeder/finisher farms with less than 100 swine
administered antimicrobials sub-therapeutically, whereas 60% of operations with 2,500 or more swine
administered antimicrobials (MacDonald and McBride 2009). Antimicrobial use in aquaculture operations
involves administration to the entire group by adding the antimicrobials directly to the water or via medicated
feed pellets, which are added to the water (Zounkova et al. 2011).
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Recognizing the importance of quantifying livestock and poultry antimicrobial use, the U.S. Government
Accountability Office (USGAO) has been advocating for better tracking and reporting mechanisms of
antimicrobial use in livestock and poultry since 1999 (USGAO 2011a). In accordance with a 2008 amendment
to the Animal Drug User Fee Act, the USFDA released estimates of the annual amount of antimicrobial
drugs sold and distributed for use in livestock and poultry in 2009 and 2010 (USFDA 2010 and 201 la). The
USFDA estimates that approximately 29.2 million pounds of antimicrobials were sold for livestock and
poultry use in the U.S. in 2010 (USFDA 201 la), or a 62% increase over 1985 use estimates (U.S. Congress,
OST 1995). Tetracyclines and ionophores were the largest class of antimicrobials reported, accounting for
over 70% of all livestock and poultry antimicrobials sold during that year (USFDA 2011a). Overall,
estimations of annual antimicrobial use in food animals in the U.S. range from 11 to 29.2 million pounds as
reviewed in Table 4-2.
Given that many human health antimicrobials are also administered to livestock and poultry, and
subtherapeutic use can select for resistance (Sapkota et al. 2007), it is important to understand the ratio
between livestock and human antimicrobial use. The USFDA's (2010) reported sales of livestock and poultry
antimicrobial use (approximately 28.8 million pounds in 2009) is estimated to be four times greater than what
is used for human health protection (approximately 7.3 million pounds in 2009) (Loglisci 2010). A slightly
higher ratio between livestock and human antimicrobial use was reported by Mellon et al. (2001), which
estimated that livestock and poultry antimicrobial use in 1997 represented 87% of all antimicrobials used in
the U.S.
The following subsections review antimicrobial use for cattle (beef and dairy), swine, poultry, and aquaculture
to provide information on common diseases and infections that affect each animal type, and also provide
estimates of the extent of antimicrobial use for therapeutic and sub-therapeutic purposes. Table A-10 in
Appendix 2 summarizes animal life stages and definitions.
Table 4-2. Estimates of antimicrobial use or sales for livestock in the U.S.
Total Mass Used/Sold
11 million pounds sold (in 1985)
18 million pounds used (in 1985)
29.6 million pounds used (in 1997)
17.8 million pounds used (in 1998)
28.8 million pounds sold (in 2009)
29.2 million pounds sold (in 2010)
Specific Use
Not Reported
12.2% for treating disease
63.2% for disease prevention
24.6% for growth promotion
7% for treating disease
93% for growth promotion and disease
prevention
83% for prevention and treating disease
17% for growth promotion
Not Reported
Not Reported
Source
Swartz 1989
U.S. Congress, Office of Technology
Assessment 1995
Mellon etal. 2001
Animal Health Institute 2000
U.S. Food and Drug Administration
2010
U.S. Food and Drug Administration
2011a
Adapted from Rogers and Raines (2005).
4.2.1. Cattle (Beef and Dairy)
Beef cattle can be administered antimicrobials to treat or prevent common ailments such as respiratory
disease (shipping fever and pneumonia), liver abscesses, bacterial enteritis (diarrhea), and coccidiosis (Table
4-3). Farming operations also administer prophylactic antimicrobials to beef cattle to promote feed efficiency
and animal growth. An estimated 83% of beef cattle operations administered antimicrobials through animal
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feed or water for either animal growth or therapeutic purposes in 1999 (USDA 2000). During that same year,
nearly all small (99%) and all large (100%) cattle feedlots used at least one parasiticide (USDA 2000).
Parasiticides, such as ivermectin and doramectin, for example, are not antimicrobials but are used to kill
parasites. A more recent USDA survey found that nearly 70% of beef cattle and calf operations vaccinated
their animals and almost 70% of operations administered oral or injectable antimicrobials for disease
treatment during 2007-2008 (USDA 2010b). Beef cattle operations with 200 or more cattle are more than
twice as likely to vaccinate for bovine viral diarrhea virus (BVDV) than smaller operations with less than 50
cattle (USDA 201 Ob). Table 4-3 presents commonly used antimicrobials in beef cattle and their intended use.
Table 4-3. Commonly used antimicrobials administered to beef cattle.
Class/Group
Aminoglycoside
(3-lactam
Bambermycin
Fluoroquinolone
lonophore
Macrolide
Polypeptide
Sulfonamide
Tetracycline
Antimicrobial
Gentamicin*, Neomycin*,
Streptomycin*
Amoxicillin*, Ampicillin*,
Penicillin*
-
Enrofloxacin
Lasalocid, Monensin
Erythromycin*, Tilmicosin,
Tylosin
Bacitracin*
Sulfamethazine
Chlortetracycline,
Oxytetracycline*
Life stage
Cattle
Cattle and calves
Cattle
(slaughter,
feed lot)
Cattle
Unspecified
Calves
Cattle
Feedlot
Growing
Calves
Cattle
Calves
Cattle
Intended Use
• Treat bacterial enteritis and pink eye
• Treat respiratory disease, bacterial enteritis, and foot rot
• Promote animal growth
• Promote feed efficiency and animal growth
• Treat respiratory disease
• Control coccidiosis
• Control liver abscesses
• Promote feed efficiency and animal growth
• Control calf diphtheria
• Control metritis and liver abscesses
• Treat foot rot and respiratory disease
• Promote feed efficiency and animal growth
• Control liver abscesses
• Promote feed efficiency and animal growth
• Treat calf diphtheria
• Treat respiratory disease, bacterial sores, foot rot, acute
metritis, coccidiosis
• Promote animal growth in the presence of respiratory
disease
• Treat bacterial pneumonia, bacterial enteritis, and
diphtheria
• Promote feed efficiency and animal growth
• Control liver abscesses and anaplasmosis
• Treat bacterial enteritis, foot rot, wooden tongue, and
acute metritis
• Prevent bacterial pneumonia
• Promote feed efficiency and animal growth
(*) indicates that the antimicrobial is approved for use in humans.
This table is meant to provide general antimicrobial use information. Antimicrobials listed within each class may be used for
different purposes during particular animal life stages. Consult the USFDA's website for more specific information about
livestock antimicrobial use. Inferences: USGAO 1999, Herman and Stokka 2001', McGuffey et al. 2001, Apley 2004, and
USFDA 2011 b.
Similarly to beef cattle, dairy cows may be treated for respiratory disease and bacterial enteritis, but dairy cows
may also be treated for other common ailments such as lameness and mastitis, which is a teat infection (Table
4-4; USDA 2008a). Most antimicrobials are prohibited for use on lactating cows when producing milk for
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human consumption (Watanabe et al. 2010). In 2007, 90% of dairy operations administered intramammary
antimicrobials (e.g., lincosamide) during non-lactating periods, and 80% of those operations treated all cows
at the facility (USDA 2008a). Approximately 85% of dairy operations used antimicrobials to treat mastitis,
administering the antimicrobials to 16% of the cows on those operations (USDA 2008a). Preweaned heifers
tend to be treated with antimicrobials more often than weaned heifers due to their increased susceptibility to
diseases (USDA 2008a). Approximately 11% of preweaned heifers received antimicrobials to treat for
respiratory disease, compared to 6% of weaned heifers (USDA 2008a). For growth promotion and disease
prevention, 58% of dairy operations fed preweaned heifers dairy milk replacer, which was typically a
combination of neomycin and oxytetracycline (USDA 2008a). In weaned heifers, approximately 45% of dairy
operations used ionophores in feed for growth promotion and disease prevention (USDA 2008a).
Table 4-4. Commonly used antimicrobials administered to dairy cows.
Class/Group
Aminoglycoside
p-lactam
Fluoroquinolone
lonophore
Lincosamide
Macrolide
Sulfonamides
Tetracycline
Antimicrobial
Neomycin*,
Streptomycin*
Amoxicillin*,
Cephalosporin,
Penicillin*
Enrofloxacin
Lasalocid, Monensin
Pirlimycin Hydrochloride
Tilmicosin, Tylosin
Sulfadimethoxine*,
Sulfamethazine
Chlortetracycline,
Oxytetracycline*
Life stage
Preweaned
Unspecified
Preweaned
Non-lactating
Unspecified
Non-lactating
Weaned
Non-lactating
Non-lactating
Dairy calves and
heifers
Non-lactating
Preweaned
Non-lactating
Intended Use
• Treat bacterial enteritis and other digestive problems
• Promote animal growth
• Treat mastitis
• Prevent Staphylococcus aureus
• Treat bacterial enteritis and other digestive problems
• Treat mastitis and lameness
• Treat respiratory disease and foot rot
• Treat respiratory disease
• Treat for respiratory disease and bacterial enteritis
• Improved feed efficiency and growth promotion
• Increased milk production efficiency
• Treat mastitis
• Treat respiratory disease, foot rot, and metritis.
• Treat bacterial enteritis and other digestive problems
• Treat calf diphtheria, shipping fever complex, and foot
rot
• Treat acute mastitis and metritis
• Treat bacterial enteritis and other digestive problems
• Promote animal growth
• Treat mastitis and lameness
• Treat bacterial enteritis and pneumonia
(*) indicates that the antimicrobial is approved for use in humans.
This table is meant to provide general antimicrobial use information. Antimicrobials listed within each class may be used for
different purposes during particular animal life stages. Consult the USFDA 's website for more specific information about
livestock antimicrobial use. References: USDA 2008a and USFDA 2011 b.
4.2.2. Swine
Swine can be treated with antimicrobials to promote animal growth and to treat or prevent common
infections such as respiratory diseases, swine dysentery, and bacterial enteritis (Table 4-5). According to the
USDA, most hogs are raised in confinement, and large operations with 10,000 hogs or more typically
administer antimicrobials through feed to promote animal growth, particularly in starter and grower hogs
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(USDA 2002b, USDA 2008b). As with other types of livestock, antimicrobial administration varies by life
stage (see Table 4-5). An estimated 89% of operations administer antimicrobials to grower/finisher pigs (hogs
grown to market weight for slaughter) (USDA 2002b) and 85% of operations use antimicrobials in feed for
nursery pigs (USDA 2008b). In the USDA (2008b) study, over half (54%) of the operations administered
antimicrobials in the nursery pig feed continuously, while 33% of operations did so for grower/finisher pigs.
Table 4-5. Commonly used antimicrobials administered to swine.
Class/Group
Aminoglycoside
(3-lactam
Bambermycin
Macrolide
Pleuromutilin
Polypeptide
Tetracycline
Streptogramin
Sulfonamide
Antimicrobial
Gentamicin*
Amoxicillin*,
Ampicillin*, Penicillin*
-
Erythromycin*,
Lincomycin, Tylosin
Tiamulin
Bacitracin*
Chlortetracycline,
Oxytetracycline*
Virginiamycin
Sulfamethazine
Life stage
Preweaned
Unspecified
Growing/Finishing
Starting/Growing/
Finishing
Unspecified
Growing/Finishing
Pregnant
Growing
Breeding
Unspecified
Swine excluding
breeders
Unspecified
Intended Use
• Treat colibacillosis
• Promote feed efficiency and animal growth
• Treat bacterial enteritis, porcine colibacillosis, and
salmonellosis
• Promote feed efficiency and animal growth
• Promote feed efficiency and animal growth
• Treat bacterial enteritis and infectious arthritis
• Control swine dysentery and the severity of swine
mycoplasmal pneumonia
• Treat swine dysentery and pneumonia
• Promote feed efficiency and animal growth
• Control swine dysentery
• Control clostridial enteritis
• Promote feed efficiency and animal growth
• Prevent/treat cervical lymphadenitis (jowl abscesses)
• Prevent/treat leptospirosis
• Treat bacterial enteritis and pneumonia
• Reduce incidences of cervical abscesses
• Promote feed efficiency and animal growth
• Treat swine dysentery
• Promote feed efficiency and animal growth
• Control Bordetella bronchiseptica rhinitis
• Prevent swine dysentery and pneumonia
• Treat porcine colibacillosis and bacterial pneumonia
(*) indicates that the antimicrobial is approved for use in humans.
This table is meant to provide general antimicrobial use information. Antimicrobials listed within each class may be used for
different purposes during particular animal life stages. Consult the USFDA 's website for more specific information about
livestock antimicrobial use. References: Herrman and Sundberg 2001, Mellon et al. 2001, Kumar et al. 2005, and USFDA
2011 b.
4.2.3. Poultry
Poultry may be treated with antimicrobials to promote growth and to cure or prevent respiratory disease and
infections, including E. coli and protozoan parasites such as coccidiosis (Table 4-6). The extensive use of
antimicrobials in poultry, much of which is used for non-therapeutic purposes, has sparked consumer interest
related to public health and antimicrobial resistance. For example, 3-Nitro (Roxarsone), the most commonly
used arsenic-based drug for animals, promotes animal growth, improves pigmentation, and prevents
coccidiosis in poultry (USFDA 201 Ic). In 2011, an USFDA study reported higher levels of inorganic arsenic
(a known carcinogen) in broiler chickens treated with Roxarsone than non-treated broiler chickens,
prompting the company producing the drug to suspend sales of Roxarsone for use in poultry (USFDA
2011c). Other arsenic-based drugs are still approved for use in poultry and swine, including nitarsone,
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arsanilic acid, and carbarsone (USFDA 2011c). In another instance, the use of fluoroquinolones in poultry
was effectively banned by the USFDA in 2005 after research indicated an increase in human infections with
fluoroquinolone-resistant Campylobacter related to poultry consumption (see Chapter 2 and Section 6.3 for
further information) (Nelson et al. 2007).
Table 4-6. Commonly used antimicrobials administered to poultry.
Class/Group
Aminocyclitol
Aminoglycoside
p-lactam
Bambermycin
lonophore
Macrolide
Polypeptide
Streptogramin
Tetracyclines
Antimicrobial
Spectinomycin*
Gentamicin*,
Neomycin*
Penicillin*
-
Lasalocid, Monensin
Erythromycin*,
Tylosin
Bacitracin*
Virginiamycin
Chlortetracycline
Life stage or Poultry
Category
Chickens (not laying
eggs for human
consumption)
Chickens and turkeys
Chickens/turkeys (not
laying eggs for human
consumption)
Broilers/growing
turkeys
Broilers/turkeys
Broilers/ replacement
chickens
Layers
Chickens and turkeys
Broilers/replacement
chickens
Layers
Growing turkeys
Broilers/turkeys
Chickens
Growing turkeys
Turkeys
Intended Use
• Promote feed efficiency and animal growth
• Treat chronic respiratory disease
• Prevent mortality associated with Arizona group
infection
• Prevent bacterial contamination and omphalitis
• Prevent early mortality caused by E. coli and Salmonella
typhimurium
• Promote feed efficiency and animal growth
• Promote feed efficiency and animal growth
• Prevent coccidiosis
• Improve pigmentation
• Control of coccidiosis
• Control chronic respiratory disease
• Increase egg production
• Promote feed efficiency and growth promotion
• Promote feed efficiency and animal growth
• Prevent necrotic enteritis
• Increase egg production
• Promote feed efficiency
• Promote feed efficiency and animal growth
• Promote feed efficiency and growth promotion
• Promote feed efficiency and animal growth
• Control synovitis, chronic respiratory disease, air sac
infections, and £ coli infections
• Promote feed efficiency and animal growth
• Control synovitis, hexamitiasis, and bacterial organisms
associated with bluecomb
(*) indicates that the antimicrobial is approved for use in humans.
This table is meant to provide general antimicrobial use information. Antimicrobials listed within each class may be used for
different purposes during particular animal life stages. Consult the USFDA's website for more specific information about
livestock antimicrobial use. References: Tanner 2000, McGuffej et al. 2001', Mellon et al. 2001 ,Apley 2004, Kumar et al.
2005, and USFDA 2011 b.
Estimates of antimicrobial use in poultry are limited. The 2010 poultry survey conducted by USDA's National
Animal Health Monitoring System (NAHMS) program includes limited data on vaccine administration in
breeder facilities, and no information is available on the types of drugs used or the extent of antimicrobial use
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in the poultry industry (USDA 201 la). According to the USDA's survey, in 2010, an estimated 80% of
breeder chicken farms in the U.S. vaccinated pullets against Salmonella, bronchitis, and coccidiosis, among
other infectious diseases (USDA 201 la). While the types of antimicrobials, including vaccines, were not
reported in the USDA's poultry survey, as of 2009, at least 50 active pharmaceutical ingredients had been
approved by the USFDA for use in poultry (USFDA 2009). Mellon et al. (2001) estimates that nearly 40%
(10.5 million Ibs.) of all antimicrobials used for non-therapeutic purposes in livestock and poultry during 1997
were administered to poultry. The study also suggests that the majority of poultry receive antimicrobials
during at least one life stage. For example, layer eggs may be dipped in gentamicin to minimize bacterial
contamination, and day-old chicks may be injected with gentamicin or other antimicrobials to prevent
omphalitis, a yolk sac infection (Tanner 2000). Table 4-6 provides further information about commonly used
antimicrobials in the poultry industry.
4.2.4. Aquaculture
Antimicrobials may be used in aquaculture to prevent and treat bacterial infections and diseases (McEwen
and Fedorka-Cray 2002). Primary antimicrobials used in aquaculture include oxytetracycline, sulfamerazine,
sulfadimethoxine-ormetoprim combination, and formalin (Table 4-7). Estimates of total antimicrobial use in
U.S. aquaculture vary widely. MacMillan et al. (2003) estimates that 54,000 to 72,000 pounds per year of
antimicrobials are used in aquaculture, while Benbrook (2002) estimates that use is closer to 200,000 to over
400,000 pounds per year. Both estimates are significantly less than livestock and poultry antimicrobial use
estimates; however, in contrast to livestock and poultry use, antimicrobials used in aquaculture enter surface
waters directly, since they are added to the water through simple addition or via feed pellets (Lee et al. 2007,
Zounkova et al. 2011). Research suggests that, an estimated 70% to 80% of drugs administered in aquaculture
operations are released into the environment, related to over-feeding and poor adsorption in the gut (Boxall
et al. 2003, Gullick et al. 2007). As noted by Daughton and Ternes (1999) and Zounkova et al. (2011),
antimicrobials are designed to kill bacteria and may do so at multiple trophic levels, potentially impacting
other, non-target, aquatic organisms. An assessment of the aquatic toxicity of 226 antimicrobials using
USEPA's Ecological Structure Activity Relationships (ECOSAR) Class Program, predicted that a large
portion of antimicrobials are toxic to aquatic life - algae, crustaceans, and fish (Sanderson et al. 2004). This is
an area that needs further research.
Table 4-7. Commonly used antimicrobials and parasiticides in aquaculture.
Class/Group
Parasiticide
(formaldehyde
solution)
Sulfanomide
Tetracycline
Antimicrobial
Formalin
Sulfadimethoxine*-
Ormetoprim
Combination,
Sulfamerazine
Oxytetracycline*
Life Stage or Species
Salmon, salmonids,
and salmon eggs;
trout and trout eggs;
catfish, largemouth
bass, bluegill, other
fin fish, and shrimp
Trout, salmonids,
catfish
Salmonids, catfish,
lobster
Intended Use
• Control of external protazoa, fungi,
and protazoan parasites
• Control furunculosis and enteric
septicemia
• Control ulcer disease, furunculosis,
bacterial hemorrhagic septicemia, and
pseudomonas disease
(*) indicates that the antimicrobial is approved for use in humans.
This table is meant to provide general antimicrobial use information. Antimicrobials listed within each class may i
used for different purposes during particular animal life stages. Consult the USFDA's website for more specific
information about livestock antimicrobial use. References: Benbrook 2002 and USFDA 2011 b.
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According to the USDA's 2005 Census of Aquaculture, catfish production is the dominant sector in U.S.
aquaculture (USDA 2006). Approximately 50% of catfish hatcheries treated egg masses to control fungal and
bacterial infections in 2009, with larger facilities more likely to administer antimicrobials than smaller ones
(USDA 2010c). Additionally, approximately 29% of catfish fingerling operations administered antimicrobials
in 2009 to treat and prevent enteric septicemia, a common bacterial infection in farm-raised catfish (USDA
2010c, USDA 201 Ib). Table 4-7 provides further information on antimicrobials used in aquaculture.
4.3. Antimicrobial Excretion Estimates
Antimicrobials are often only partially metabolized in livestock and poultry and can be excreted virtually
unchanged as the parent compound (Kumar et al. 2005, Boxall 2008, Khan 2008, Perez and Barcelo 2008).
For example, up to 80% of tetracyclines may be excreted by swine and poultry as the parent compound
(Kumar et al. 2005, Khan 2008). Additionally, up to 67% of the macrolide tylosin, which is approved for use
in beef cattle, dairy cows, swine, and poultry (see Table 4-3 to Table 4-6), may be excreted by livestock and
poultry when the antimicrobial is administered orally (Feinman and Matheson 1978).
Several challenges are presented when attempting to estimate the types of antimicrobials present in livestock
manure (i.e., dairy cow vs. beef cattle manure). First, as evidenced in the preceding tables (Table 4-3 to Table
4-7), the types of antimicrobials used at each operation differ depending on animal life stage and which
ailments are most common at the operation. Second, dosage differs by operation, and excretion estimates
vary by compound (McEwen and Fedorka-Cray 2002, Kumar et al. 2005). Finally, while hundreds of
antimicrobial agents are approved for animal use, our understanding of which compounds are excreted is
partly a function of which antimicrobials are tested for their presence in manure, as well as analytical
detection limits. For example, Sapkota et al. (2007) estimated which antimicrobials to test for in ground water
and surface water near a swine operation based on the types of antimicrobials approved for use by the
USFDA. The actual antimicrobials used at the operation were deemed proprietary information, presenting a
challenge to researchers in the environmental health field. Despite these limitations, recent research indicates
that the most common antimicrobial classes found in manure include tetracyclines, macrolides, sulfonamides,
ionophores, and [3-lactams, some of which are also used for human health (Kumar et al. 2005, Lee et al.
2007).
4.4. Antimicrobial Stability and Transport in the Environment
After excretion, antimicrobials and their degradates can enter the environment in a variety of ways, including
through direct land application via excretion from grazing animals or application of manure or lagoon slurry
on cropland (Boxall 2008, Klein et al. 2008). Spills and overflow from manure lagoons, wash-off from indoor
animal housing facilities or hard surfaces, and wash-off from animals treated externally also present pathways
for antimicrobial transport to the environment (Boxall 2008, Klein et al. 2008). Additionally, antimicrobials
can enter the atmosphere during the spraying of manure on fields, dust from scraping solid manure, or when
antimicrobials bind to air particles during animal excretion (Boxall 2008, Chee-Sanford et al. 2009).
Antimicrobials are chemically diverse, though they tend to be hydrophilic and do not easily biodegrade;
therefore these compounds tend to be more mobile in aquatic environments (Chee-Sanford et al. 2009,
Zounkova et al. 2011). However, because antimicrobials are organic compounds with a range of chemical
properties, their stability and mobility in the environment varies considerably, with half-lives ranging from a
few days to over a year (Kumar et al. 2005). Generally, antimicrobials tend to have a high affinity for soils and
clays (Chee-Sanford et al. 2009). Tetracyclines, fluoroquinolones, and lincosamides are not considered to be
very mobile related to their high sorption potential, while sulfonamides appear to be the most mobile of
antimicrobials (Chee-Sanford et al. 2009). Antimicrobials with a high sorption potential may be less mobile in
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the environment, potentially persisting in cropland soil or at the bottom of manure lagoons for longer periods
of time (Boxall et al. 2003, Lee et al. 2007, Adams et al. 2008, Carmosim and Lee 2008). Additionally,
environmental factors such as pH, temperature, oxygen availability, and microbial populations can influence
antimicrobial behavior and degradation in the environment (Gu and Karthikeyan 2005, Kumar et al. 2005,
Carmosini and Lee 2008). Antimicrobials tend to degrade during manure storage, and the process appears to
be more rapid under higher temperatures and aerobic conditions (Kumar et al. 2005, Lee et al. 2007, Boxall et
al. 2008). Therefore, prolonged manure storage and avoiding manure land application during colder winter
months may allow for further degradation, potentially reducing antimicrobial transport to the environment
and surface waters. Given the limited number of field studies, further research in this area is warranted to
determine optimal conditions for antimicrobial degradation in manure.
The majority of research on antimicrobial stability in the environment has been conducted in controlled
laboratory experiments (Kumar et al. 2005, Lee et al. 2007). Some researchers are concerned that findings
from these studies may not be directly applicable to actual conditions in the field since environmental factors,
such as temperature and pH, fluctuate both spatially and temporally, influencing the behavior of
antimicrobials in the environment (Sarmah et al. 2006). Further research on antimicrobial excretion and
degradation in differing medias, including manure, soil, and water, may help researchers better quantify the
amount of antimicrobials that enter the environment each year.
4.5. Antimicrobial Occurrence in the Environment
The occurrence of antimicrobials in soils, sediment, surface water, and ground water has been documented,
particularly in close proximity to livestock and poultry operations. Campagnolo et al. (2002) found
antimicrobial compounds present in 67% of ground water and surface water samples collected near poultry
operations and 31% of ground water and surface water samples collected near swine operations. In that
study, Campagnolo et al. (2002) detected lincomycin, chlortetracycline, and sulfadimethoxine, among other
antimicrobials near both the swine and poultry operations. In another study, tetracyclines were detected in
soils, and sulfonamides were detected in shallow ground water near large dairy livestock production facilities,
which, in general, use significantly fewer antimicrobials per unit animal weight than other large livestock and
poultry production facility types since most antimicrobials are prohibited for use on lactating cows (Watanabe
et al. 2010). Additionally, Batt et al. (2006) detected two types of sulfonamides, which are approved only for
veterinary use, in private drinking water wells near a large beef cattle livestock production facility and irrigated
agriculture fields in Idaho. Lincomycin was measured in a ground water well near a swine lagoon in North
Carolina (Harden 2009). In a study of North Carolina drinking water systems, fluoroquinolones as well as
sulfonamides, lincomycin, tetracyclines, and macrolides were the most frequently detected antimicrobials in
source water (Weinberg et al. 2004). In addition to livestock wastes, suspected sources also included
wastewater treatment plants.
The concentrations of antimicrobials measured in the environment vary considerably, ranging from non-
detectable concentrations to levels in the mg/L range. Overall, concentrations in soil tend to be much higher
than in water because most antimicrobials bind well to soil (Lee et al. 2007). However, because antimicrobials
tend to be hydrophilic, they can be transported in aquatic systems (Chee-Sanford et al. 2009, Zounkova et al.
2011). It is important to note that our understanding of the occurrence of antimicrobials in the environment
is limited by the fact that research tends to focus on the most commonly used antimicrobials (e.g.,
tetracyclines, sulfonamides), rather than degradates and less commonly used compounds. Numerous
antimicrobial agents have been approved for livestock use, though many have not yet been researched in
terms of their prevalence in the environment.
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4.6. Summary and Discussion
Antimicrobial use is widespread in livestock and poultry production - both to treat infections and diseases,
and also to increase feed efficiency and animal growth. An estimated 60% to 80% of livestock and poultry
routinely receive antimicrobials (NRG 1999, Carmosini and Lee 2008), and several USDA surveys and
publications suggest that larger, confined livestock and poultry operations rely more heavily on antimicrobial
use than smaller facilities (MacDonald and McBride 2009, USDA 2010b). There are currently no reporting
requirements for antimicrobial use on livestock and poultry operations, though according to the USFDA, an
estimated 29.2 million pounds of antimicrobials were sold for livestock use in 2010 (USFDA 2011a). Gaining
a more thorough understanding of the quantity of antimicrobials used in livestock and poultry production as
well as the behavior and stability of antimicrobials in the environment may provide guidance for manure
management to promote antimicrobial degradation prior to land application, thereby potentially reducing
antimicrobial transport to the environment and surface waters. The possible link between livestock and
poultry antimicrobial use and the proliferation and evolution of antimicrobial resistance (WHO 2000, Swartz
2002, USGAO 2011a) is discussed in Section 6.3.
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5. Hormones in Manure
Hormones are endocrine disrupters that are naturally produced by, and in some cases artificially administered
to, livestock and poultry. As with all mammals including humans, livestock and poultry excrete hormones in
their waste, which has the potential to enter water resources through runoff and discharges from animal
production facilities and fertilized cropland. The purpose of this chapter is to provide estimates of livestock
and poultry hormone use and excretion rates as well as the occurrence and mobility of hormones in the
environment. Section 6.4 provides information on endocrine disruption and potential impacts to aquatic life
and human health.
5.1. Introduction
Hormones are naturally synthesized in the endocrine systems
of all mammals and regulate metabolic activity and
developmental processes. Beef cattle may also be
administered additional natural and synthetic exogenous
hormones to improve beef quality and promote animal
growth. Dairy cows may be treated with additional hormones
to control reproduction and increase milk production
(USFDA 2002, Bartelt-Hunt et al. 2012). The USFDA has
not approved the use of exogenous steroid hormones for
growth promotion purposes in swine, poultry, veal calves, or
dairy cows (USFDA 201 Id). Natural hormones include
estrogens, androgens, and progestogens (Table 5-1), and their synthetic versions include zeranol, trenbolone
acetate, and melengestrol acetate (Table 5-2).
Table 5-1. Natural hormones and select metabolites as well as the functional purpose of
the hormone.
^Livestock excreted an estimated
722,852 pounds of endogenous
hormones in 2000.
v Beef cattle feedlot operations may
administer synthetic hormones as
implants and feed additives to promote
animal growth.
Hormone
Estrogens
Androgens
Progestogens
Select Hormone Metabolites
Estrone, 17p-estradiol, and estriol
Testosterone, 5a-
dihydrotestosterone, 5a-androstane-
3P, 17p-diol, 4-androstenedione,
dehyroepiandrosterone, and
androsterone
Progesterone
Purpose
• Natural reproductive hormone
• Stimulates and maintains female
characteristics
• Natural reproductive hormone
• Stimulates and maintains male
characteristics
• Natural reproductive hormone
• Produced during the estrous cycle
• A metabolic precursor to
estrogens
Hormones are naturally excreted by livestock and poultry in manure and bile (USEPA 2004a, Zhao et al.
2008). Therefore, hormones and their metabolites can enter aquatic ecosystems through runoff from pasture
and rangeland used by grazing cattle and cropland fertilized with manure, as well as via leaks/overflow from
manure lagoons (Kolodziej and Sedlak 2007, Bartelt-Hunt et al. 2012). Because hormones are endocrine
disrupting compounds, Lee et al. (2007) and Zhao et al. (2008), among others, have noted concern regarding
the potential adverse impacts of aquatic organism exposure to manure. Specifically, hormones can affect the
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reproductive biology, physiology, and fitness of fish and other aquatic organisms (Zhao et al. 2008). It is
important to note that all mammals excrete hormones, thus other possible sources of steroid hormones to the
environment include wastewater treatment plant discharges and leaky septic systems (Shore and Shemesh
2003).
Table 5-2. Synthetic hormones that may be administered to and excreted by beef cattle and/or
dairy cows.
Synthetic Hormone
Zeranol
Trenbolone acetate
Melengestrol acetate
Mimics the Behavior of Which
Natural Hormone Metabolite?
17(3-estradiol
Testosterone
Progesterone
Purpose
• Administered as an implant (typically without other hormones)
• Used to improve feed efficiency and animal growth
• Administered as an implant either alone or with 17(3-estradiol
• Used to improve feed efficiency and animal growth
• Administered as a feed additive
• Used for estrous synchronization and to induce lactation
• Used to improve feed efficiency and animal growth
5.2. Estimates of Exogenous Hormone Use
The USFDA has approved the use of patented forms of natural hormones and synthetic steroid hormones
for use in beef and dairy cattle, as included in the Code of Federal Regulations (CFR), Title 21, Parts 522, 556,
and 558 (see also Table 5-1 and Table 5-2). Hormones may be administered through implants, or pellets
containing doses of one or more hormones that are implanted into the ear of an animal (USFDA 201 Id).
Typical implants on beef cattle feedlots contain doses of approximately 140 mg of trenbolone acetate and 14
mg of 17[3-estradiol benzoate (Bartelt-Hunt et al. 2012). Beef cattle on feedlots may also receive daily doses of
approximately 0.45 mg of melengestrol acetate in feed (Bartelt-Hunt et al. 2012). Intravaginal controlled
internal drug release (CIDR) inserts, which contain progesterone, may be used in dairy operations to control
estrous (menstrual cycle), or to treat anestrous (non-menstruating) females and females with cystic ovaries
(USDA2009c).
The USFDA has also approved the use of the genetically engineered hormone, recombinant bovine growth
hormone (rBGH), also referred to as recombinant bovine somatotropin, to increase milk production in dairy
cows (USFDA 2011e). Estimates of rBGH use in dairy cows are unknown; however, a 2006 USDA article
reported that 33 million doses are sold annually by the manufacturer (Gray 2006) (note that this estimate may
include sales outside of the U.S.). Information on the extent of rBGH treatments at U.S. dairy operations
would allow for an understanding of trends in usage.
Estimates of hormone use in beef and dairy cattle are limited because there are no reporting requirements;
however, recent USDA NAHMS surveys have provided insight into common practices in beef and dairy
operations. Approximately 39% of steers and heifers weighing less than 700 pounds and 82% of those
weighing 700 pounds or more received at least one hormonal implant in 1999 (USDA 2000). Of those,
livestock operations with 8,000 or more cattle were more likely to use implants than smaller ones.
Additionally, approximately 33% of dairy operations used CIDR inserts in 2007 (USDA 2009c). The USDA's
NAHMS 2007 Dairy Survey mentions that rBGH is the most common production enhancement injection
used in dairy operations, though use estimates are not provided (USDA 2009d). Beyond these estimates,
research to-date (though limited) has focused primarily on livestock and poultry excretion, since hormones
are also produced naturally, and use estimates therefore would not necessarily accurately reflect amounts
entering the environment.
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5.3. Hormone Excretion Estimates
Approximately 2.2 billion cattle, swine, and poultry generated an estimated 1.1 billion tons of manure in 2007
(see Chapter 2), and livestock excrete hormones that are naturally-produced and synthetic (in the case of
cattle). Quantifying the total amount of hormones excreted by livestock and poultry is challenging because
daily excretion rates vary by animal type, season, diet, age, gender, breed, health status, reproductive state, and
whether or not the animal is castrated (Schwarzenberger et al. 1996, Lange et al. 2002, Khan et al. 2008). One
of the most extensive estimates of hormone excretion currently available suggests that cattle, swine, and
poultry (excluding turkeys), excreted approximately 722,852 Ibs. of estrogens, androgens, and progestogens
(excluding synthetic hormones) during the year 2000 (Table 5-3) (Lange et al. 2002). Cattle account for the
majority of estrogen and progestogen excreted by livestock (93% and 92%, respectively), related to
differences in excretion rates and the higher quantity of manure generated by cattle compared to other animal
types. Androgens are predominantly excreted by cattle and poultry, followed by swine. Lange et al. (2002)
estimate that adding excretion of exogenous hormones to the above figures may increase the total excretion
values by as much as 0.2% for estrogens and 20% for androgens. Using these estimates, livestock excreted an
estimated 724,900 Ibs. of hormones in 2000 (an approximate 0.3% increase over the estimates in Table 5-3).
Table 5-3. Estimated livestock and poultry endogenous hormone excretion in the U.S. in 2000.
Animal Type
Cattle
Swine
Poultry (broilers,
layers)
Total
Estrogens
Lbs.
99,208
1,830
5,952
106,990
% of Total
92.7%
1.7%
5.6%
100%
Androgens
Lbs.
4,189
772
4,630
9,590
% of Total
43.7%
8.0%
48.3%
100%
Progestogens
Lbs.
557,770
48,502
-
606,271
% of Total
92.0%
8.0%
-
100%
Total
Lbs.
661,166
51,103
10,582
722,852
% of Total
91.5%
7.1%
1.5%
100%
(-) indicates that no estimate is available from Lange et al. (2002). Adapted from Lange et al. (2002).
The following subsections provide information on hormone excretion rates for different animal types and
aquaculture. Overall, limited data are available on hormone excretion, particularly for swine and poultry, and
few studies have investigated aquaculture hormone contributions. Also, the majority of research has focused
on estrogen excretion and, to a lesser extent, androgen excretion. Limited information is available on
livestock progesterone and synthetic hormone excretion. Importantly, identifying trends and comparing data
between livestock types is difficult because hormone excretion rates vary depending on the animal type and
life stage.
5.3.1. Cattle (Beef and Dairy)
Hormone excretion in cattle varies by life stage and reproductive state, among other factors. For example,
androgen excretion ranges from 0.0003 Ibs./yr (120 mg/yr) in calves to 0.001 Ibs./yr (390 mg/yr) in bulls
(Lange et al. 2002). The majority (58% to 90%) of estrogen excreted by cattle is via feces, most of which is
excreted during the final three months of pregnancy (Ivie et al. 1986, Lange et al. 2002, Shore et al. 2009).
While pregnant cows produce significantly more hormones than non-pregnant cows, mean estrogen excretion
rates within the first 80 days of pregnancy (first trimester) are similar to those of non-pregnant cattle
(Hoffman et al. 1997). Pregnant cattle are estimated to excrete 0.01 Ibs./yr (4,400 mg/yr) of progestogens
(Lange et al. 2002).
Regarding excretion of synthetic, exogenous hormones, an estimated 8% of applied trenbolone acetate may
be recovered in heifer liquid manure, and 3% to 42% may be recovered in solid dung (feces and straw)
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(Schiffer et al. 2001). An estimated 12% of applied melengestrol acetate is excreted by heifers via feces
(Schiffer et al. 2001). Limited information is available on zeranol and rBGH hormone excretion.
5.3.2. Swine
In contrast to cattle, which excrete the majority of total estrogen in feces, swine excrete nearly 96% of total
estrogen in urine (Palme et al. 1996). Estrogen concentrations in swine manure tend to increase after three to
four weeks of pregnancy (Choi et al. 1987, Szenci et al. 1997). Progestogen excretion can be as high as 0.009
Ibs./yr (3,900 mg/yr) for pregnant swine, and 0.004 Ibs./yr (1,700 mg/yr) for pigs in estrous (Lange et al.
2002).
5.3.3. Poultry
Similar to swine, the majority (69%) of total estrogen released into the environment by poultry is excreted via
urine rather than feces (Ainsworth et al. 1962). Layers generally excrete more estrogen than broiler hens:
0.000016 Ibs./yr (7.1 mg/yr) compared to only 0.00000075 Ibs./yr (0.34 mg/yr) from broiler hens (Lange et
al. 2002). Broilers generally excrete fewer androgens than laying hens and cocks. Androgen excretion by
broilers is estimated to be 0.0000015 Ibs./yr (0.7 mg/yr), while laying hens excrete 0.0000075 Ibs./yr (3.4
mg/yr) and cocks excrete 0.0000196 Ibs./yr (8.9 mg/yr) (Lange et al. 2002).
5.3.4. Aquaculture
As with mammals, fish and other aquatic organisms also naturally excrete hormones, though hormone
contributions from aquaculture operations have been far less studied than livestock. Kolodziej et al. (2004)
estimates that hormone discharge from a standard aquaculture operation (i.e., 55 to 220 tons of fish) may be
comparable to the amount of hormones produced by several hundred cattle, or a wastewater treatment plant
serving several thousand people. Hormone excretion may be higher during spawning periods, though further
research is needed. In a study of hormone concentrations in aquaculture operations, Kolodziej et al. (2004)
found that concentrations of estrone, testosterone, and androstenedione (a precursor to sex steroid
hormones) ranged from 0.1 to 0.8 ng/L in hatchery effluents. Note that the rate of effluent production was
not reported in the Kolodziej et al. (2004) study; therefore an estimate of hormone production reported as
mass per year, cannot be calculated for these hatcheries. Effluent from aquaculture operations may enter
natural surface waters untreated, either through direct discharge or overflow (Kolodziej et al. 2004).
5.4. Hormone Stability and Transport in the Environment
Because mammals, including livestock, poultry, and humans, produce and excrete hormones, key sources of
hormones to the environment include manure and bile from livestock and poultry operations as well as
biosolids and discharges from wastewater treatment facilities. As previously discussed, manure and biosolids
are often land applied, which can lead to concentrated releases of hormones and other compounds (e.g.,
nutrients, pathogens, and antimicrobials) to the environment (Bevacqua et al. 2011). Related to the typically
higher total weight of manure compared to biosolids, as well as the more extensive treatment of biosolids, the
contribution of hormones to the environment from manure compared to biosolids can be higher. A recent
analysis estimated that poultry litter application to farmland in Maryland is nearly two times greater than
biosolids application, contributing approximately two times more progesterone (35.27 Ibs./yr versus 17.6
Ibs./yr) and six times more estrone (24.3 Ibs./yr versus 4.2 Ibs./yr) to the environment (Bevacqua et al. 2011).
The occurrence and stability of hormones in the environment have only recently been investigated, partly
related to improvements in laboratory methods allowing for the detection of hormones at low (ng/L)
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concentrations. However, available monitoring data indicate that hormones and their metabolites have been
detected in the environment in close proximity to livestock and poultry operations and generally degrade at
different rates depending on the media and environmental conditions. Both estrogens and testosterone may
degrade to other compounds after excretion (Zhao et al. 2008). While estrogens may be degraded by biotic or
abiotic processes under either aerobic or anaerobic conditions, a key route of degradation for testosterone is
through microbial activity (Zhao et al. 2008). Limited information is available on progesterone degradation,
though some studies indicate that they may be actively transformed by spores and vegetative cells of
microorganisms in soil, as well as some fungi (Plourde et al. 1974, Pokorna and Kasal 1990).
Hormones are lipophilic (fat soluble) organic molecules that generally do not readily dissolve in water (Casey
2004, Arnon et al. 2008). Because of these characteristics, hormones tend to sorb to sediment, soil particles,
and organic matter (Arnon et al. 2008). Sorption potential measures how tightly the compound binds with
soil particles and can thus be an indication of how likely the compound will leach from the soil. In a study of
soil sorption potentials of estrogens in a range of soil types on cultivated land, Caron et al. (2010) found a
significantly positive correlation between sorption potential and soil organic carbon content. While further
research is needed, this finding suggests that hormone leaching and contributions to runoff may be
minimized in soils with higher carbon content.
Hormones in the environment typically degrade over time. The extent and rate of degradation can depend on
a variety of factors such as the media's moisture content, temperature, and organic carbon content, as well as
the availability of light (Zhao et al. 2008). Microbial breakdown also appears to be a key route for the
degradation of hormones; therefore, it is possible that hormones may persist for longer periods of time
during colder, winter temperatures when microbial activity tends to be slower than during warmer months
(Zhao etal. 2008).
Table 5-4. Half-lives of natural and synthetic hormones in the environment.
Hormone (Metabolite)
Estrogen (17(3-estradiol)
Androgen (Testosterone)
Zeranol
Trenbolone acetate
Trenbolone acetate (17a-
trenbolone)
Trenbolone acetate (17(3-
trenbolone)
Melengestrol acetate
Half-Life (days)
69
24
0.2-9
43
56
49-91
267
0.2-2
0.2-.6
0.16-1
Media
Poultry manure compost
Anaerobic soil
River
Clay-amended compost
Manure
Soil
Liquid manure
Aerobic soil
Aerobic soil
Water
Source
Hakk etal. 2005
Yingand Kookana 2005
Jiirgensetal. 2002
Hakk etal. 2005
USFDA 1994
USFDA 1994
Schiffer etal. 2001
Khan and Lee 2010
Khan and Lee 2010
USFDA 1996
Adapted from Zhao et al. (2008), Table 13.11.
Manure storage may facilitate the degradation of natural and synthetic hormones. For example, the
degradation of estrogen in manure during storage has been observed in broiler litter (Shore et al. 1995),
manure from pregnant and non-pregnant cows (Schenkler et al. 1998), and dairy manure (Raman et al. 2001).
However, research suggests that synthetic hormones may persist at low concentrations even after months of
storage and land application. Schiffer et al. (2001) measured the fate of trenbolone acetate and melengestrol
acetate in solid and liquid lagoon manure from cattle that had received hormone implants. Trenbolone acetate
and melengestrol acetate were detected in the solid manure after excretion and also after 4.5 months of
storage. Likewise, trenbolone was detected in the liquid manure, decreasing in concentration after 5.5 months
of storage. However, trenbolone was still detected in the soil up to two months after the liquid manure was
applied to corn fields and had an estimated half-life of 267 days during storage. As shown in Table 5-4, half-
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lives of natural and synthetic hormones vary considerably, ranging from several hours to over 260 days
depending on the type of hormone and media.
5.5. Hormone Occurrence in the Environment
While limited, recent studies have detected hormones in manure, runoff, and in surface waters near livestock
and poultry operations (e.g., Durhan et al. 2006, Kolodziej and Sedlak 2007, Bartelt-Hunt et al. 2012).
However, analyzing trends and making definitive statements about hormone occurrence is challenging
because many studies focus on the occurrence of one type of hormone or metabolite in one type of medium
rather than researching the occurrence of an array of natural and synthetic hormones in the same study.
Further, most studies involve the use of bioassay methods, which quantify total concentrations of 17|3-
estradiol and testosterone; in contrast, chemical identification liquid chromatography-tandem mass
spectrometry allows for more precise quantification of specific hormone compounds including estriol, 17oc-
estradiol and progesterone (Bevacqua et al. 2011).
Estrogen content in poultry litter (manure and bedding materials) is variable, ranging from 14,000 to 500,000
ppb (ug/kg) (Shore et al. 1993, 1995). Likely related to the higher portion of total estrogen that is excreted by
poultry via urine (69%) rather than feces (Ainsworth et al. 1962), estrogen levels detected in dry broiler litter
are substantially lower, at 28 ppb (Shore et al. 1995). The concentration of estrogen in manure from pregnant
cows is around 36 ppb, with the estrogen content in bull manure estimated to be nearly four times lower
(Shore 2009). The level of testosterone in dairy cow manure is estimated to be 25 ppb; concentrations in
broiler litter vary from 30 to 133 ppb; in breeder layer litter, concentrations range from approximately 20 to
250 ppb (Shore et al. 1995, Lorenzen et al. 2004). The variability may be attributed to differences in breed,
manure treatment, and age (Zhao et al. 2008). Progesterone levels in manure have been far less studied than
other hormone compounds. However, Bevacqua et al. (2011) reported an average progesterone concentration
of 63.4 ppb in poultry litter from 12 broiler chicken farms in the Mid-Atlantic.
Relatively few studies have focused on concentrations of synthetic hormones in manure, though a recent
controlled experiment on feedlot beef cattle conducted by Bartelt-Hunt et al. (2012) provides insight into
concentrations of synthetic hormones in manure. In that study, feedlot cattle were treated with exogenous
hormones via implants and feed additives during two study seasons in 2007 and 2008. Average
concentrations of melengestrol acetate ranged from 1.7 to 6.5 ppb in fresh manure, with concentrations
generally decreasing from day seven of the study to day 109 (Bartelt-Hunt et al. 2012). The average
concentration of 17a-trenbolone (a metabolite of trenbolone acetate) in fresh manure after 46 days was 31
ppb; average concentrations of a-zearalanol and a-zearalenol (metabolites of the synthetic hormone zeranol)
were 47 ppb and 46 ppb respectively after 46 days.
Both natural and synthetic hormones and their metabolites have also been measured in runoff from livestock
and poultry operations. Runoff from a Nebraska beef cattle feedlot with hormone-treated cattle had
concentrations of testosterone of up to 420 ng/L, 17a-estradiol up to 720 ng/L, and estrone up to 1050 ng/L
(Bartelt-Hunt et al. 2012). In another study, concentrations of 17a-trenbolone were detected in 67% of runoff
samples from a beef cattle feedlot in Ohio with concentrations ranging from <10 to approximately 120 ng/L
(Durhan et al. 2006).
A USGS nationwide reconnaissance survey of streams known, or suspected to be, susceptible to human,
animal, or industrial impacts, reported that nearly 6% of streams had measureable concentrations of 17a-
estradiol, with a median concentration of 30 ng/L (Kolpin et al. 2002). According to Hanselman et al. (2003)
and Kolodziej and Sedlak (2007), the source of 17a-estradiol is likely cattle operations, given that this steroid
is predominantly excreted by cattle and not by other types of livestock or humans. Shore et al. (1995)
reported concentrations of up to 5 ng/L of estrogen and 28 ng/L of testosterone in small streams draining
fields which had recently been fertilized with poultry litter. Runoff from cattle grazing rangeland may also
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contribute hormones to surface waters. Kolodziej and Sedlak (2007) detected steroid hormones in 86% of
samples from rangeland creeks where cattle had access to the creeks. Though few studies are available,
hormones have also been detected in ground water impacted by dairy farms (Arnon et al. 2008) and swine
CAFOs (Harden et al. 2009). Concentrations of estrone and 17[3-estradiol have been detected in manure
storage ponds, with higher concentrations at increasing depths (Raman et al. 2004), and testosterone and
estrogen have been detected in sediments below a dairy wastewater lagoon at depths of up to 148 ft and 105
ft, respectively (Arnon et al. 2008). Few studies have investigated the presence and stability of progesterone in
the environment, though Zheng et al. (2008) found that progesterones were present in dried manure piles on
a dairy operation, but not in dairy lagoon samples.
5.6. Summary and Discussion
Hormones are naturally synthesized by all mammals, including livestock and poultry. Estimates suggest that
over 720,000 Ibs. of natural and synthetic hormones were excreted in manure and bile by cattle, swine and
poultry (excluding turkeys) in 2000 (Lange et al. 2002) (Table 5-3). Research (while limited) indicates that
hormones and their metabolites may be present in the environment proximal to livestock and poultry
operations, including streams, creeks draining cattle grazing rangeland, and surface waters downstream from
beef cattle feedlots (Kolpm et al. 2002, Durhan et al. 2006, Kolodziej and Sedlak 2007, Arnon et al. 2008,
Harden et al. 2009, Bartlet-Hunt et al. 2012). While hormones are typically detected at low concentrations,
such chemicals are biologically active at low levels (ng/L) and are classified as endocrine disrupters (see
Section 6.4). Manure storage prior to land application may promote hormone degradation (see Chapter 8),
possibly minimizing the amount that enters the environment (Shore et al. 1995, Raman et al. 2001, Schiffer et
al. 2001). However, the nature of the degradation products is not completely understood yet. More research
on the use, occurrence, fate, and transport of natural and synthetic hormones is necessary in order to fully
understand their potential impact on human and ecological health.
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6. Potential Manure-Related Impacts
Manure from livestock and poultry is a source of a number of contaminants including nutrients, pathogens,
hormones, and antimicrobials (see Table 1-1). As reviewed in the previous chapters, these contaminants have
been detected in manure and environmental media such as soil, sediment, and water resources near livestock
and poultry operations. Manure can be viewed as a source of nutrients to water, and it may be related to the
development of harmful algal blooms (HABs) in some cases. HABs can produce cyanotoxins — also
contaminants of emerging concern. The purpose of this chapter is to review the potential and documented
human health and ecological impacts associated with these contaminants. This is not a comprehensive
discussion of human health issues related to manure and livestock and poultry operations. Additional health
issues for people living in the vicinity of large animal feeding operations or working in livestock and poultry
operations and handling manure are associated with air quality (see Donham et al. 2007, Merchant et al. 2005,
Mirabelli et al. 2006, PCIFAP 2008).
6.1. Harmful Algal Blooms and Cyanotoxin Production
Nitrogen and phosphorus (nutrients) are perhaps the most widely researched pollutants from livestock and
poultry manure. Nutrients from manure may reach surface water and ground water through runoff from
pasture and cropland, infiltration through soil, or volatilization during manure decomposition leading to
atmospheric deposition of nitrogen (Jordan and Weller 1996, Bouwman et al. 1997, Aneja et al. 2001).
Nutrients are necessary for all biological growth, but excess nutrients may lead to eutrophication in aquatic
ecosystems. Characterized in part by
excessive algal growth and potentially
harmful algae blooms (HABs),
eutrophication can alter the biology,
chemistry, and aesthetic quality of the
waterbody. HABs can also produce toxins,
which may be harmful to wild animals and
aquatic life as well as to humans and pets
when exposed to them from drinking
water supplies or recreational waters (see
Grand Lake St. Marys case study) (Lopez
etal. 2008).
Manure-Related Harmful Algal Blooms in
Grand Lake St. Marys, Ohio
Grand Lake St. Marys (GLSM) is a public drinking water
supply in Ohio that has experienced recurring HABs since
2009 related to livestock manure runoff and nutrient
loading (OEPA 2009). The watershed is 90% agricultural,
with nearly 300,000 animal units of poultry, swine, and
cattle. The HABs have caused fish kills, waterfowl and pet
deaths, and have also been linked to over 20 cases of human
illness. The state of Ohio has issued recreation, boating, and
fish consumption advisories related to the blooms. The
$150 million annual lake-based recreational and tourism
industries have been compromised, park revenues have
decreased by more than $250,000 per year, and several
lakeside businesses have closed. To date, millions of state,
federal, and local dollars had been leveraged toward lake
restoration and watershed management projects. Technical
assistance and funding programs have also been developed
to minimize manure runoff to the lake. (References: OEPA
2007, OEPA 2009, OEPA 2011, Gibson 2011).
While livestock and poultry manure
contributes nutrients to the environment,
there have been limited cases where
manure has been documented as the
primary cause of HABs and associated
formation of cyanotoxins. Additionally,
livestock and poultry manure must be
placed in context relative to all the
nutrients used in agricultural production.
The National Research Council (NRC)
estimated nitrogen and phosphorus
balances for croplands by USDA Region and for the U.S. The NRC reported that in the U.S., 45% of
nitrogen and 79% of phosphorus inputs to cropland may be attributed to synthetic fertilizers, whereas 8% of
nitrogen and 15% of phosphorus inputs are from livestock and poultry manure (NRC 1993). However,
because manure production is more localized (refer to Chapter 2), associated nutrient contributions can be
higher in particular watersheds. For example, a USGS study found that animal manure was the primary
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source of nitrogen in several Mid-Atlantic and southern watersheds, contributing 54% and 56% of total
nitrogen loads to the Susquehanna River in Pennsylvania and the White River in Arkansas, respectively
(Puckett 1994).
The majority of HABs in freshwater in the U.S. and throughout the world are caused by cyanobacteria,
commonly referred to as blue-green algae. USEPA's 2007 National Lakes Assessment found that microcystin,
a hepatotoxin produced by cyanobacteria that is harmful to animals and humans, was detected in
approximately one third of the lakes studied (USEPA 2010b). It is important to note that the presence of
cyanobacteria is not necessarily an indication of cyanotoxins because not all cyanobacteria, and not all blooms
produce toxins. Table 6-1 reviews the various types of nuisance and harmful algae, the toxins they can
produce, and the associated adverse human health and aquatic life impacts.
Table 6-1. Types of harmful or nuisance inland algae, toxin production, and potential adverse
impacts.
Algae Group
Cyanobacteria
Haptophytes
Chlorophytes,
Microalgae
Macroalgae
Euglenophytes
Raphidophytes*
Dinoflagellates
Cryptophytes
Diatom
Genera/Taxa
Anabaena, Aphanocapsa,
Hapalosiphon, Microcystis, Nostoc,
Oscillatoria, Planktothrix, Nodularia
spumigena, Aphanizomenon,
Cylindrospermopsis, Lyngbya,
Umezakia
Prymnesium parvum,
Chrysochromulina polylepis
Volvox, Pandorina
Cladophora
Euglena sanguinea
Chattonella
Peridinium polonicum
Cryptomonas, Chilomonas,
Rhodomonas, Chroomonas,
Hemiselmis, Proteomonas,
Teleaulax0
Didymosphenia geminata
Toxins
Hepatotoxins,
neurotoxins,
cytotoxins,
dermatoxins,
endotoxins,
respiratory and
olfactory irritant
toxins
Ichthyotoxins
-
-
Ichthyotoxins
Ichthyotoxins
Ichthyotoxins
-
-
Potential Adverse Impacts
• Human and animal health impacts (i.e.,
gastrointestinal disorders, liver
inflammation/failure, tumor promotion,
cardiac arrhythmia, skin irritation,
respiratory paralysis, etc.)
• Water discoloration
• Unpleasant odors and aesthetics
• Hypoxia from high biomass blooms
• Taste and odor problems in drinking
water and in farm-raised fish
• Fish mortalities
• Water discoloration
• Localized hypoxia
• Unpleasant odors and aesthetics
• Localized hypoxia
• Clogged water intakes
• Water discoloration
• Fish mortalities
• Fish mortalities
• Fish mortalities
• Water discoloration
• Localized hypoxia
• Produce large quantities of extracellular
stalk material resulting in ecosystem and
economic impacts
* Raphidophytes are a marine algae, but can bloom in inland saline waters
Q Information from Marin et al. (1998).
Adapted from Lope% et al. 2008.
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6.2. Fish Kills
Manure discharges to surface waters have been implicated in fish kills nationwide (Mulla et al. 1999). Such
discharges can be caused by rain events, equipment failures (e.g., lagoon ruptures/leaks), or the application of
manure to frozen ground or to tile drained fields, and subsequent discharges to surface waters. Fish
mortalities from runoff containing manure may be caused by ammonia toxicity and/or oxygen depletion with
large loadings of manure.
In Minnesota, a top swine producing state, an estimated 20 manure spills occur annually, one of which
involved 100,000 gallons of liquid hog manure washing into Beaver Creek, killing nearly 700,000 fish
(DeVore 2002). Similarly, in Lewis County, New York, millions of gallons of manure from a dairy CAFO
spilled from a lagoon in 2005, contaminating approximately 20 miles of the Black River and killing
approximately 375,000 fish (NYSDEC 2007). In 1995, spills from poultry and swine lagoons entered Cape
Fear River basin in North Carolina, causing fish kills, algal blooms, and microbial contamination (Mallin and
Cahoon 2003). Osterburg and Wallinga (2004) reported over 300 manure spills within ten years in Iowa alone,
24% of which were caused by manure storage overflow and equipment failures. Large livestock and poultry
operations often store large volumes of untreated manure in lagoons, which can rupture or overflow, leading
to a greater potential for fish kills (Armstrong et al. 2010). Between 1995 and 1998 alone, there were an
estimated 1,000 manure spills at animal feedlots in ten states and 200 manure-related fish kills in the U.S.
(Marks 2001). Proper management and maintenance of lagoons and minimization of winter land application
of manure will help prevent manure discharges to surface waters.
6.3. Antimicrobial Resistance
Antimicrobials are typically administered to livestock therapeutically for disease treatment, control, and
prevention, as well as sub-therapeutically for growth promotion (refer to Chapter 3) (Kumar et al. 2005). The
USFDA estimates that 29.2 million Ibs. of antimicrobials were sold for livestock and poultry use in 2010
(USFDA 201 la). The use of antimicrobials in livestock and poultry has been increasing over the past four
decades (Perez and Barcelo 2008). This increase is partly related to the shift towards fewer, larger confined
animal facilities, which may increase disease susceptibility among livestock because the livestock are routinely
in close contact (Perez and Barcelo 2008). The overuse and/or misuse of antimicrobials (in general) can
facilitate the development and proliferation of antimicrobial resistance (i.e., when bacteria have the ability to
survive exposure to certain types of antimicrobials) (Levy and Marshall 2004). Research conducted by the
WHO and others suggest that antimicrobial use in livestock and poultry, which is typically administered at
low doses for extended periods of time for sub-therapeutic purposes, has contributed to the prevalence of
antimicrobial-resistant pathogens found in food animal operations and nearby environments (WHO 2000,
Swartz 2002, Hayes et al. 2004, Levy and Marshall 2004, Nelson et al. 2007, USGAO 2011a). However,
antimicrobial resistance can develop in a number of ways, and while resistant infections in humans have been
linked to livestock and poultry production (Swartz 2002), the relationship between livestock and poultry
antimicrobial use and resistant infections in humans is not well understood. This section focuses on
antimicrobial resistance and the potential human health implications. Note that research also indicates that
antimicrobials are toxic to aquatic life; this topic has been reviewed elsewhere (e.g., Sanderson et al. 2004,
Kummerer 2009a and 2009b) and is not the focus of this chapter.
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6.3.1. Development and Spread of Antimicrobial Resistance
Each class of antimicrobials operates differently: some attack cell walls and membranes, some act on cellular
components responsible for protein synthesis, and others interrupt biochemical pathways within the cell
(Rogers and Haines 2005). Bacteria may develop resistance to antimicrobials when their deoxyribonucleic acid
(DNA) changes through the mutation of existing genetic material. Bacteria may also develop resistance
through conjugation (i.e., the transfer of genetic material between living bacteria), transformation (i.e.,
obtaining genetic material from the environment), or transduction (i.e., the transfer of genetic material
between bacteria via a bacteriophage) (Rogers and Haines 2005). Because of the multiple methods by which
resistance can spread, exposure of bacteria to increasingly large pools of antimicrobial resistant genes can
further expand the pool of resistant strains of pathogens.
Antimicrobial-resistant bacteria are generally shed in
animal manure, but they may also be present in the
mucosa of livestock animals. Once a resistant strain is
present in a bacterial community, it can spread among
livestock, wild animals, pets, and humans (Figure 6-1).
For example, resistance can spread between herds of
animals, particularly when in close confinement, or via
vectors such as insects and rodents (McEwen and
Fedorka-Cray 2002). Antimicrobial-resistant
pathogens can also survive on food products, such as
vegetables and fruit grown on fields fertilized with
manure containing resistant pathogens, or meat from
slaughterhouses; such pathogens can also spread
through soil or water that has been contaminated with
manure containing resistant bacteria (USGAO 201 la).
It is important to note that ingested bacteria will not
always cause illness, in part because many strains of
bacteria are naturally present in the human and/or
animal digestive tract (e.g., certain strains of E. coE)
(USGAO 2011a).
» The sub-therapeutic use of antimicrobials in
livestock contributes to the development of
antimicrobial resistant pathogens.
» The U.S. Department of Agriculture
reported that 74% of Salmonella and 62% of
Campjlobacter isolates from swine manure were
resistant to two or more antimicrobials.
* Resistant strains of pathogens tend to be
less responsive to treatment and can cause more
severe and prolonged illness in humans than
susceptible strains.
» The U.S. Food and Drug Administration
banned the use of fluoroquinolones in poultry
in 2005 related to human health concerns;
livestock antimicrobial use has previously been
banned in European countries related to
perceived human health concerns.
Most antimicrobial resistance related to human health
is likely the result of overuse and misuse of certain
medications in humans (Levy and Marshall 2004).
However, evidence suggests that the use of antimicrobials in livestock and poultry operations selects for
antimicrobial resistance in certain pathogens and bacteria such as Salmonella and Enterococcus (McEwen and
Fedorka-Cray 2002). These bacteria may be transferred to humans through the food chain and via
contaminated water (McEwen and Fedorka-Cray 2002).
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Figure 6-1. Potential pathways for the spread of antimicrobial-resistance from animals to humans.
loath instant ana susce
in tarm ?n>ra>s
r
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ited 3nirtiais
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baftena; 'es«tan1 bactena
survw? n c^rtarmr atea a-mras,
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to*jim woiM; and food to ;cilal"'ii
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*-
•; batter'a s^read
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R^iistait tacts \a
spiearltc *i^h, ttuits
an.1 vogetab is
CLi'iSlillfrttJV
humsiis
*As indicated in the figure, antimicrobial-resistant pathogens can spread to humans through several pathways. Certain pathogens
with resistance can infect humans, increasing the severity and decreasing the treatability of the resulting illness I infection. Source:
USGAO (2011a), Figure 1.
6.3.2. Antimicrobial Resistance in Manure and the Environment
Antimicrobial-resistant pathogen strains can be shed by livestock and poultry and are therefore generally
found in manure and nearby environments such as surface water, ground water, and fertilized cropland.
Antimicrobial-resistant Enterococcus spp. isolates were found to be prevalent in broiler and layer chicken
operations in the Netherlands, with over 90% of isolates resistant to oxytetracyline or erythromycin (van den
Bogaard et al. 2002). In that study, 80% of Enterococcus spp. isolates from broiler litter were also resistant to
vancomycin, which is typically the first line drug used in humans to treat Enterococcus infections. Note that
vancomycin has not been approved by the USFDA for use by livestock and poultry in the U.S. In a separate
survey of poultry litter from more than 80 broiler operations, approximately 99% of Enterococcus spp. isolates
were resistant to lincomycin, 68% were resistant to tetracycline, 54% were resistant to erythromycin, and 27%
were resistant to penicillin (Table 6-2) (Hayes et al. 2004). Each of these medications is also used to treat
human infections, and some may be used to treat infections from Enterococcus, specifically. Importantly,
whether or not antimicrobial use in the poultry was a direct cause of the high prevalence of resistance is
unclear because the types and quantities of antimicrobials used on the farms in the Hayes et al. (2004) study
were not known/reported.
Research indicates that increased use of antimicrobials in livestock and poultry may be related to a greater
prevalence of resistant pathogens in manure. Jackson et al. (2004) reported that 59% of Enterococcus spp.
isolates were erythromycin-resistant in manure from a swine farm administering tylosin continuously through
feed for animal growth, compared to 28% in a swine farm that administered tylosin for disease treatment for
only five days (both tylosin and erythromycin are macrolides). The percent occurrence of erythromycin-
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resistant isolates was only 2% on a swine farm that did not use tylosin. Similarly, Sapkota et al. (2011)
reported a significantly lower occurrence of antimicrobial-resistant strains of Enterococcus spp. on organic,
antimicrobial-free poultry farms compared to conventional poultry operations. On the conventional
operations, 42% of Enterococcus faecalis (E. faecalis) and 84% of Enterococcus faedum (E. faedum) isolates were
multidrug-resistant (Table 6-2), compared with only 10% of E. faecalis and 17% of E. faedum isolates on the
organic operations.
Results from USDA's NAHMS studies on the occurrence of antimicrobial-resistant pathogens in livestock
and poultry manure, suggest a higher prevalence of antimicrobial-resistant pathogens in manure from swine,
compared to other animal types (see USDA sources in Table 6-2). This finding was also reported by Sayah et
al. (2005), which researched antimicrobial resistance patterns in livestock and poultry, companion animals,
human septage, wildlife, surface water, and farm environments (e.g., manure storage facilities, lagoons, and
livestock holding areas) in a watershed in Michigan. In that study, E. coli isolates from livestock manure were
resistant to the greatest number of antimicrobials, and multidrug resistance was most common in isolates
from swine manure (Table 6-2). Resistance was demonstrated most frequently to tetracycline, sulfisoxazole,
streptomycin, and cephalothin (a type of cephalosporin that has since been voluntarily withdrawn from the
U.S. market by the drug manufacturer). In terms of Salmonella and Campylobacter, the USDA's NAHMs studies
also indicate that antimicrobial-resistant strains of these pathogens are less prevalent in beef cattle manure
compared to dairy cow and swine manure (Table 6-2).
Table 6-2. Occurrence of antimicrobial-resistant isolates in livestock and poultry manure from
conventional livestock operations.
Pathogen
Salmonella spp.
Escherichia coli
Enterococcus spp.
Campylobacter sp.
Animal Type
Beef cattle
Dairy cows
Swine
Swine
Dairy cows
Beef cattle
Poultry (broilers)
Poultry (broilers)
Poultry (broilers)
Beef cattle
Dairy cows
Swine
% of Resistant Isolates
0% resistant to any antimicrobials
2% resistant to 1 antimicrobial
6% resistant to > 2 antimicrobials
80% resistant to 1 antimicrobial
74% resistant to > 2 antimicrobials
32% resistant to 1 antimicrobial
60% resistant to > 2 antimicrobials
31% resistant to 1 antimicrobial
15% resistant to > 3 antimicrobials
28% resistant to 1 antimicrobial
6% resistant to > 3 antimicrobials
28% resistant to 1 antimicrobial
6% resistant to > 3 antimicrobials
28% resistant to 1 antimicrobial
12% resistant to > 3 antimicrobials
53% resistant to 4 antimicrobials
42% (E faecalis) resistant to > 3 antimicrobials
84% (E faedum) resistant to > 3 antimicrobials
8% resistant to > 2 antimicrobials
62% resistant to 1 antimicrobial
2% resistant to > 2 antimicrobials
91% resistant to 1 antimicrobial
62% resistant to > 2 antimicrobials
Source
USDA 2009e
USDA 2009f
USDA 2009g
USDA 2009h
Sayah etal. (2005)
Hayes etal. (2004)
Sapkota etal. 2011
USDA 2009i
USDA 2009f
USDA 2008c
Antimicrobial-resistant pathogens have also been detected in surface water and ground water near livestock
and poultry operations. In the Sayah et al. (2005) study previously described, antimicrobial-resistant isolates of
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E. coli were detected throughout the farm environment as well as in surface water near farming operations.
Among the surface water samples, 81% of E. coli showed resistance to cephalothin (Sayah et al. 2005). Ash et
al. (2002) reported that over 40% of bacteria in 16 rivers in the U.S. were resistant to at least one
antimicrobial. Chee-Sanford et al. (2001) reported resistant bacteria in swine lagoons and underlying ground
water, with the bacteria detected over 800 ft. down-gradient from the lagoons. In a study of the presence of
resistant bacteria near a concentrated swine operation, median levels of enterococci and E. cotiwete up to 33
times higher in surface water and ground water down-gradient from the operation. A higher percentage of the
enterococci were resistant to erythromycin and tetracycline in surface water samples, and a higher percentage
of resistance to tetracycline and clindamycin were observed in down-gradient ground water samples. The
surface water was used for recreational purposes, and the ground water had been used as a primary drinking
water source but was taken offline due to pollution from the swine operation (Sapkota et al. 2007). The
presence of antimicrobial-resistant bacteria in flowing systems such as streams, rivers, and ground water may
facilitate the spread of resistant bacteria in the environment (McEwen and Fedorka-Cray 2002).
The presence of antimicrobial-resistant bacteria in drinking water source water and tap water has been
documented. Bacteria resistant to amoxicillin, chloramphenicol, ciprofloxacin, gentamicin, sulfisoxazole, and
tetracycline were found in surface water sources of drinking water in Michigan and Ohio (Xi et al. 2009). The
percent of resistant bacteria ranged from 1.66% to 14.42% in source water, and from 1.17% to 47.98% in
finished (treated) water. The study found that the levels of antibiotic-resistant bacteria were higher in tap
water compared to finished water, suggesting that bacteria continued to grow in the drinking water
distribution system (Xi et al. 2009).
The presence of antimicrobial-resistant bacteria in air, soil, and on cultivated land has also been documented.
Gibbs et al. (2004) detected antimicrobial-resistant bacteria in air samples inside and downwind of a
concentrated swine operation, but not upwind, suggesting that the swine operation was the source of the
resistant bacteria. Multidrug-resistant bacteria have also been detected in topsoil from dairy farms,
demonstrating resistance to chloramphenicol,
penicillin, nalidixic acid, and tetracycline
(Burgos et al. 2005). In soil from farmland
amended with swine manure slurry, there was
an increase in tetracycline-resistant bacteria
following manure application, though the
amount of resistant bacteria decreased during
the eight months of the study (Sengelov et al.
2003).
The USFDA Bans Prophylactic Use of
Cephalosporin in Livestock
Cephalosporins are antimicrobials used to treat
pneumonia, pelvic inflammatory disease, and skin
infections in humans. They are also widely used in
livestock production; the USFDA reported that over
54,000 Ibs. were sold for use in food-producing animals
in 2010. Also, a USDA survey reported that in 2007, over
half (53%) of dairy operations administered
cephalosporins to treat mastitis (an increase from 37% of
operations in 2002). There has been growing concern
over the increased prevalence of cephalosporin-resistant
pathogens (i.e., Salmonella and E. coli) related to
widespread livestock use. To preserve the effectiveness
of cephalosporins for human use, the USFDA has
moved to ban their prophylactic use (among other uses)
in cattle, swine, and poultry. The new rule became
effective in April, 2012. (References: USDA 2008a,
USFDA 201 la and 2012. Gilbert 20121.
The period of time between antimicrobial
introduction and the emergence of
antimicrobial-resistant pathogens on a
livestock operation varies. Because of the
numerous ways in which bacteria can gain
resistance (see subsection 6.3.1), once the
pool of resistant genes reaches a certain
magnitude, reversal of the problem can be
challenging (Swartz 2002). While limited,
available research suggests that certain
antimicrobial-resistant pathogens may be
more persistent in the environment than
others. However, research on the persistence of resistant pathogens appears to be focused primarily on
Campylobacter and Enterococcus in the poultry industry, so there is a strong need for more research in this area.
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Fluoroquinolone-resistant Campylobacter appears to be persistent in poultry operations. Price et al. (2005, 2007)
researched the prevalence of resistant strains of Campylobacter in chicken meat products from two prominent
poultry companies that had discontinued the use of fluoroquinolones in drinking water to treat entire flocks.
In the study, even one year after discontinuing the use of the drug, fluoroquinolone-resistant Campylobacter
was detected in 43% to 96% of the chicken products from the two producers. Chicken products from one of
the producers were over 450 times more likely to carry fluoroquinolone-resistant Campylobacter than products
from an antimicrobial-free poultry operation involved in the study (Price et al. 2005). There was no significant
change in the proportion of resistant Campylobacter strains three years later (i.e., four years after the operations
had discontinued the use of fluoroquinolones) (Price et al. 2007). The persistence of fluoroquinolone-
resistant Campylobacter is of interest, because this pathogen is a primary cause of bacterial gastroenteritis in the
U.S., causing approximately 1.4 million infections annually (Nelson et al. 2007). Fluoroquinolones are
commonly prescribed to adults infected with Campylobacter (Nelson et al. 2007). Thus, resistance compromises
the effectiveness of these antimicrobials in treating Campylobacter infections in humans. As described in
subsection 6.3.3, the USFDA has since banned the use of fluoroquinolones in poultry due to fluoroquinolone
resistance and human health concerns.
Research conducted in the U.S. and in Europe indicates that antimicrobial-resistant Enterococcus spp. may be
less persistent than Campylobacter. For example, one study found that five newly organic and antimicrobial-free
large-scale poultry operations in the U.S. experienced a substantial drop in the prevalence of antimicrobial-
resistant Enterococcus spp. in feed, litter, and water samples, compared to five conventional operations (see
subsection 6.3.2) (Sapkota et al. 2011). Similarly, tylosin-resistant Enterococcus spp. isolates detected in swine
manure in Denmark were high (around 90% occurrence) prior to Denmark's ban of the use of tylosin for
growth promotion (Aarestrup et al. 2000). However, the percent occurrence of tylosin-resistant Enterococcus
spp. isolates decreased to 28% and 47% for E.faecalis and E.faecium, respectively, three years after the ban. It
is important to note that a more substantial drop in occurrence may not have been observed because
macrolides, such as tylosin, were still being administered to swine for therapeutic purposes (Aarestrup et al.
2000). In the same study, similar drops in occurrence were observed for erythromycin- and virginiamycin-
resistant Enterococcus spp. isolates in broilers, and for glycopeptides-resistant E. faecium isolates in swine
(Aarestrup et al. 2000). These findings were further confirmed by similar research conducted by Emborg et al.
(2003) in Denmark on the occurrence of antimicrobial resistant Enterococcus spp. in broilers. One of the ways
in which resistant pathogens can be transferred to humans is via the consumption of meat products, which is
beyond the scope of this report. The National Antimicrobial Resistance Monitoring System (NARMS), a
collaboration between the USFDA, the USD A, and the Centers for Disease Control and Prevention (CDC),
conducts annual surveys of the prevalence of resistant pathogens on meat products (see NARMS, 2009) and
provides further information.
Research indicates a higher prevalence of antimicrobial-resistant strains of pathogens in livestock and poultry
handlers compared to the general public (Swartz 2002). Levy et al. (1976) found that after tetracycline-
supplemented feed was introduced on a poultry farm, tetracycline-resistant E. coli isolates increased in fecal
samples from both the poultry and farm family members. After introducing the medicated feed, 80% of the
isolates in the family members were tetracycline-resistant, compared to only 7% of isolates from neighbors.
The percent of resistant isolates found in the family members decreased to levels closer to the percent
detected in neighbors approximately six months after discontinuing the use of tetracycline in the animal feed.
Similar findings were reported by van den Bogaard et al. (2002), who found significant correlations between
the prevalence of antimicrobial-resistant Enterococcus spp. in broilers and broiler farmers and also between
broilers and poultry slaughterers.
6.3.3. U.S. and International Responses to Livestock Antimicrobial Use
Making the direct link between livestock and poultry antimicrobial use and resistant infections in humans is
challenging and controversial, in part because bacteria can develop resistance naturally or from antimicrobial
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Federal Court Ruling Requires USFDA to Evaluate Human
Health Risks Associated with Livestock Antimicrobial Use
Recent federal court decisions ordered the USFDA to re-evaluate
the human health implications of the use of antimicrobials in
livestock feed. The U.S. District Court for the Southern District
of New York rulings came in response to a suit brought by the
Natural Resources Defense Council, the Union of Concerned
Scientists, and others. In a March, 2012 ruling, which USFDA is
currently appealing, the federal judge required USFDA to
withdraw its approval for most non-therapeutic uses of
tetracyclines and penicillin in livestock feed, unless the practices
are proven to be safe for humans. Following the court order,
USFDA called for drug manufacturers to voluntarily place
restrictions on the use of certain drugs in livestock feed. The
most recent ruling, in June, 2012, requires USFDA to withdraw
its approval of the use of antimicrobials in livestock unless
industry can prove they are safe. (References: Jacobs 2012,
use in humans (Levy and Marshall
2004). However, in specific cases,
years of research and evidence have
demonstrated the link between
livestock and poultry antimicrobial
use and resistant infections in
humans, leading to limitations or
bans on certain antimicrobials. Most
recently, because of the relationship
between livestock and poultry
antimicrobial use and the evolution
and proliferation of antimicrobial-
resistant pathogens, a federal court
ordered the USFDA to evaluate the
human health risks associated with
livestock and poultry antimicrobial
use (see Federal Court Ruling text
box). The USFDA also recently
banned the use of cephalosporin in
livestock and poultry, related to
antimicrobial resistance (see Cephalosporin text box). In 2005, the USFDA banned the use of
fluoroquinolone in the poultry industry because substantial data and research indicated that an increase in
human infections caused by fluoroquinolone-resistant Campylobacter was associated with poultry consumption
(Nelson et al. 2007). The fluoroquinolone ban is anticipated to reduce the selective pressure not only on
fluoroquinolone-resistant Campylobacter but also on non-typhodial Salmonella species and other foodborne
pathogens that can cause infections in humans (Nelson et al. 2007).
In other countries, bans on the use of certain antimicrobials in livestock and poultry related to human health
concerns have been in effect for decades. The sub-therapeutic use of antimicrobials in food animals has been
banned in Sweden since 1986 and in Denmark since 1998 (Emborg et al. 2003, PCIFAP 2008). In 2006, the
European Union banned the use of all growth-promoting antimicrobials after having already previously
banned the use of human medicines from being added to livestock feed (Europa 2005). Studies conducted by
Aarestrup (2000) and Emborg et al. (2003) suggest that, as a result of these bans, there have been
demonstrated reductions in the occurrence of antimicrobial-resistant pathogens in livestock and poultry.
However, the European Union still considers the prevalence of antimicrobial resistance a growing health
problem. In November 2011, it published the Action Plan on Antimicrobial Resistance, which, among other
goals, calls on European Union countries to ensure that antimicrobials are only available via prescription and
to better track cases of resistance (Europa 2011).
6.3.4. Summary and Discussion
Livestock and poultry antimicrobial use in the U.S. is an estimated four times greater than the amount used to
treat human infections (Loglisci 2010). Research conducted by the USGAO, the WHO, and others
demonstrate that overuse and misuse of antimicrobials - in humans and/or livestock and poultry - may
contribute to the prevalence of antimicrobial resistance (WHO 2000, Levy and Marshall 2004, USGAO
2011a). Research has demonstrated an increased prevalence of antimicrobial-resistant bacteria on and near
livestock and poultry production facilities related to the use of antimicrobials (Hayes et al. 2004, Kumar et al.
2005, Sapkota et al. 2011). Antimicrobial-resistant pathogens have been detected in meat products (NARMS
2009). What is less clear is the extent to which antimicrobial-resistant human infections are related to the use
of antimicrobials in livestock and poultry. Making that connection is challenging - USFDA reviewed decades
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of scientific research before banning fluoroquinolone use in poultry in 2005 and prohibiting prophylactic use
of cephalosporin in certain types of livestock in 2012 (Nelson et al. 2007, USFDA 2012b).
As noted by Kumar et al. (2005), significant costs incur when antimicrobials used to treat human, pet and/or
livestock and poultry bacterial infections become ineffective because of resistant bacteria. These costs are
related to increased health costs and loss of livestock and poultry, as well as the need to develop new drugs.
More representative data about the occurrence of antimicrobial resistance in different types of livestock and
food products will help researchers and agencies identify trends and better understand the relationships
between livestock and poultry antimicrobial use, the prevalence of resistant pathogens, and the occurrence of
human infections caused by resistant pathogens.
6.4. Endocrine Disruption
Livestock excrete natural hormones (i.e., estrogens, androgens, and progestogens), and synthetic hormones
(i.e., trenbolone acetate, zeranol, and melengestrol acetate in the case of some cattle). These hormones can
enter aquatic ecosystems through runoff following manure land application, wash-off from farming
operations, or via spills, overflow, and leaks from manure lagoons (Perez and Barcelo 2008). To regulate
metabolic and developmental processes in animals, hormones are naturally biologically active at very low
concentrations (ng/L). Even low levels of hormones detected in surface water have been implicated in
endocrine disruption, adversely impacting the reproductive biology, physiology, and fitness of fish and other
aquatic organisms (Zhao et al. 2008). To date, the majority of research has been conducted on the
environmental impacts of hormones from human waste
streams (e.g., municipal wastewater treatment plant
discharges). However, recent research suggests that
exposure to animal manure can also have endocrine-
disrupting effects on aquatic organisms (Lee et al. 2007,
Cipansetal. 2012).
Sex steroids regulate the differentiation and structural
development, as well as behavior and function, of the
reproductive system in vertebrates (Lange et al. 2002).
Specifically, estrogens are responsible for the
development and maintenance of female sex organs and
» Hormones are endocrine system regulators
that are biologically active even at low
concentrations.
» Fish exposure to estrogens can cause
defeminization in females and
demasculinization in males, reducing
reproductive fitness.
* The biological activity of the synthetic
hormone melengestrol acetate is estimated to
characteristics, while androgens are responsible for male , , 10c^.- ^ j j ^ r ^ i
' & F be nearly 125 times greater than that of natural
organs and characteristics. Progestogens are involved in
the female menstrual cycle and pregnancy. An
investigation into the ecological toxicity of 92 types of
hormones using USEPA's ECOSAR program found that hormones exhibited the greatest toxicity to aquatic
biota, compared to several other classes of pharmaceuticals (Sanderson et al. 2004). The study predicted that
80% of the compounds were very toxic and 52% extremely toxic to fish based on impacts on species survival
and reproduction. The study found that only 1% of hormone compounds were non-toxic to fish, daphnids,
or algae, illustrating the potential ecological effects associated with hormones in surface waters.
The majority of research on hormones in surface waters has been conducted on estrogens, which can cause
physiochemical changes in sensitive fish and other aquatic organisms. Fish exposure to exogenous estrogens
can induce the production of egg yolk precursor proteins (vitellogenin) and eggshell proteins (zona radiata),
which are associated with reduced testicular growth, reduced testicular and ovary size, decreased egg
production, and liver and kidney damage (Lange et al. 2002). Exposure to exogenous estrogen can also lead to
reduced reproductive fitness, intersex (the presence of both male and female sex characteristics), skewed
population sex ratios, abnormal spawning behavior, and compromised immune systems in fish (Iwanowicz
and Blazer 2011). The most potent estrogen metabolite is 17[3-estradiol, which has been associated with
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adverse impacts on gamete production, maturation, spawning, and sexual differentiation in a variety of fish
species (Lange et al. 2002, Zhao et al. 2008).
Exposing fish to animal manure containing natural hormones has also been shown to cause adverse impacts
on fish, though research on hormones in manure is limited at this time (the majority of research is focused on
aquatic life impacts from hormones in wastewater treatment plant discharges). Orlando et al. (2004) found
that exposure of wild fathead minnows to animal feedlot effluent caused defeminization in females and
demasculinization in males (i.e., reduced testicular size and testosterone synthesis, and altered head
morphometrics). As suggested by the author, results from this study indicate that there were potent
androgens and estrogens in the feedlot effluent. A separate study reported a high intersex prevalence in male
smallmouth bass in the Potomac River Basin in the Mid-Atlantic region. This was partly explained by
hormone contributions from runoff containing livestock (primarily poultry) manure within the watershed
(Blazer et al. 2007).
Exposure to synthetic hormones and their metabolites from livestock and poultry manure can also adversely
impact the reproductive endocrinology of some fish. Fathead minnow fecundity can be reduced when
exposed to 17[3-trenbolone and 17a-trenbolone (metabolites of trenbolone acetate) at concentrations greater
than 27 ng/L, and 16 ng/L for 21 days, respectively (Ankley et al. 2003, Jensen et al. 2006). For perspective,
concentrations of 17[3-trenbolone have been detected in runoff from beef cattle feedlots at concentrations of
up to 20 ng/L, which is slightly lower than the documented levels of concern (Durhan et al. 2006). However,
17a-trenbolone has been documented at concentrations ranging from <10 to 120 ng/L, which are high
enough levels to potentially have adverse impacts (Durhan et al. 2006). Importantly, this information is based
on a limited number of studies, and further research is needed to truly understand whether levels observed in
surface waters are sufficient to cause adverse effects on aquatic life.
The hormone 17(3-trenbolone is considered a potent androgen because it binds with greater affinity to the
androgen receptor of fathead minnows than naturally-produced testosterone (Ankley et al. 2003). Research
conducted by Jensen et al. (2006) suggests that 17a-trenbolone may be just as potent as 17[3-trenbolone.
Exposure to the trenbolone acetate metabolites can also result in the formation of dorsal (nuptial) turbercles
on females: these tubercles are normally present on spawning males (Ankley et al. 2003, Jensen et al. 2006). In
another study, male fathead minnows exposed to fecal slurry from cattle implanted with trenbolone acetate
and estradiol experienced demasculinizing and feminizing effects (Sellin et al. 2009). Currently, there are no
published studies on the potential adverse impacts of synthetic progestins on aquatic organisms. However,
Schiffer et al. (2001) and Lee et al. (2007) provide evidence suggesting that the progestinal activity of
melengestrol acetate is estimated to be nearly 125 times greater than that of progesterone.
The presence of hormones in aquatic ecosystems is not new since all mammals naturally produce and excrete
hormones. In the past decade, a number of studies, most of which have been focused downstream from
wastewater treatment plant discharges, have suggested potential adverse impacts of hormones on the
endocrinology offish (Lee et al. 2007). Additionally, a limited number of case studies suggest that hormones
from manure specifically, may have similar endocrine-disrupting impacts on aquatic life (i.e., Blazer et al.
2007). Little is known about the potential adverse impacts of long-term exposure to hormone doses lower
than those exhibiting a response over a 21 day test, such as in the previously discussed studies conducted by
Ankley et al. (2003) and Jensen et al. (2006). Importantly, the detection of hormones in the environment is
relatively new because recent advancements in laboratory methods and analytical techniques have made it
possible to detect hormones, which are often present in low concentrations (ng/L) in the environment (Lee
et al. 2007). The ability to detect hormones in the environment has allowed for more research on the
potential impacts of hormones from human and animal waste streams on aquatic organisms. Given the
adverse impacts of exogenous hormones on aquatic organisms, the increasing amount of both natural and
synthetic hormones entering the environment through livestock animal manure needs additional review,
particularly because some synthetic hormones (e.g., trenbolone acetate) appear to be more stable in the
environment than natural hormones (Ankley et al. 2003, Lee et al. 2007).
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6.5. Waterborne Disease Outbreaks
Livestock and poultry manure can contain pathogens with zoonotic potential (transferred to humans from
other animals) (e.g., Rogers and Haines 2005). Land application of manure presents opportunities for those
pathogens to enter recreational waters and drinking water sources, potentially leading to a waterborne disease
outbreak (see Chapter 3). Exposure of crops to manure or contaminated water can also lead to foodborne
illness.
Although the majority of waterborne disease outbreaks have been attributed to human fecal contamination
(Rosen 2000), investigations have identified pathogens in manure as a possible or confirmed source in a
number of outbreaks (Rosen 2000, Guan and Holley 2003). A number of examples of outbreaks are briefly
described in Table 6-3, which also includes outbreaks caused by contamination of food with manure. This
chapter reviews waterborne disease outbreaks, presents examples of notable outbreaks, and notes
informational gaps, particularly in the ability to trace the origin of waterborne diseases in many cases.
Table 6-3. Waterborne and foodborne disease outbreaks. (Table 6-3 continues on the followingpage.)
Location
Nova Scotia,
Canada
Carrollton,
GA
Ayrshire, UK
Swindon &
Oxfordshire,
UK
Cabool, MO
Bradford, UK
Year
1981
1987
1988
1989
1990
1992
Pathogen
Listeria
monocytogenes
Cryptosporidium
parvum
Cryptosporidium
parvum
Cryptosporidium
parvum
£co//0157:H7
Cryptosporidium
parvum
Suspected Source of
Contamination
Cabbages grown on a farm
fertilized with Listeria-
contaminated sheep
manure.
Runoff from cattle grazing
areas and a sewage
overflow-contaminated river
water used for drinking
water supply. Also, drinking
water treatment
deficiencies.
Post-treatment
contamination of a
municipal drinking water
tank with runoff; cattle
manure slurry sprayed
nearby.
Oocysts in runoff from fields
with cattle entered water
supply (Thames River) after
Contamination of
distribution system with
human sewage overflow via
water main breaks and
meter replacements.
Community practices dairy
farming.
Cryptosporidium oocysts in
the water supply after heavy
rains in the catchment area.
Also, deficiencies in drinking
water treatment.
Predominant Illness
and Impact
41 cases of listeriosis,
18 deaths
13,000 cases of
cryptosporidiosis
27 confirmed cases
hundreds more
suspected
516 cases of
cryptosporidiosis over
5 months, mostly
children, 8%
hospitalized
243 cases of diarrhea,
including 86 with
bloody diarrhea, 32
hospitalized, 2
Hemolytic-uremic
syndrome (HUS), 4
deaths
125 cases of
cryptosporidiosis
References
Health Canada 2009
Solo-Gabriele et al.
1996, USEPA 2004a
Smith etal. 1989
Richardson et al.
1991, USEPA 2004a
Geldreich et 3!
1992, Swerdlowet
al. 1992, Cotruvoet
al ?nn4
Athertonetal. 1995,
USEPA 2004a
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Location
Maine
The
Netherlands
Milwaukee,
Wi
Sakai City,
Japan
Connecticut
and Illinois,
USA
Washington
Co., NY
California,
USA
Walkerton,
Canada
Cornwall,
U.K.
Year
1992
1993
1993
1995
1996
1999
1999
2000
2004
Pathogen
£co//0157:H7
£co//0157:H7
Cryptosporidium
parvum
£co//0157:H7
£co//0157:H7
£co//0157:H7and
Campylobacter spp.
£ co// 0157: NM
£co//0157:H7and
Campylobacter spp.
E. co//0157:H7
Suspected Source of
Contamination
Cow manure spread in a
vegetable garden.
Illness was contracted
swimming in a semi-natural
shallow lake. Possible
sources include human
excrement and water from
ditches draining meadows
with cattle.
Cryptosporidium oocysts in
drinking water source,
related to heavy rain and
increased turbidity. Source
may have been animal
manure and /or human
excrement.
Animal manure used in fields
growing alfalfa sprouts.
Consumption of mesclun
lettuce. Cattle were found
near the lettuce fields.
Contamination of un-
chlorinated water supply
well used by food vendors
for ice and drinks. Possible
sources are of cattle or
human origin.
Recreational exposure to lake
water; fecal contamination
may have been from humans,
cattle, or deer.
Runoff from farm fields
entering a shallow well used
for the town's water supply.
Exposure to a freshwater
stream crossing a seaside
beach; the stream had cattle
grazing upstream.
Predominant Illness
and Impact
4 cases of bloody
diarrhea, one adult and
3 children
12 cases of enteritis, 5
children with HUS
403,000 cases of
cryptosporidiosis, 54
deaths
12,680 cases among
schoolchildren, most
with diarrhea or bloody
diarrhea. 121 cases of
HUS, 425 hospitalized,
3 deaths
53 cases, 40 with
bloody diarrhea, and 3
HUS cases
Bopp et al. cite 775
cases, 65 hospitalized,
11 HUS cases, 2 deaths
CDC cites 921 persons
with diarrhea after
attending fair
7 cases of diarrhea in
children
2,300 cases of diarrhea,
more than 100
hospitalized, 27 HUS
cases, 6 deaths
7 cases in children,
diarrhea and bloody
diarrhea, 4 hospitalized
References
Cieslaketal. 1993,
USEPA 2004a
Cransberg et al.
1996, Cotruvo etal.
2004
MacKenzie etal.
1994, Hoxieetal.
1997
Fukushima et al.
1999, USEPA 2004a,
Rogers and Haines
2005
Hilborn etal. 1999
CDC 1999, Bopp et
al. 2003, Cotruvo et
al. 2004
Feldman etal. 2002,
Cotruvo et al. 2004
Valcour etal. 2002,
Hrudey etal. 2003,
Cotruvo et al. 2004,
USEPA 2004a, PHAC
2000
Ihekweazu etal.
2006
6.5.1. Routes of Exposure and Example Outbreaks
A waterborne disease outbreak is defined by two criteria: 1) two or more persons experience an illness and are
linked epidemiologically by time, location of exposure to water, and illness characteristics, and 2) the
epidemiological evidence implicates water as the source of illness (Hlavsa et al. 2011). Humans may be
exposed to waterborne pathogens via contact with treated or untreated recreational water or ingestion of
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drinking water (Bowman 2009). Although exposure may also occur through inhalation of some organisms
(e.g., Legionellapneumophila, Naeg/eria fon/leri, Acanthamoeba), this method of exposure is outside of the scope of
this report and is not discussed further. Surface waters may become contaminated by zoonotic pathogens
from agricultural or urban runoff, although dilution and die-off can help mitigate the possibility of illness
(Rosen 2000). Ground water may become contaminated through infiltration of agricultural runoff or leaching
of land-applied manure (Marks et al. 2001), with shallow aquifers and fractured rock and karst aquifers being
especially vulnerable. Agricultural or urban runoff may also enter inadequately protected private or municipal
wells (Rosen 2000).
Large and/or intense precipitation events can increase the likelihood of contamination of water with
microorganisms carried in runoff and/or through impacts on drinking water treatment processes. Such
hydrologic conditions in an agricultural watershed raise the possibility of waterborne disease outbreak due to
zoonotic organisms in manure. Curriero et al. (2001) analyzed the relationship between precipitation and
waterborne disease based on all reported waterborne disease outbreaks in the U.S. from 1948 to 1994. Of 548
waterborne disease outbreaks analyzed, 51% were
observed to coincide with extreme precipitation
events. A number of examples can be found in which
a combination of heavy rainfall and deficient
treatment of a surface water supply resulted in a
waterborne disease outbreak; some were outbreaks in
which manure was a suspected source. For example,
insufficient chlorination related to increased turbidity
from heavy precipitation was implicated in a 1978
Campylobacter outbreak in Bennington, Vermont, with
» Many waterborne disease outbreaks are
undetected or unreported.
v^ From 1991-2002, the pathogens for almost
40% of gastrointestinal illness outbreaks
associated with drinking water were not
identified.
» Many if not most outbreaks for which the
pathogen is known are attributable to human
sources of infection.
» The number of manure-related outbreaks is
not known, but contamination from manure has
been suggested as a possible causative agent in a
number of outbreaks involving zoonotic
pathogens.
3,000 cases (Vogt et al. 1982). In this outbreak, the
main water source for the town was vulnerable to
deficient sewer systems as well as animal excrement
on the banks (animal type unknown); increased
runoff from the watershed provided contamination,
and the additional turbidity decreased the
effectiveness of the disinfection.
The Milwaukee outbreak (March and April, 1993)
was the largest drinking water-related Cryptosporidium
outbreak on record and was related to heavy precipitation and drinking water treatment deficiencies. An
estimated 403,000 people were affected, and 54 deaths were reported (Hoxie et al. 1997). Milwaukee uses
water from Lake Michigan and has two treatment plants; the locations of cases of illness suggested that one
of the two plants (Howard Avenue) was responsible (USEPA 2004, Bowman 2009). It is believed that heavy
rainfall and snow runoff may have transported Crypto sporidium oocysts to Lake Michigan in addition to causing
high turbidity (Rosen 2000). Plant operators may not have used adequate coagulant to treat the water
(MacKenzie et al. 1994, Bowman 2009). Also, the plant recycled its filter backwash water, possibly
concentrating oocysts in the plant. At the time of the outbreak, the plant met all drinking water quality
standards (MacKenzie et al. 1994, Rosen 2000), but the treatment processes were not adequate to remove or
inactivate Cryptosporidium oocysts. After the outbreak, the intake was moved and the plant was upgraded to
prevent future Cryptosporidium outbreaks by the addition of ozone for disinfection and enhanced filter beds
with continuous turbidity meters (MacKenzie et al. 1994, Bowman 2009). Also, the practice of recycling filter
backwash water has been discontinued (MacKenzie et al. 1994). Possible sources of the Cryptosporidium
include cattle manure in the watershed, slaughterhouse waste, and sewage overflow (MacKenzie et al. 1994).
Genetic testing has implicated human sewage, but the analysis was based on only four isolates and may not be
representative of the entire outbreak (Peng et al. 1997). Thus, the sources of the oocysts remain unclear.
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Contamination of ground water supplies has also resulted in waterborne disease. In August of 1999, a large
outbreak of E. coli O157:H7 and Campylobacterjejuni occurred in association with the Washington County Fair
in New York State. According to the CDC (1999), 921 individuals reported diarrhea after attending the fair.
E. coli O157:H7 was cultured from stools from 116 persons, with 13 also infected with Campy lob acter. Two
deaths were reported. Water at the fairgrounds was supplied by six shallow wells, four of which were un-
chlorinated (Bopp et al. 2003). One of the un-chlorinated wells was implicated in the outbreak. Two possible
sources of contamination were located near the well: a cow manure storage site and a dormitory septic tank.
The well may have been contaminated by runoff resulting from a heavy rainfall that occurred during one day
of the fair.
An E. coli O157:H7 outbreak linked to cattle manure contamination of a ground water supply occurred in
May 2000 in Walkerton, Ontario, resulting in more than 2,000 cases. Of those, 27 people developed
hemolytic-uremic syndrome (HUS), and there were six deaths. Both E. coli O157:H7 and Campylobacter were
confirmed in stool samples from those infected (PHAC 2000). Testing of one of the town's production wells
and the distribution system demonstrated evidence of fecal contamination of the drinking water, and DNA
analyses by polymerase chain reaction (PCR) confirmed the presence of E. coli O157:H7 (PHAC 2000). To
determine the origin of the E. coli O157:H7, 13 livestock farms were investigated in the area. Campylobacter^rzs,
found on nine farms, and both E. coli O157:H7 and Campylobacter were found on two farms, including a farm
near the tested drinking water well (PHAC 2000). Typing of isolates, including the use of genetic
fingerprinting, matched the isolates from the farm near the well to those found in most of the patients
(PHAC 2000, Clark et al. 2003). The analysis indicates that the outbreak was caused by a combination of
factors including flooding from heavy rainfall, runoff contaminated by cattle manure, a well vulnerable to
surface water contamination (as further indicated by historic records), and decreased disinfection efficacy due
to increased turbidity (PHAC 2000, Clark et al. 2003).
Contamination can also occur post-treatment, as was the case with a Cryptosporidium outbreak in Ayrshire,
England in 1988. Twenty-seven cases of cryptosporidiosis were confirmed, although inquiries by local health
authorities suggested that there may have been hundreds of cases. The contamination was traced to
intermittent seepage of runoff into a clay pipe that fed into a water tank. Cattle manure slurry had been
sprayed nearby, and there had been heavy rain, which would have increased water leakage into the tank
(Smith etal. 1989).
If contaminated irrigation water or runoff reaches crops or if manure is applied to fields, foodborne
outbreaks may also occur; two thirds of deaths from food-borne outbreaks are attributed to zoonotic
bacterial pathogens: Salmonella sp., Usteria monocytogems, Campylobacter, and E. coli O157:H7 (Bowman 2009). A
variety of fresh fruits, vegetables, and nuts may be affected (Rogers and Haines 2005, CDC 2013).
6.5.2. Outbreak Statistics
Data on waterborne disease outbreaks in the U.S. are compiled and reported by the CDC, the Council of
State and Territorial Epidemiologists, and the USEPA through the Waterborne Disease and Outbreak
Surveillance System (WBDOSS), a voluntary system in place since 1978. Reports are published by the CDC as
surveillance summaries, allowing for an assessment of trends in the prevalence of different types of pathogens
in recreational and drinking waters. Although these reports do not identify potential animal vs. human
sources for outbreaks, they do provide information on the types of illness and the etiologic agents, some of
which can be zoonotic. These reports, however, are recognized as underestimates of the true number of
outbreaks because of unreported or unrecognized cases (see subsection 6.5.3).
During 2007 and 2008, 36 drinking water-related disease outbreaks were reported to the CDC (Hlavsa et al.
2011); 12 were related to untreated ground water used for drinking, and seven were attributed to treatment
failures; these 19 outbreaks all resulted in acute gastrointestinal illness. For recreational water, 134 outbreaks
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causing nearly 14,000 cases of illness were reported in the same time period (Hlavsaet al. 2011). Outbreaks of
acute gastrointestinal illness can be caused by pathogens with zoonotic potential (Rosen 2000). For example,
among 21 bacterial outbreaks associated with drinking water during 2007-2008, four were caused by
Campy lob acter, three by Salmonella (including one outbreak with 1,300 cases), and one by E. coli O157:H7.
(Other bacterial outbreaks were caused by Legiomllapneumophila, which is not considered zoonotic). Two of
the three parasitic outbreaks were caused by Giardia intestinatis (synonymous with Giardia lamblia). Norovirus
was responsible for four of the five viral outbreaks. Among 134 recreational water disease outbreaks in 2007-
2008, Cryptosporidium caused 60 outbreaks, most of which were caused by exposure to treated water such as
chlorinated swimming pools and spas (Hlavsa et al. 2011).
6.5.3. Limitations Associated with Detection of Zoonotic Waterborne Disease Outbreaks
Determining the pathogen and tracing the origin of a waterborne disease outbreak can be challenging.
Therefore, the causes of outbreaks often remain unknown, including those that may be related to livestock
and poultry operations. Between 1991 and 2000, for example, the pathogens associated with nearly 40% of
drinking water outbreaks were not identified (Craun et al. 2006). Without knowing which pathogen is
responsible for the outbreak, it is even more difficult to trace the pollution source. Livestock and poultry
manure is a source of pathogens, but because of the limitations associated with tracing an outbreak back to
the source, manure-related outbreaks may be left undetected or attributed to another source incorrectly or by
default. For example, if an outbreak cannot be traced to water or if the route of transmission is unclear, the
source may be attributed to food (Bowman et al. 2009). It is also generally recognized that reported outbreaks
represent only a small portion of total outbreaks (Craun et al. 2006); more research as well as better
monitoring and surveillance are needed to better understand the possible extent of underestimation.
Several factors affect whether an outbreak is recognized. Not all infected patients seek medical attention,
making the number of cases difficult to track. The local health department needs to have adequate resources
for surveillance and investigation (Craun et al. 2006). Also, many outbreaks may simply be too small to notice.
Importantly, by the time an outbreak is discovered, the contamination may have already flushed through the
water source, making it difficult to conclusively link the outbreak to water or identify the source of pollution
(e.g., Hunter et al. 2003, Perdek et al. 2003). Pathogen detection methods also present challenges in terms of
time requirements, method sensitivities, the abilities of the pathogens to grow in culture, and indications of
viability (Perdek et al. 2003, Cotruvo et al. 2004, Yu and Bruno 1996, Pyle et al. 1999, Hunter et al. 2003,
Perdek et al. 2003). These factors compound the difficulty in assessing to what degree (and where)
waterborne illnesses may be caused by zoonotic pathogens transported in manure. A number of serotyping
methods and molecular methods, however, may be used to attempt to determine the source of a pathogen
(e.g., Hunter et al. 2003). An example of a useful development has been the identification of Cryptosporidium
genotypes that can help determine if the source is zoonotic (e.g., Royer et al. 2002).
6.5.4. Summary and Discussion
Waterborne disease outbreaks can occur from exposure to contaminated recreational water or ingestion of
contaminated drinking water. Although many, if not most, outbreaks are believed to be associated with
human fecal contamination, livestock and poultry manure contains pathogens that may contaminate water.
The number of waterborne disease outbreaks that may be associated with zoonotic pathogens from livestock
and poultry manure is not understood. This is in part because confirming the source of an outbreak is
challenging, and many outbreaks may not even be recognized. Not all persons will seek medical attention,
some outbreaks may be too small to be noticed, and reporting to the WBDOSS is voluntary. Furthermore,
among recognized outbreaks of acute gastrointestinal illness, the causative agent remains unidentified for a
substantial portion (Craun et al. 2006, Hlavsa et al. 2011).
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Routes of exposure to waterborne pathogens may involve entry of pathogen-contaminated water into
drinking water supplies, either via runoff or infiltration, or into recreational water via runoff. Heavy rainfall in
particular has been implicated in a number of outbreaks; the possibility of manure-related contamination may
be greater if manure has been recently applied, allowing runoff contaminated with manure to reach
recreational waters or drinking water supplies.
Agricultural sources such as runoff containing manure have been suspected in a number of waterborne
outbreaks caused by pathogens with zoonotic potential (Table 6-3). It is not generally possible to confirm
unequivocally that the source is agricultural as opposed to human, but watershed characteristics, such as
nearby livestock and poultry operations and their proximity to recreational or drinking water resources
suggest possible zoonotic transmission. Greater surveillance is needed to understand the degree to which
manure-related pathogens may be implicated in waterborne disease outbreaks.
6.6. Potential Manure-Related Impacts Summary and Discussion
Livestock production has become increasingly concentrated in the U.S., which in turn has resulted in greater
volumes of manure and associated contaminants in local areas (MacDonald and McBride 2009). This chapter
reviews some of the potential and documented impacts associated with emerging contaminants, including
antimicrobials and hormones. To a lesser extent, this chapter reviews pathogens and indirect effects of
nutrients, which have been reviewed in detail elsewhere (e.g. Rogers and Haines 2005, Camargo and Alonso
2006, NITG 2009). The research provided in the preceding chapters indicates both documented and potential
ecological and human health impacts associated with livestock and poultry manure, though overall impacts
are largely unknown. Importantly, research indicates that manure runoff can contribute to water quality
degradation, and the magnitude of manure generated (1.1 billion tons in 2007) may be of concern.
Aquatic communities can be adversely impacted by manure runoff or discharges to surface waters in a
number of ways. Nutrient loading is the typical impact discussed, though large manure spills have been
implicated in fish kills and degraded water quality (Mulla et al. 1999). Manure can also be a source of
hormones, which are known endocrine disrupters. While research is limited, exposure to hormones from
livestock and poultry manure has been implicated in adverse impacts on reproduction, fitness, and behavior
in fish (Zhao et al. 2008, Iwanowicz and Blazer 2011).
Manure contamination of drinking and recreational water resources can be a human health concern and/or
incur increased drinking water treatment costs. Nutrient loadings to surface waters may also contribute to the
growth of HABs, which can produce toxins that can be harmful to human and ecological health (Lopez et al.
2008). Waterborne disease outbreaks have been associated with pathogen contributions from manure, though
source detection is challenging (Rosen 2000, Guan and Holley 2003). The human health impacts related to
potential long-term exposure via drinking water to low levels of hormones and antimicrobials (from all
sources) are unknown. Furthermore, little is known about the potential synergistic effects between
antimicrobials and hormones, which may be present in drinking water systems (Weinberg et al. 2008).
A topic of increasing interest has been the issue of widespread antimicrobial use in livestock and poultry.
Such widespread use may select for antimicrobial-resistant bacteria (Swartz 2002). Many antimicrobials are
also used in human clinical medicine (Sapkota et al. 2007). Related to antimicrobial resistance and human
health concerns, the USFDA has banned the use of certain types of antimicrobials for livestock and poultry
use (Nelson et al. 2007, Gilbert 2012).
Research pertaining to the human health and ecological impacts associated with livestock and poultry manure
is relatively limited, particularly in terms of antimicrobials and hormones. However, as reviewed in this
chapter, these contaminants have been detected in manure and environments proximal to livestock and
poultry operations. A more thorough understanding of livestock and poultry antimicrobial and hormone use
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and excretion and better source tracking of waterborne disease outbreaks is needed to fully address the
ecological and human health impacts associated with manure generation.
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7. Drinking Water Treatment Techniques for Agricultural Manure
Contaminants
Drinking water resources may be contaminated with livestock and poultry manure through overland runoff,
soil infiltration, direct discharges or atmospheric deposition. Key manure contaminants reviewed in this
report include pathogens, antimicrobials, hormones, and nutrients, though Table 1-1 provides a more
complete list. Because of their acute negative human health impacts, much research and regulatory attention
has been given to ensuring the removal and/or inactivation of pathogens and nutrients such as nitrate and
nitrite. For example, MCLs and treatment technique requirements have been established under USEPA's Safe
Drinking Water Act, focusing on the removal or inactivation of pathogens from drinking water sources (see
USEPA's current drinking water regulations
website: http: /7water.epa.gov/lawsregs/rulesregs /sdwa/currentregulations.cfrn). While extensive research
has been conducted on pathogens, emerging contaminants, such as hormones and antimicrobials, have only
recently been studied. This is largely because of recent developments in analytical techniques that allow for
the detection of such contaminants at low levels (e.g., ng/L). Research is limited, though hormones and
antimicrobials have been detected in drinking water supplies (Stackelberg et al. 2007, Benotti et al. 2009), and
understanding how effectively these compounds are removed by drinking water treatment processes is
important for preventing potential long-term public health impacts (Snyder et al. 2008, Weinberg et al. 2008).
Ingestion of antimicrobials and hormones via drinking water is likely low over the course of a lifetime, though
short- and long-term effects related to low-level exposure or synergisms between different compounds are
not fully understood (Weinberg et al. 2008).
This chapter provides a brief overview of watershed management techniques and drinking water treatment
processes that can help to reduce surface water pollution and remove contaminants. Importantly, this chapter
focuses primarily on antimicrobial and hormone removal from drinking water, because our understanding of
removal of these contaminants from drinking water is relatively new given recent advancements in analytical
techniques allowing for measurement of these compounds. Information on the removal of pathogens and
nutrients is covered briefly, but is well established and available from other sources (USEPA's Alternative
Disinfectants and Oxidants Guidance Manual (1999), AWWA's Removal of Emerging Waterborne Pathogens (2001),
USEPA's Effect of Treatment on Nutrient Availability (2007).
7.1. Source Water Protection
A multi-barrier approach including source water protection efforts in addition to drinking water treatment
can help minimize exposure to animal manure contaminants. The first step in this approach is to utilize
source water contamination prevention measures related to livestock and poultry manure that can improve
water quality and reduce the burden on drinking water treatment utilities. Management strategies include
preventing animals and their manure from coming into contact with runoff and water sources; properly
applying manure as fertilizer on crop or pastures during growing seasons to match crop nutrient needs (based
on well-developed Nutrient Management Plans), and appropriately managing pastures (USEPA 2001).
A variety of intervention practices may be employed to minimize manure contact with precipitation and
runoff. Specific practices include lining and maintaining manure storage lagoons, constructing litter storage
facilities, diverting precipitation and surface water away from manure, composting, and treating runoff
(Armstrong et al. 2010) (see also Chapter 8 for further information). The goal of pasture management is to
protect water resources from direct livestock contact and runoff from animal feeding operations. Fencing can
be used to keep livestock and poultry from defecating in or near streams or wells. Additionally, providing
alternative water sources and hardened stream crossings for use by livestock lessens their impact on water
quality (USEPA 2001). For more information on livestock and poultry management strategies designed to
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protect water resources, refer to the USEPA's Source Water Protection Practices bulletin Managing Livestock, Poultry,
and Horse Waste to Prevent Contamination of Drinking Water (2001).
7.2. Drinking Water Treatment Techniques
While source water protection efforts can help to reduce the burden for contaminant removal on drinking
water treatment plants, appropriate treatment processes must also be in place. Conventional drinking water
treatment facilities typically incorporate: 1) coagulation and flocculation, in which dirt, colloids and other
suspended particles in the water column bind to alum or other chemicals that are added to the water to form
floe; 2) sedimentation, in which the coagulated particles (floe) settle to the bottom; 3) filtration, in which
particles including clays, silt and organic matter are physically removed; and 4) disinfection, in which
microorganisms are killed or inactivated (USEPA 2004b). In addition, treatment facilities may utilize
advanced treatment options such as nanofiltration and ultrafiltration, reverse osmosis, ion exchange and
carbon adsorption to remove contaminants not removed by conventional filtration (USEPA 2004b).
The following subsections provide a brief overview of pathogen and nutrient removal and a more detailed
review of recent research findings on antimicrobial and hormone removal.
7.2.1. Pathogen and Antimicrobial-Resistant Bacteria Removal
Coagulation and filtration processes have been demonstrated to remove bacteria, protozoa and viruses.
Maximum removal of pathogens is associated with optimized coagulant dosing and production of water with
a very low turbidity. Chlorine, the most common disinfectant in the U.S., is an effective bactericide and
viricide. Protozoan cyst and oocysts have been found to be more resistant to chlorine disinfection, and high
contact time (CT) values are required for their inactivation. Crypstosporidium parvum and Giardia lamblia are
resistant to chlorine disinfection, though UV light has been found to be an appropriate disinfection
alternative. For more information on pathogen removal, refer to the USEPA's Alternative Disinfectants and
Oxidants Guidance Manual (1999) and AWWA's Removal of Emerging Waterborne Pathogens (2001).
The process of chlorination during drinking water treatment has been associated with an increase in
antimicrobial-resistant bacteria in treated water. During testing of drinking water source, treated, and tap
water, Xi et al. (2009) found that during the treatment process, there was a significant increase in the
prevalence of bacteria resistant to amoxicillin, and chloramphenicol. Chlorine-induced formation of
multidrug-resistant bacteria has also been documented by Armstrong (1981) and (1982). The process by
which this occurs, is not entirely known, though one potential explanation is that in the presence of chlorine,
the bacteria increase their expression of efflux pumps, which pump toxins and antibiotics outside of the cell
(Xi et al. 2009). Further research in this area will help elucidate the impacts of chlorination on the prevalence
of antimicrobial-resistant bacteria.
7.2.2. Nutrient Removal
Nutrient removal in drinking water is focused on nitrate and nitrite, related to the human health impacts
briefly discussed in Chapter 6. The USEPA has established a drinking water MCL for nitrite of 1 mg/L and
for nitrate-nitrogen of 10 mg/L. Ion exchange, reverse osmosis, and electrodialysis have been shown to
remove nitrates/nitrite concentrations to below their MCL. For more information on nitrates and nitrites,
please refer to USEPA's Basic Information about Nitrate in Drinking Water, available online
at http://water.epa.gov/drink/contaminants/basicinformation/nitrate.cfm. For information on other
nutrients, please see USEPA's Effect of Treatment on Nutrient Availability (2007).
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7.2.3. Antimicrobial and Hormone Removal
Each step of the drinking water treatment process differs in its efficacy in removing antimicrobials and
hormones. Generally, concentrations of antimicrobials and hormones tend to be lower in finished (i.e.,
treated) water than in source water, either due to degradation or removal (Stackelberg et al. 2007, Snyder et al.
2008). For example, Stackelberg et al. (2007) measured the removal of antimicrobials in a conventional
drinking water treatment plant and found that, out of seven antimicrobials detected in source water, only one
persisted at detectable concentrations after treatment. In that study, erythromycin, erythromycin-H2O (an
erythromycin degradate), lincomycin, sulfadimethoxine, sulfamethazine, and sulfamethoxazole, all decreased
from <0.1 ug/L in source water to non-detectable concentrations in finished, treated water. Sulfathiazole
persisted through treatment, though maximum concentrations decreased from 0.08 ug/L in source water to
0.01 ug/L in finished water. Reporting levels for this study ranged from 0.01 ug/L to 0.1 ug/L for the
aforementioned antimicrobials.
Importantly, even when treatment appears to remove nearly all of a compound from source water, those
compounds are likely still present in the treated effluent, either as degradates or in concentrations below the
method detection limit (Snyder et al. 2008, Weinberg et al. 2008). Furthermore, most research has focused on
commonly used antimicrobials and naturally produced, rather than synthetic, hormones. Therefore, our
knowledge of the amount of antimicrobials and hormones in drinking water is essentially a function of which
compounds are analyzed and the analytical methods used. According to Snyder et al. (2008), no water is 'drug
free' given the variety of sources of these compounds to the environment. Although some antimicrobials may
be degraded during treatment, their degradates may remain biologically active, potentially having long-term
public health impacts (Dodd et al. 2005, Weinberg et al. 2008). The following subsections review available
research on each treatment process in terms of its effectiveness in removing antimicrobials and hormones
from source water.
7.2.3.1. Coagulation and Sedimentation
The effectiveness of coagulation and sedimentation in antimicrobial and hormone removal appears to vary,
though the processes are generally considered to be relatively ineffective in overall removal (Westerhoff et al.
2005, Stackelberg et al. 2007). Using ferric chloride as a coagulant, Stackelberg et al. (2007) reported 33%
removal of sulfamethoxazole, 47% removal of erythromycin-LbO, and 60% removal of acetaminophen from
source water. However, in a separate study, coagulation using ferric salt or alum did not result in any
statistically significant removal of carbadox, trimethoprim, or various types of sulfonamides (Adams et al.
2002). The relative ineffectiveness of coagulation and sedimentation in antimicrobial removal is not surprising
because these processes remove hydrophobic compounds, and antimicrobials tend to be hydrophilic
(Weinberg et al. 2008, Chee-Sanford et al. 2009).
Coagulation using alum or ferric salt appears to be even less effective in hormone removal (Westerhoff et al.
2005). Using alum, ethynlestradiol, and androstenedione were not removed in measurable amounts, and only
approximately 2% of estradiol, 5% of estrone, and 6% of progesterone were removed from source water
(Westerhoff et al. 2005). Using ferric salt during coagulation resulted in similar low removals.
7.2.3.2. Filtration and Adsorption
Nanofiltration and reverse osmosis (RO) have been shown to be effective at removing organic compounds
(Snyder et al. 2008), while ion exchange is relatively ineffective in antimicrobial removal (Adams et al. 2002).
The use of nanofiltration has been shown to remove as much as 80% of chlortetracycline, but only 11% to
20% of sulfonamides (Koyuncu et al. 2008). Removal of the hormones estriol, estradiol, estrone, 17a-
ethinylestradiol, and testosterone through nanofiltration range from 22% to 46% (Koyuncu et al. 2008). In a
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separate study, Nghiem et al. (2004) also reported effective removal of estradiol, estrone, testosterone, and
progesterone by nanofiltration.
Using RO, Adams et al. (2002) reported 90% removal of carbadox, trimethoprim, and sulfonamides from
Mississippi River water. Currently, limited research on RO in terms of hormone and antimicrobial removal
has been conducted, and despite its apparent effectiveness, RO implementation is costly and may not always
be economically feasible.
The use of activated carbon appears to be effective in removing organic compounds; however, activated
carbon must be regularly replaced or regenerated in order to maintain effectiveness, and the contact time and
dose are also important factors in its capacity to remove compounds (Snyder et al. 2006, 2008). As much as
21% of sulfamethoxazole and 65% erythromycin-H2O may be removed through powdered activated carbon
(PAC) adsorption (Westerhoff et al. 2005). The PAC dosage may be an important factor in antimicrobial
removal efficacy. Using PAC doses of 10 mg/L, Adams et al. (2002) reported that antimicrobial removal
ranged from 49% to 73% in Mississippi River source water, while removal rates ranged from 65% to 100%
using a PAC dose of 20 mg/L. The use of PAC also appears to be effective in removing hormones from
source water, with as much as 88% of testosterone, 93% of progesterone, and 94% of estradiol removed after
four hours of PAC contact time (Westerhoff et al. 2005). PAC is typically only used during certain times of
the year, such as during algal blooms in the late spring or summer. The use of granular activated carbon
(GAC) is expected to be effective (Adams et al. 2002), though limited research has been conducted on this
process in terms of antimicrobial and hormone removal.
7.2.3.3. Disinfection
Research indicates that the disinfection process is instrumental in antimicrobial and hormone
removal/degradation during water treatment (Adams et al. 2002, Stackelberg et al. 2007, Snyder et al. 2008,
Weinberg et al. 2008). Depending on the treatment facility, disinfection may involve the use of chlorine
compounds, ozone, or UV light treatment. Chlorine disinfectants tend to react with antimicrobials such as
sulfamethoxazole, trimethoprim, ciprofloxacin, and enrofloxacin, leading to their degradation, but potentially
not completely eliminating their biological effect because of the formation of degradation products (Dodd et
al. 2005, Weinberg et al. 2008). Disinfection through the use of sodium hypochlorite can significantly
decrease the concentration of sulfathiazole in source water (Stackelberg et al. 2007). Regarding hormone
removal, Snyder et al. (2008) reported higher removal rates of estrogen than testosterone and progesterone
during chlorine treatment; over 20% of testosterone and progesterone were removed, while upwards of 100%
of estradiol, estriol, and estrone were removed during bench-scale analyses. Although chlorination provides
critical benefits in the disinfection process, it may also lead to the formation of undesirable disinfection
byproducts, which can be carcinogenic. The costs and benefits of chlorination in this regard should be further
evaluated.
Ozone may be more rapid and effective than chlorine compounds in organic compound removal (Weinberg
et al. 2008). Adams et al. (2002) found that concentrations of antimicrobials in Mississippi River water
decreased by over 95% through the use of ozone, demonstrating the effectiveness of this disinfection
method. Similarly, Snyder et al. (2005) found that sulfamethoxazole concentrations in drinking water
decreased from 9.7 ng/L in source water to below the detection limit (<1 ng/L) in treated water after
ozonation. Ozone has also been shown to oxidize nearly 100% of testosterone, progesterone, and estrogen
hormonal compounds, suggesting that ozonation is more efficient in removing hormones than is chlorination
(Snyder et al. 2008). Similar results were observed by Westerhoff et al. (2005) in terms of hormone removal
through the use of ozonation.
UV light alone appears to be less effective than chlorination and ozonation in removing hormones and
antimicrobials (Snyder et al. 2008). Also, the dose of UV light typically used for disinfection to kill
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microorganisms is orders of magnitude lower than what would be required to remove micropollutants such as
organic compounds (Snyder et al. 2003). However, a combination of UV light and hydrogen peroxide appears
to be effective in hormone removal (Rosenfeldt and Linden 2004) and antimicrobial removal (Weinberg et al.
2008, Giri et al. 2011). Certain antimicrobials including tetracycline, chlortetracycline, and oxytetracycline may
undergo photodegradation under UV light, the rate of which markedly increases when low concentrations of
hydrogen peroxide are added to the disinfection process (Lopez-Penalver et al. 2010).
7.3. Summary and Discussion
Conventional drinking water treatment processes are effective at removing pathogens, and some treatment
plants employ additional processes that effectively remove nutrients. Recent research indicates that
conventional drinking water treatment practices are also effective in decreasing the concentrations of
hormone and antimicrobials in source water, particularly during disinfection (Adams et al. 2002, Snyder et al.
2008). Filtration using nanofiltration and reverse osmosis is highly effective in antimicrobial and hormone
removal (Koyuncu et al. 2008), though these processes are not always used in conventional drinking water
treatment facilities, and limited research is available. Antimicrobials and hormones, as with all organic
compounds, vary widely in physical and chemical characteristics and may be rapidly removed or unaffected by
certain drinking water treatment processes. Therefore, antimicrobial and hormone removal from drinking
water may be enhanced through the implementation of multiple treatment and disinfection methods (Snyder
et al. 2008). Whereas public water systems are subject to drinking water treatment processes, private drinking
water wells are typically not tested or treated for these compounds, so antimicrobials and hormones in private
groundwater drinking water systems affected by livestock and poultry production may remain undetected. A
stronger understanding of the prevalence and concentrations of antimicrobials and hormones in drinking
water, as well as more research on which treatment processes best remove these compounds, will help in
planning strategies to minimize their consumption and any potential associated health effects.
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8. Managing Manure to Control Emerging Contaminants
Historically, the focus of manure management has been on utilizing the nutrients in manure for crop
production. In recent decades, livestock and poultry producers, land grant universities, and government
agencies have worked together to develop practices and systems to minimize the impact of manure
production and utilization on air and water quality, including drinking water. Though the practices and
systems promoted by these programs typically do not focus specifically on the potential connections between
manure, pathogens, emerging contaminants, and water quality, they do address many of the potential
pathways described in this report (e.g., erosion, runoff, infiltration). Widespread implementation of
appropriate practices and systems will help to reduce agricultural runoff and minimize the potential
environmental problems associated with emerging contaminants from livestock and poultry manure.
This chapter provides a brief overview of the standard basic strategies for managing manure and a summary
of additional approaches that can provide further benefits, including economic benefits. Many of the existing
programs and standards described within this chapter are managed by the USDA Natural Resources
Conservation Service (NRCS). Partnerships between federal agencies (including USDA and USEPA),
conservation professionals, university extension offices, and local producers have formed to develop
programs and technical standards that conserve natural resources, reduce soil erosion, decrease pollutant
loading to the nation's surface waters, and improve source water protection. This overview is not intended to
be exhaustive; the objective is to highlight information that is most relevant to individuals working to
improve water quality. To learn more about tools, policies, technical standards, and programs that may not be
listed here and may be more relevant to a specific location, contact your state or local NRCS District
Conservationist or your area's Cooperative Extension Service. A sampling of online resources that are
available to help planners and producers related to manure management are listed in Appendix 3.
8.1. Land Application of Manure
Manure serves as a nutrient-rich natural fertilizer and is commonly applied to cropland. In some cities,
however, facilities that serve as holding pens before slaughter may discharge to wastewater treatment
operations instead of land-applying the manure. Variations in the operational characteristics of livestock and
poultry facilities (e.g., layout, herd size, access to forage crops and pastures, etc.) make it challenging to
identify specific practices that implement widely-accepted principles regarding the timing, location, and rate
of manure land application. Thus, NRCS has placed increased emphasis on meeting overarching resource
conservation objectives through the development and implementation of nutrient management plans that
determine the location and amount of manure applied to meet crop needs and keep manure out of surface
and ground water resources. Appropriately managing manure as part of a nutrient management plan should
also minimize the loading of other emerging contaminants, though there is relatively little research available
that specifically addresses the consequences of manure management on emerging contaminants. In addition,
there are many financial incentives to developing and implementing a nutrient management plan, including
cost savings within the operation and increased access to federal financial assistance programs.
The NRCS Conservation Practice Standard 590 provides criteria for nutrient management through land
application (http://www.nrcs.usda.gov/Internet/FSE DOCUMENTS/stelprdbl046433.pdf). Producers
receiving financial support from USDA for nutrient management must follow this standard.
The USEPA also requires nutrient management plans for any operation seeking a permit under the national
pollutant discharge elimination system (NPDES) program. (See discussion under 8.5. CAFO Discharge
Regulations). Any operation seeking NPDES permit coverage must submit a nutrient management plan as
part of its permit application to be covered by an individual permit or a notice of intent to be covered by a
general permit (40 CFR 122.23(h) and 122.42(e)(l)). A nutrient management plan is a manure and wastewater
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management tool that every permitted CAFO must use to properly manage discharges from the production
or land application areas through the use of best management practices.
The regulations specify nine minimum requirements that must be included in the nutrient management plan,
to the extent that they are applicable (40 CFR 122.42(e)(l)). The NPDES nutrient management practices were
developed to be consistent with the content of comprehensive nutrient management plans as defined by
USDA in the Comprehensive Nutrient Management flan Technical Guidance. However, there are some differences
between the requirements of a nutrient management plan for NPDES permitting and a comprehensive
nutrient management plan as defined by USDA. The USEPA describes nutrient management planning
requirements in the 2012 Technical Manual for Concentrated Animal Feeding Operations, available
athttp://cfpub.epa.gov/npdes/afo/info.cfm#guide docs.
There are many resources available to assist producers with the development of nutrient management plans,
including online tools (see Appendix 3) and individual consultation services provided by crop consultants,
NRCS, conservation districts, and university extension personnel.
8.2. Manure Storage
Manure storage enables livestock and poultry producers with confined operations to better implement their
nutrient management plans and apply their manure to address crop needs. Adequate storage capacity enables
operators to store manure during times of the year when no crops are growing and avoid applying manure on
frozen or snow-covered ground, immediately before, during, or after precipitation events, or when the land is
saturated (Zhao et al. 2008). Storing manure for extended periods of time may also minimize pathogen loads
and promote degradation or adsorption of antimicrobials and hormones (Shore et al. 1995, Lee et al. 2007).
Thoughtful design of manure storage infrastructure is critical for ensuring there is adequate capacity to
prevent spills and over-topping of an open structure. Operational practices, such as covering open storage
lagoons, are also important for preventing the addition of precipitation and managing manure volumes. The
NRCS provides additional location-specific information about the design and operation of manure storage
structures in their Technical Standards.
II. Constructing diversions and gutters around animal lots and buildings are inexpensive and
effective ways to minimize the amount of water falling on and washing across manure covered areas.
Diverting rainfall from areas with manure is often the first step in reducing the amount of runoff that must be
managed to avoid pollution issues. The USEPA requires diversion of clean water, as appropriate, for
operations with NPDES permit coverage. Clean water includes, but is not limited to, rain falling on the roofs
of facilities and runoff from adjacent land.
Structures. There are many common types of storage structures, including walled enclosures, lagoons,
earthen ponds, above-ground tanks and under-floor storage pits. The size and choice of storage structure
depends on multiple factors, including the animal production system, precipitation patterns, siting or design
limitations, bedding materials, availability of on-site and off-site transportation options, local and state
regulations, and costs. Following construction, storage structures should be checked periodically for leaks to
prevent contamination of surface water and ground water. Also, insufficient storage capacity increases the risk
of runoff from manure piles and spills from lagoons and other containment structures. Furthermore, it
increases the possibility that an operation will have to land apply during periods of increased risk to surface
water (e.g., during rainfall events).
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8.3. Treating Manure
On some farms and in some geographic areas, the amount of manure produced from livestock and poultry
operations exceeds what can be safely applied to nearby croplands or pastures to meet nutrient needs. To
manage surplus manure, technologies have been developed to treat manure nutrients such that additional
options for disposition of nutrients become viable. Recent research indicates that some of these technologies
and processes may also promote removal and degradation of pathogens, antimicrobials, and hormones.
Although many of these technologies have been proven from an engineering perspective, the costs are
generally prohibitive for most producers. Livestock and poultry producers need to analyze the economic
viability of any of these technologies for their specific operations. However, potential economically beneficial
options do exist such as the sale of electricity generated through the manure-to-energy process. In some
cases, nutrients from manure, such as phosphorus byproducts, can be recovered, sold and transported to
locations low in phosphorus (Szogi et al. 2010). Given that phosphorus is a nonrenewable resource, it is
anticipated that these byproducts could become an increasingly valuable source of income (Chesapeake Bay
Commission 2012).
8.3.1. Physical and Chemical Treatments
Physical and chemical treatments are designed to separate the solids and liquids in manure slurry to make the
manure easier to utilize, handle, and transport. For example, as recommended in an Ohio State University
Extension manure management guide, solids may be reused for livestock bedding material, and liquids can be
recycled for washing down hard surfaces (James et al. 2006).
"Physical treatment of manure involves separating solids from liquid manure through settling, filtration,
screening, or drying. Settling basins are used to separate solids through natural settling so that the solids can
be removed (James et al. 2006). Solids may also be separated out in a mechanical centrifuge or through
filtering and screening systems that remove solids as the liquid waste passes through. Filtering systems may be
constructed with sand drying beds, stationary or vibrating screens, or vacuum filters (James et al. 2006).
Manure may also be dried passively (i.e., spread in a manner that allows water to evaporate), though this
method is more time consuming and is more likely to result in the emission of foul odors and greenhouse
gases unless additional steps are taken to capture the emissions. The effects of physical treatment on
emerging contaminants are unknown.
I treatment involves the addition of coagulants, such as lime, alum, and organic polymers to manure
(James et al. 2006). Coagulants are effective at separating solids and liquids, but the agents may persist in the
manure and may reach surface waters and ground water through runoff and infiltration, if land applied. Some
coagulants decrease the presence of pathogens, such as quick lime (CaO) or hydrated lime (CaOH), which
increase pH and kill most microorganisms (James et al. 2006). Adding lime, however, results in an immediate
loss of ammonia from the manure through volatilization (James et al. 2006), reducing its quality as a fertilizer
and creating air quality concerns. The effects of chemical treatment on emerging contaminants in manure are
largely unknown.
8.3.2. Biological Treatment Techniques
Biological treatment of manure occurs within traditional manure storage structures and other less traditional
methods such as composting and anaerobic digestion. These methods remove pathogens and can reduce the
total volume of manure. This subsection focuses on less traditional treatments: composting and anaerobic
digestion.
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8.3.2.1. Composting of Manure
Composting is the process of aerobic biological decomposition of manure in a controlled environment.
During composting, microorganisms decompose the manure, increasing the temperature and inactivating
pathogens. Numerous factors influence the effectiveness of composting, including nutrient balance (i.e.,
carbon to nitrogen ratio), water content, oxygen availability, porosity, and temperature (James et al. 2006).
Composting manure prior to land application provides some benefits, including reduction of odor and fly
problems and weed seeds (USDA 2009J). When composting is properly controlled, most pathogens are
inactivated at higher temperatures (i.e., greater than 55° F), with the exception of some viruses and worm
eggs (Rosen 2000, Olson 2001, Venglovsky et al. 2009). Also, the quality of the manure as a fertilizer
increases when composted, because the nitrogen becomes more stable and nutrients are released more slowly
than they are from raw manure (Zhao et al. 2008, USDA 2009J), though nitrogen volatilization during
composting reduces the total amount of nitrogen available in the manure. When composting is used as part
of a system that includes separation of liquids and solids, the practice can reduce the total amount of dry
matter by 50% to 75%, with greater reductions for swine and dairy cow manure, and the total volume of
manure can be reduced by as much as 85% (USDA 2007c).
Recent research suggests that composting may promote antimicrobial degradation (Zhao et al. 2008,
Ramaswamy et al. 2010), although given the structural diversity of antimicrobials, degradation rates likely vary
among compounds. A recent USDA study found that concentrations of extractable oxytetracycline in beef
cattle manure mixed with straw and wood chips decreased by over 99% during 35 days of composting
(Arikan et al. 2007). Additionally, populations of oxytetracycline-resistant bacteria were ten times lower in the
manure after composting. This study suggests that adding straw and wood chips to manure, thereby
increasing the temperature during composting, may allow for more rapid antimicrobial and pathogen
reduction and/or adsorption. Arikan et al. (2009) documented declines of 99% and 98% in concentrations of
extractable chlortetracycline and ^'-chlortetracycline, respectively, in composted and sterile incubated manure
mixtures. In another study, rates of antimicrobial decline in turkey litter extracts were measured during
manure stockpiling, managed composting (i.e., routine mixing and managed moisture content), and in-vessel
composting (i.e., controlled composting in a rotating steel drum) (Dolliver et al. 2008). In that study,
chlortetracycline concentrations rapidly declined during all three treatments, with more than 99% removal
within ten days. Concentrations of monensin and tylosin also decreased, but more gradually, with reductions
ranging from 54% to 76% during the three treatments. In contrast, concentrations of sulfamethazine
remained stable during all three treatments (Dolliver et al. 2008). In combination with recent research
indicating that sulfonamides may be the most mobile antimicrobials (Chee-Sanford et al. 2009), the
persistence of sulfamethazine (a type of sulfonamide) merits further study of its environmental occurrence
and potential effects.
Composting is presumed to be an effective means of reducing hormone concentrations in manure via aerobic
digestion (Zhao et al. 2008), though limited research has been conducted. One USDA study found that
concentrations of 17[3-estradiol and testosterone decreased by 84% and 90%, respectively, in chicken layer
manure during composting (Hakk et al. 2005). In that study, testosterone concentrations declined at a faster
rate than the 17[3-estradiol concentrations. A more recent USDA study reported degradation of 17[3-estradiol
in poultry litter composted under heated conditions and at room temperature (Hakk et al. 2011). Limited
research in this area is available, however, and further research on the degradation and adsorption of both
natural and synthetic hormones in manure from various animal types would help elucidate the effectiveness
of composting in removing hormones.
8.3.2.2. Anaerobic Digesters/Methane Capture
Anaerobic digesters, or biogas recovery systems, are oxygen-free environments in which bacteria break down
manure, generating gases that may be captured for energy use. One of the primary gaseous byproducts of
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anaerobic digestion, methane, is combustible and may be used to generate electricity needs on the farm (e.g.,
to warm on-site buildings or heat water), sold to a local electric utility, or converted to compressed natural gas
for fueling needs (USEPA 201 Ib). Liquid effluent from the digester may be spread on fields as fertilizer, since
the digester does not reduce the nutrients in the manure. Digested solids may be used as livestock bedding
material, or they may be sold for use as a soil amendment or for use in building materials such as particle
board (USEPA 201 Ib).
There are a variety of types of anaerobic digesters; in 2010, the most commonly used types in the U.S. were
mixed plug flow digesters (54%), complete mix digesters (42%), and covered lagoons (27%) (USEPA 201 Ic).
A plug flow digester is a long, narrow, covered concrete tank and is used at dairy facilities that collect manure
through scraping. A complete mix digester is an enclosed heated tank with a gas mixing system; this type of
digester is optimal when manure is diluted with water. A covered lagoon digester is a lagoon with a flexible
cover that minimizes atmospheric gas exchange and allows the recovered gas to be piped to a combustion
device (USEPA 20lib).
The number of digesters in the U.S. has been
steadily increasing since 2000 (USEPA
2011c). In 2010, there were 162 anaerobic
digesters in the U.S., generating over 450
million kilowatt hours (kWh) of energy; this is
equivalent to the amount of energy used to
power 25,000 average American homes for a
year. Additionally, the amount of methane
emissions avoided due to use of digesters in
2010 was equivalent to reducing annual oil
consumption by nearly 2.8 million barrels
(USEPA 2011c). The majority of digesters are
on dairy farms in the Midwest and Northeast,
with 33 states having digesters in 2010
(USEPA 201 Ic).
The benefits of using anaerobic digesters
include reductions in pathogens, reduced
greenhouse gas emissions (methane and
carbon dioxide), and minimization of odors
(USDA 2011c). As reviewed by Sahlstrom
(2003), while time and temperature (among
other factors) influence pathogen
inactivation, anaerobic digestion has been
shown to be effective in reducing 90% of viable counts of microorganisms in hours (120-130°F) to days (86-
100°F). Limited available research also suggests that anaerobic digesters may facilitate hormone and
antimicrobial degradation. For example, concentrations of 17[3-estradiol in dairy manure have been shown to
decrease by 40% during anaerobic digestion (Zhao et al. 2008). A separate USDA experiment found that
concentrations of oxytetracycline decreased by nearly 60% during 56 days in an anaerobic digester (Arikan et
al. 2006). The study also reported that manure laden with 62 [ig/g oxytetracycline and diluted 5-fold with
water resulted in a 27% decrease in biogas production, indicating potential consequences of antibiotic use on
the cost-effectiveness of anaerobic digestion. Levels of chlortetracycline in swine manure and monensin in
cattle manure were also reduced by varying degrees after 21 days in anaerobic digesters set at different
temperatures (Varel et al. 2012).
Anaerobic Digester Provides Farm a Source of
Income and Reduces Environmental Impact:
Brubaker Dairy Farms in Pennsylvania was named the
2011 Innovative Dairy Farmer of the Year by the
International Dairy Foods Association for implementing
an anaerobic digester powered by solar panels. The farm
has over 1,400 cows and also produces 250,000 broilers
annually. The digester kills fly larvae and weed seeds,
reduces odors by 75% to 90%, and reduces the farm's
methane and other greenhouse gas emissions.
All undigested fibers are reused as bedding for the cows
or sold to other dairy farmers for bedding or gardening.
The digester also generates enough energy in the form of
electricity to power 150 to 200 homes per day. The
majority of the energy is sold to a local utility, generating
more income for the farm. Brubaker Dairy Farms has
shown that these systems can work to minimize
environmental impact and increase profit margin.
(References: Brubaker 2009, IDFA 2011).
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8.4. Financial and Technical Assistance Programs
Financial and technical assistance programs are available to help offset the costs of manure management. The
table below highlights a few of the key federal programs managed by NRCS that provide financial assistance
to producers. In addition to these resources, there are many state and local programs that provide loans and
grants for reducing the environmental risks associated with manure.
Table 8-1. Key USDA-NRCS programs that may provide financial assistance to producers.
Program Name
Description
Website
Agricultural
Management
Assistance (AMA)
Provides financial and technical assistance to agricultural
producers to voluntarily address issues such as water
management, water quality, and erosion control by
incorporating conservation into their farming operations.
http://www.nrcs.usda.gov/wps/portal/nrcs/rn
ain/national/programs/financial/ama/
Agricultural Water
Enhancement
Program (AWEP)
Voluntary conservation initiative that provides financial
and technical assistance to agricultural producers to
implement agricultural water enhancement activities on
agricultural land to conserve surface and ground water
and improve water quality.
http://www.nrcs.usda.gOV/wps/portal/nrcs/d
etail/national/programs/financial/awep/?&cid
=nrcs!43 008334
Conservation
Innovation
Grants (CIG)
Voluntary program intended to stimulate the
development and adoption of innovative conservation
approaches and technologies while leveraging Federal
investment in environmental enhancement and
protection, in conjunction with agricultural production.
http://www.nrcs.usda.gOV/wps/portal/nrcs/d
etail/national/programs/financial/cig/?&cid=n
rcs!43 008205
Environmental
Quality Incentives
Program (EQIP)
Voluntary program that provides financial and technical
assistance to agricultural producers through contracts up
to a maximum term often years in length.
http://www.nrcs.usda.gov/wps/portal/nrcs/rn
ain/national/programs/financial/eqip/
Source: NRCS, 2012. http://www.nrcs.usda.gov/wps/portal/nrcs/main/national/programs/financial
8.5. CAFO Regulations
The USGAO (201 Ib) noted that discharges from CAFOs share many of the traits of a diffuse, nonpoint
source but are treated and regulated as a point source. The Clean Water Act specifically includes the term
"concentrated animal feeding operation" in the definition of point source (Clean Water Act, Section 502(14)),
and the NPDES program regulates discharges of pollutants from point sources. Under the NPDES
permitting program, regulations governing CAFOs consist primarily of two different sets. The regulations at
40 CFR 122.23 set the framework for CAFO permitting by establishing criteria that define CAFOs and
specifying whether and when a CAFO must have permit coverage. The second set of regulations, which are at
40 CFR Part 412, are the effluent limitations guidelines and standards for CAFOs, which establish discharge
limits and certain management practice requirements that must be included in NPDES permits for CAFOs.
Any CAFO seeking NPDES permit coverage must submit a nutrient management plan as part of its permit
application to be covered by an individual permit or a notice of intent to be covered by a general permit (40
CFR 122.23(h) and 122.42(e)(l)). A nutrient management plan is a manure and wastewater management tool
that every permitted CAFO must use to properly manage discharges from the production or land application
areas through the use of best management practices.
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For more detailed information on CAFO regulations, refer to USEPA's CAFO rule history
website: http://cfpub.epa.gov/npdes/afo/aforule.cfm. For further information on aquaculture NPDES
regulations, visit: http: /7water.epa.gov/scitech/wastetech/guide/aquaculture/index.cfm.
8.6. Additional Technical Resources
A sampling of available on-line resources that are obtainable to help planners and producers related to
manure management are listed in Appendix 3.
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Adams, C., Y. Wang, K. Loftin, and M. Meyer. 2002. Removal of antibiotics from surface and distilled water
in conventional water treatment processes. Journal of Environmental Engineering. 128(3) :253-260.
Adams, C. 2008. Treatment of antibiotics in swine wastewater. p. 331-348. In D.S. Aga (ed.) Fate and
transport of pharmaceuticals in the environment and water treatment systems. 1st ed. CRC Press,
Boca Raton, FL.
Ainsworth, L., R.H. Common, and R.L. Carter. 1962. A chromatographic study of some conversion products
of estrone-16-C-14 in the urine and feces of the laying hen. Canadian Journal of Biochemistry and
Physiology. 40:123-135.
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Appendix 1. Livestock Animal Unit and Manure Production Calculations
Livestock manure production was estimated using standard methods and conversion factors developed by the
USDA's NRCS (see for example Kellogg et al. 2000, Gollehon et al. 2001, and Midwest Planning Service
1985), converting livestock and poultry head counts to animal units (AU). Animal units are a common unit of
measure based on animal weight, allowing for the calculation of manure generation and a method for
aggregating across animal types and life stages. For this report we used USDA's 2007 Census of Agriculture
livestock count data for cattle, swine, chickens (layers and broilers), and turkeys as well as acreage of land in
farms for each state. "Land in farms" is defined by the USDA (2009a) as primarily agricultural land used for
grazing, pasture, or crops, but it may also include woodland and wasteland that is not under cultivation or
used for grazing or pasture, provided it is on the farm operator's operation. For cattle, three categories were
used: beef cows, milk cows, and "cattle excluding cows" (e.g., breeding and replacement stock). The total
inventory numbers (head of animals) from the end of December, 2007 were used to generate the final
numbers of AUs in each state. Similar, but more complex, methods were employed by Kellogg et al. (2000)
which used USDA's Census of Agriculture data to calculate livestock and poultry manure generation and
manure nutrient contributions, evaluate trends in livestock production, and quantify the extent to which
manure nutrient contributions exceed crop assimilative capacity. Additionally, Kellogg et al. (2000) calculated
AUs using 16 livestock categories/life stages from more detailed marketing statistics to refine estimates of
manure generation and nutrient recovery, and make estimates of confinement operations. (Note: the overall
state and national estimates of this report are within a few percentage points of the estimates of these reports
for total manure generated).
The AU and manure production conversion factors were then related to the appropriate animals for breeding
and marketing for each livestock type (see Table A-l). Following the procedures, three quarters of the "cattle
excluding cows" were treated as "Steers, Calves, & Bulls" and the remaining quarter were treated as "Heifers
& Dairy Calves," which assumes that roughly half of the animals in this category are adult animals slated for
slaughter, and the remaining half is equally split between young females (heifers) and males (steers). Turkey
counts were treated as slaughters to provide a more conservative estimate for this animal type (i.e., there are
more AUs per slaughter turkey than breeder turkey, therefore providing lower manure generation estimates;
see Table A-l).
Table A-l. The number of animal units (AU)
and associated manure generation per animal
type as defined by USDA's NRCS.
Animal Type
Beef Cattle
Dairy Cows
Heifers & Dairy Calves
Steers, Calves, & Bulls
Swine, Breeders
Swine, Market
Chickens, Layers
Chickens, Broilers
Turkeys for Slaughter
Turkeys Hens for Breeding
Animals per AU
1
0.74
1.82
1.64
2.67
9.09
250
455
67
50
Manure
Generation
perAU
(tons)
11.5
15.24
12.05
10.59
6.11
14.69
11.45
14.97
8.18
8.18
Kellogg et al. 2000, Gollehon et al. 2001.
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Converting all the animal types to AUs allows the total number of all AUs to be summed as well as the total
estimated manure produced to be summed, so a "total" comparison among the states can be done, as shown
in the tables in this appendix. Also, livestock and poultry manure generation was estimated by dividing state
manure generation by the sum of land in farms both owned and rented in each state — the most likely land-
base for the application of the manure — using data from the USDA's 2007 Census of Agriculture, as
discussed in Chapter 2. To illustrate the AU and manure generation calculations, the following example is
provided using beef cattle counts in Texas. Calculated data for all states are shown in Tables A-2 to A-9.
2007 USDA Census of Agriculture inventory
Animals per AU
5,259,843
Texas beef AUs = = 5,259,843 AUs
State inventory
Percentage of U.S. livestock = x 100
Sum of inventory in all reporting states
5,259,843
Texas'percentage of U.S. beef stock = x 100 = 16.02%
P a J J 32,834,801
Tons of manure produced = AUs x tons manure produced per AU
Texas'beef manure production = 5,259,843 x 11.5 = 60,488,195 tons
Total AUs = (Beef Cow + Milk Cow + Cattle Excluding Cows AUs)
+ (Swine Breeder + Swine Market AUs) + (Layer + Broiler AUs) + (Turkey AUs)
Texas'AUs = (5,259,843 + 404,399 + 4,784,377)+ (35,550 + 116,708)+ (76,467+ 260,686)
+ (29,654)= 11,109,770 AUs
AUs or tons manure AUs or tons manure
acre land owned, in farms + land, rented, in farms
AUs 11,109,770 AUs
inTexas = = 0.09
acre 75,578,240 + 54,299,426 acre
Tables A-2 through A-9 present summaries of livestock AUs and estimated total manure generated by those
livestock for all 50 states. The states are listed in rank-order in the different categories.
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Table A-2. Total animal units and estimated tons of manure produced for beef and dairy cattle in
2007.
National
Rank
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
State
TEXAS
MISSOURI
OKLAHOMA
NEBRASKA
SOUTH DAKOTA
MONTANA
KANSAS
TENNESSEE
KENTUCKY
ARKANSAS
FLORIDA
NORTH DAKOTA
IOWA
COLORADO
WYOMING
VIRGINIA
ALABAMA
CALIFORNIA
OREGON
GEORGIA
NEW MEXICO
MISSISSIPPI
LOUISIANA
IDAHO
ILLINOIS
MINNESOTA
NORTH CAROLINA
UTAH
OHIO
WASHINGTON
WISCONSIN
NEVADA
INDIANA
SOUTH CAROLINA
WEST VIRGINIA
ARIZONA
PENNSYLVANIA
MICHIGAN
NEW YORK
HAWAII
MARYLAND
MAINE
VERMONT
NEWJERSEY
MASSACHUSETTS
ALASKA
CONNECTICUT
NEW HAMPSHIRE
DELAWARE
RHODE ISLAND
U.S. TOTAL
Total Beef
Cattle AUs
5,259,843
2,089,181
2,063,613
1,889,842
1,649,492
1,522,187
1,516,374
1,179,102
1,166,385
947,765
942,419
930,023
904,100
735,014
732,141
695,061
678,949
662,423
604,069
554,099
530,173
521,517
510,837
476,292
429,111
399,768
373,024
364,744
293,757
274,001
269,820
238,662
235,299
230,419
203,711
197,060
158,430
109,500
103,620
86,000
44,015
12,114
10,002
9,298
8,646
6,468
5,982
4,981
3,668
1,800
32,834,801
Percent of Total
Beef Cattle AUs
16.02%
6.36%
6.28%
5.76%
5.02%
4.64%
4.62%
3.59%
3.55%
2.89%
2.87%
2.83%
2.75%
2.24%
2.23%
2.12%
2.07%
2.02%
1.84%
1.69%
1.61%
1.59%
1.56%
1.45%
1.31%
1.22%
1.14%
1.11%
0.89%
0.83%
0.82%
0.73%
0.72%
0.70%
0.62%
0.60%
0.48%
0.33%
0.32%
0.26%
0.13%
0.04%
0.03%
0.03%
0.03%
0.02%
0.02%
0.02%
0.01%
0.01%
Total Tons
Manure
60,488,195
24,025,582
23,731,550
21,733,183
18,969,158
17,505,151
17,438,301
13,559,673
13,413,428
10,899,298
10,837,819
10,695,265
10,397,150
8,452,661
8,419,622
7,993,202
7,807,914
7,617,865
6,946,794
6,372,139
6,096,990
5,997,446
5,874,626
5,477,358
4,934,777
4,597,332
4,289,776
4,194,556
3,378,206
3,151,012
3,102,930
2,744,613
2,705,939
2,649,819
2,342,677
2,266,190
1,821,945
1,259,250
1,191,630
989,000
506,173
139,311
115,023
106,927
99,429
74,382
68,793
57,282
42,182
20,700
377,600,212
National
Rank
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
State
CALIFORNIA
WISCONSIN
NEW YORK
PENNSYLVANIA
IDAHO
MINNESOTA
TEXAS
MICHIGAN
NEW MEXICO
OHIO
WASHINGTON
IOWA
ARIZONA
INDIANA
VERMONT
COLORADO
FLORIDA
OREGON
KANSAS
MISSOURI
ILLINOIS
VIRGINIA
KENTUCKY
SOUTH DAKOTA
UTAH
GEORGIA
OKLAHOMA
TENNESSEE
MARYLAND
NEBRASKA
NORTH CAROLINA
MAINE
LOUISIANA
NEVADA
NORTH DAKOTA
MISSISSIPPI
CONNECTICUT
SOUTH CAROLINA
MONTANA
ARKANSAS
MASSACHUSETTS
NEW HAMPSHIRE
ALABAMA
WESTVIRGINIA
NEWJERSEY
WYOMING
DELAWARE
HAWAII
RHODE ISLAND
ALASKA
U.S. TOTAL
Total Dairy
CowAUs
2,487,473
1,688,255
846,561
747,731
724,950
621,286
546,485
465,180
441,081
367,484
328,557
291,069
248,303
224,526
188,809
171,546
161,968
157,822
156,262
149,132
134,699
133,672
122,246
116,545
115,219
104,315
89,220
82,609
77,259
73,527
64,309
43,955
38,295
37,378
35,782
30,486
27,953
24,095
23,592
22,592
20,338
19,745
17,516
15,870
13,230
8,978
8,819
3,103
1,791
780
12,522,397
Percent of Total
DairyCowAUs
19.86%
13.48%
6.76%
5.97%
5.79%
4.96%
4.36%
3.71%
3.52%
2.93%
2.62%
2.32%
1.98%
1.79%
1.51%
1.37%
1.29%
1.26%
1.25%
1.19%
1.08%
1.07%
0.98%
0.93%
0.92%
0.83%
0.71%
0.66%
0.62%
0.59%
0.51%
0.35%
0.31%
0.30%
0.29%
0.24%
0.22%
0.19%
0.19%
0.18%
0.16%
0.16%
0.14%
0.13%
0.11%
0.07%
0.07%
0.02%
0.01%
0.01%
Total Tons
Manure
37,909,088
25,729,012
12,901,587
11,395,422
11,048,238
9,468,406
8,328,433
7,089,339
6,722,076
5,600,453
5,007,205
4,435,890
3,784,133
3,421,771
2,877,456
2,614,360
2,468,386
2,405,202
2,381,435
2,272,778
2,052,807
2,037,156
1,863,028
1,776,140
1,755,936
1,589,759
1,359,717
1,258,968
1,177,434
1,120,552
980,076
669,880
583,610
569,646
545,324
464,614
425,999
367,202
359,540
344,300
309,949
300,908
266,947
241,863
201,621
136,830
134,400
47,285
27,288
11,883
190,841,335
USDA 2009a.
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Table A-3. Total animal units and estimated tons of manure produced for cattle other than beef and
dairy cattle and for all cattle combined in 2007.
National
Rank
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
State
TEXAS
KANSAS
NEBRASKA
OKLAHOMA
CALIFORNIA
IOWA
MISSOURI
SOUTH DAKOTA
COLORADO
WISCONSIN
MINNESOTA
IDAHO
KENTUCKY
MONTANA
PENNSYLVANIA
TENNESSEE
NORTH DAKOTA
ARKANSAS
VIRGINIA
NEW YORK
OHIO
ILLINOIS
NEW MEXICO
OREGON
FLORIDA
ARIZONA
MICHIGAN
WYOMING
WASHINGTON
ALABAMA
GEORGIA
INDIANA
MISSISSIPPI
NORTH CAROLINA
UTAH
LOUISIANA
WEST VIRGINIA
NEVADA
SOUTH CAROLINA
VERMONT
MARYLAND
HAWAII
MAINE
CONNECTICUT
MASSACHUSETTS
NEW JERSEY
NEW HAMPSHIRE
DELAWARE
ALASKA
RHODE ISLAND
U.S. TOTAL
Other Cattle
AUs
4,784,377
2,995,494
2,754,972
1,939,667
1,780,990
1,702,481
1,244,762
1,160,811
1,119,957
1,103,008
913,248
727,526
677,107
624,434
533,663
524,380
508,464
498,443
459,235
424,139
420,264
417,654
398,080
397,443
385,790
368,246
353,521
340,760
339,986
294,521
288,892
281,820
263,601
237,616
233,987
201,887
116,303
104,252
90,836
68,449
53,115
37,574
25,898
14,002
13,770
11,364
10,281
6,423
4,625
1,166
32,259,283
Percent ofTotal
OtherCattleAUs
14.83%
9.29%
8.54%
6.01%
5.52%
5.28%
3.86%
3.60%
3.47%
3.42%
2.83%
2.26%
2.10%
1.94%
1.65%
1.63%
1.58%
1.55%
1.42%
1.31%
1.30%
1.29%
1.23%
1.23%
1.20%
1.14%
1.10%
1.06%
1.05%
0.91%
0.90%
0.87%
0.82%
0.74%
0.73%
0.63%
0.36%
0.32%
0.28%
0.21%
0.16%
0.12%
0.08%
0.04%
0.04%
0.04%
0.03%
0.02%
0.01%
0.00%
Total Tons
Manure
52,280,036
32,732,479
30,104,233
21,195,210
19,461,300
18,603,413
13,601,808
12,684,456
12,238,042
12,052,836
9,979,278
7,949,855
7,398,911
6,823,339
5,831,465
5,730,022
5,556,104
5,446,603
5,018,169
4,634,665
4,592,329
4,563,802
4,349,920
4,342,960
4,215,621
4,023,911
3,863,009
3,723,564
3,715,110
3,218,302
3,156,797
3,079,514
2,880,428
2,596,482
2,556,837
2,206,070
1,270,874
1,139,181
992,582
747,957
580,400
410,576
282,997
153,007
150,472
124,181
112,341
70,181
50,543
12,736
352,504,907
National
Rank
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
State
TEXAS
CALIFORNIA
NEBRASKA
KANSAS
OKLAHOMA
MISSOURI
WISCONSIN
SOUTH DAKOTA
IOWA
MONTANA
COLORADO
KENTUCKY
MINNESOTA
IDAHO
TENNESSEE
FLORIDA
NORTH DAKOTA
ARKANSAS
PENNSYLVANIA
NEW YORK
NEW MEXICO
VIRGINIA
OREGON
WYOMING
OHIO
ALABAMA
ILLINOIS
GEORGIA
WASHINGTON
MICHIGAN
MISSISSIPPI
ARIZONA
LOUISIANA
INDIANA
UTAH
NORTH CAROLINA
NEVADA
SOUTH CAROLINA
WEST VIRGINIA
VERMONT
MARYLAND
HAWAII
MAINE
CONNECTICUT
MASSACHUSETTS
NEW HAMPSHIRE
NEW JERSEY
DELAWARE
ALASKA
RHODE ISLAND
U.S. TOTAL
Total Cattle
AUs
10,590,705
4,930,886
4,718,341
4,668,130
4,092,501
3,483,075
3,061,084
2,926,847
2,897,650
2,170,213
2,026,517
1,965,738
1,934,302
1,928,768
1,786,091
1,490,177
1,474,269
1,468,800
1,439,824
1,374,319
1,369,334
1,287,967
1,159,334
1,081,879
1,081,505
990,986
981,463
947,306
942,544
928,201
815,604
813,609
751,019
741,645
713,950
674,949
380,292
345,349
335,885
267,260
174,389
126,676
81,968
47,937
42,754
35,006
33,892
18,909
11,873
4,756
77,616,481
Percent ofTotal
Cattle AUs
13.64%
6.35%
6.08%
6.01%
5.27%
4.49%
3.94%
3.77%
3.73%
2.80%
2.61%
2.53%
2.49%
2.48%
2.30%
1.92%
1.90%
1.89%
1.86%
1.77%
1.76%
1.66%
1.49%
1.39%
1.39%
1.28%
1.26%
1.22%
1.21%
1.20%
1.05%
1.05%
0.97%
0.96%
0.92%
0.87%
0.49%
0.44%
0.43%
0.34%
0.22%
0.16%
0.11%
0.06%
0.06%
0.05%
0.04%
0.02%
0.02%
0.01%
Total Tons
Manure
121,096,664
64,988,253
52,957,968
52,552,215
46,286,477
39,900,167
40,884,779
33,429,753
33,436,453
24,688,030
23,305,063
22,675,367
24,045,016
24,475,451
20,548,663
17,521,825
16,796,693
16,690,201
19,048,832
18,727,881
17,168,985
15,048,526
13,694,955
12,280,016
13,570,987
11,293,163
11,551,386
11,118,694
11,873,326
12,211,598
9,342,488
10,074,234
8,664,305
9,207,223
8,507,329
7,866,334
4,453,441
4,009,602
3,855,413
3,740,436
2,264,007
1,446,861
1,092,188
647,799
559,850
470,530
432,729
246,763
136,808
60,724
920,946,454
USD A 2009a.
Page 112 of 125
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EPA-OW
Literature Review of Livestock and Poultry Manure
EPA 820-R-l 3-002
July 2013
Table A-4. Total animal units and estimated tons of manure produced for breeder and market hogs
in 2007.
National
Rank
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
State
IOWA
NORTH CAROLINA
MINNESOTA
ILLINOIS
OKLAHOMA
NEBRASKA
MISSOURI
INDIANA
KANSAS
COLORADO
SOUTH DAKOTA
OHIO
PENNSYLVANIA
MICHIGAN
TEXAS
ARKANSAS
WISCONSIN
GEORGIA
KENTUCKY
NORTH DAKOTA
VIRGINIA
WYOMING
SOUTH CAROLINA
CALIFORNIA
ALABAMA
NEW YORK
TENNESSEE
IDAHO
FLORIDA
WASHINGTON
MARYLAND
OREGON
HAWAII
DELAWARE
LOUISIANA
MASSACHUSETTS
WEST VIRGINIA
NEWJERSEY
CONNECTICUT
MAINE
NEVADA
NEW HAMPSHIRE
NEW MEXICO
RHODE ISLAND
VERMONT
ALASKA
ARIZONA
MISSISSIPPI
MONTANA
UTAH
U.S. TOTAL
Total Breeder
Hog Alls
406,815
378,608
223,606
191,057
147,216
145,798
134,134
117,465
69,309
62,551
61,980
59,837
44,924
39,404
35,550
31,477
19,726
16,521
15,863
14,302
12,055
10,416
10,399
8,001
6,851
5,005
4,857
2,282
2,025
1,694
1,619
1,474
1,451
961
875
810
580
375
354
352
284
221
219
200
193
D
D
D
D
D
2,289,694
Percent of Total
Breeder Hog AUs
17.77%
16.54%
9.77%
8.34%
6.43%
6.37%
5.86%
5.13%
3.03%
2.73%
2.71%
2.61%
1.96%
1.72%
1.55%
1.37%
0.86%
0.72%
0.69%
0.62%
0.53%
0.45%
0.45%
0.35%
0.30%
0.22%
0.21%
0.10%
0.09%
0.07%
0.07%
0.06%
0.06%
0.04%
0.04%
0.04%
0.03%
0.02%
0.02%
0.02%
0.01%
0.01%
0.01%
0.01%
0.01%
Total Tons
Manure
2,485,637
2,313,294
1,366,235
1,167,360
899,488
890,824
819,557
717,712
423,476
382,189
378,699
365,602
274,483
240,759
217,209
192,325
120,527
100,943
96,922
87,384
73,656
63,642
63,537
48,889
41,857
30,580
29,674
13,941
12,371
10,348
9,895
9,007
8,868
5,870
5,346
4,950
3,542
2,291
2,160
2,153
1,735
1,352
1,339
1,220
1,179
13,990,028
National
Rank
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
State
IOWA
NORTH CAROLINA
MINNESOTA
ILLINOIS
INDIANA
NEBRASKA
MISSOURI
OKLAHOMA
KANSAS
OHIO
SOUTH DAKOTA
TEXAS
PENNSYLVANIA
MICHIGAN
COLORADO
WISCONSIN
VIRGINIA
KENTUCKY
SOUTH CAROLINA
GEORGIA
ARKANSAS
ALABAMA
NORTH DAKOTA
CALIFORNIA
TENNESSEE
WYOMING
NEW YORK
IDAHO
WASHINGTON
OREGON
FLORIDA
HAWAII
MASSACHUSETTS
LOUISIANA
NEWJERSEY
WEST VIRGINIA
DELAWARE
MAINE
CONNECTICUT
NEW HAMPSHIRE
NEVADA
VERMONT
RHODE ISLAND
NEW MEXICO
ALASKA
ARIZONA
MARYLAND
MISSISSIPPI
MONTANA
UTAH
U.S. TOTAL
Total Market
Hog AUs
2,003,179
1,003,644
776,156
416,787
369,134
316,751
301,797
220,606
187,040
183,864
145,715
116,708
115,237
101,963
78,733
42,260
37,293
33,627
29,266
24,132
22,585
17,600
15,786
14,590
13,778
8,731
7,962
2,938
2,643
1,891
1,599
1,217
1,033
911
831
814
703
381
297
242
241
240
196
153
D
D
D
D
D
D
6,621,249
Percent of Total
Market Hog AUs
30.25%
15.16%
11.72%
6.29%
5.57%
4.78%
4.56%
3.33%
2.82%
2.78%
2.20%
1.76%
1.74%
1.54%
1.19%
0.64%
0.56%
0.51%
0.44%
0.36%
0.34%
0.27%
0.24%
0.22%
0.21%
0.13%
0.12%
0.04%
0.04%
0.03%
0.02%
0.02%
0.02%
0.01%
0.01%
0.01%
0.01%
0.01%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%
Total Tons
Manure
29,426,699
14,743,526
11,401,727
6,122,600
5,422,574
4,653,068
4,433,394
3,240,698
2,747,625
2,700,956
2,140,550
1,714,435
1,692,829
1,497,839
1,156,588
620,802
547,827
493,980
429,918
354,499
331,774
258,544
231,894
214,320
202,396
128,265
116,967
43,152
38,823
27,778
23,483
17,870
15,175
13,379
12,201
11,959
10,327
5,592
4,365
3,557
3,541
3,533
2,881
2,241
97,266,149
"D"
USDA
that the data were not disclosed (because there were too few producers in the category to protect confidentiality).
2009a.
Page 113 of 125
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EPA-OW
Literature Review of Livestock and Poultry Manure
EPA 820-R-l 3-002
July 2013
Table A-5. Total animal units and estimated tons of
manure produced for swine (breeder and market hogs
combined) in 2007.
National
Rank
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
State
IOWA
NORTH CAROLINA
MINNESOTA
ILLINOIS
INDIANA
NEBRASKA
MISSOURI
OKLAHOMA
KANSAS
OHIO
SOUTH DAKOTA
PENNSYLVANIA
TEXAS
MICHIGAN
COLORADO
WISCONSIN
ARKANSAS
KENTUCKY
VIRGINIA
GEORGIA
SOUTH CAROLINA
NORTH DAKOTA
ALABAMA
CALIFORNIA
WYOMING
TENNESSEE
NEW YORK
IDAHO
WASHINGTON
FLORIDA
OREGON
HAWAII
MASSACHUSETTS
LOUISIANA
DELAWARE
MARYLAND
WEST VIRGINIA
NEW JERSEY
MAINE
CONNECTICUT
NEVADA
NEW HAMPSHIRE
VERMONT
RHODE ISLAND
NEW MEXICO
ALASKA
ARIZONA
MISSISSIPPI
MONTANA
UTAH
U.S. TOTAL
Total Swine
AUs
2,409,994
1,382,252
999,762
607,844
486,599
462,548
435,930
367,821
256,349
243,700
207,695
160,160
152,257
141,367
141,284
61,986
54,062
49,490
49,348
40,653
39,665
30,088
24,451
22,591
19,148
18,634
12,967
5,219
4,336
3,623
3,365
2,668
1,843
1,786
1,664
1,619
1,394
1,205
733
651
525
463
433
396
372
D
D
D
D
D
8,910,943
Percent of Total
Swine AUs
27.05%
15.51%
11.22%
6.82%
5.46%
5.19%
4.89%
4.13%
2.88%
2.73%
2.33%
1.80%
1.71%
1.59%
1.59%
0.70%
0.61%
0.56%
0.55%
0.46%
0.45%
0.34%
0.27%
0.25%
0.21%
0.21%
0.15%
0.06%
0.05%
0.04%
0.04%
0.03%
0.02%
0.02%
0.02%
0.02%
0.02%
0.01%
0.01%
0.01%
0.01%
0.01%
0.00%
0.00%
0.00%
Total Tons
Manure
31,912,337
17,056,820
12,767,962
7,289,960
6,140,286
5,543,892
5,252,950
4,140,186
3,171,100
3,066,558
2,519,248
1,967,313
1,931,644
1,738,598
1,538,776
741,329
524,100
590,902
621,484
455,442
493,455
319,278
300,401
263,210
191,908
232,069
147,547
57,093
49,171
35,854
36,786
26,738
20,125
18,725
16,196
9,895
15,501
14,492
7,745
6,525
5,275
4,909
4,711
4,101
3,580
111,256,177
"D" signifies that the data were not disclosed (because there
producers in the category to protect confidentiality).
USDA 2009a.
too few
Page 114 of 125
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EPA-OW
Literature Review of Livestock and Poultry Manure
EPA 820-R-l 3-002
July 2013
Table A-6. Total animal units and estimated tons of manure produced for broiler and layer chickens
in 2007.
National
Rank
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
State
GEORGIA
ARKANSAS
ALABAMA
MISSISSIPPI
NORTH CAROLINA
TEXAS
MARYLAND
DELAWARE
KENTUCKY
MISSOURI
SOUTH CAROLINA
CALIFORNIA
OKLAHOMA
VIRGINIA
TENNESSEE
LOUISIANA
PENNSYLVANIA
FLORIDA
WEST VIRGINIA
OHIO
MINNESOTA
WISCONSIN
INDIANA
WASHINGTON
OREGON
IOWA
NEBRASKA
MICHIGAN
NEW YORK
ILLINOIS
MONTANA
SOUTH DAKOTA
CONNECTICUT
VERMONT
NEW HAMPSHIRE
KANSAS
NEWJERSEY
NORTH DAKOTA
MAINE
NEW MEXICO
COLORADO
IDAHO
UTAH
HAWAII
ALASKA
ARIZONA
WYOMING
NEVADA
MASSACHUSETTS
RHODE ISLAND
U.S. TOTAL
Total Broiler
A Us
517,363
444,830
391,953
330,982
329,498
260,686
143,964
112,291
109,399
102,537
100,642
97,548
97,395
96,142
90,198
79,750
60,459
31,041
28,162
22,026
19,010
15,517
12,169
10,214
8,804
3,964
1,699
1,500
1,031
239
237
225
221
93
53
43
39
35
33
25
24
17
6
5
5
4
3
1
D
D
3,522,083
Percent of
Total Broiler
AUs
14.69%
12.63%
11.13%
9.40%
9.36%
7.40%
4.09%
3.19%
3.11%
2.91%
2.86%
2.77%
2.77%
2.73%
2.56%
2.26%
1.72%
0.88%
0.80%
0.63%
0.54%
0.44%
0.35%
0.29%
0.25%
0.11%
0.05%
0.04%
0.03%
0.01%
0.01%
0.01%
0.01%
0%
0%
0%
0%
0%
0%
0%
0%
0%
0%
0%
0%
0%
0%
0%
Total Tons
Manure
7,744,926
6,659,104
5,867,541
4,954,799
4,932,592
3,902,473
2,155,138
1,680,999
1,637,707
1,534,984
1,506,618
1,460,290
1,458,000
1,439,247
1,350,271
1,193,850
905,067
464,685
421,581
329,733
284,580
232,292
182,171
152,899
131,799
59,335
25,431
22,448
15,429
3,584
3,552
3,363
3,308
1,398
796
643
589
520
489
369
364
261
84
70
69
66
50
10
52,725,576
National
Rank
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
State
IOWA
OHIO
INDIANA
PENNSYLVANIA
CALIFORNIA
GEORGIA
TEXAS
ARKANSAS
NORTH CAROLINA
FLORIDA
MINNESOTA
NEBRASKA
ALABAMA
MICHIGAN
MISSOURI
MISSISSIPPI
WASHINGTON
ILLINOIS
WISCONSIN
SOUTH CAROLINA
KENTUCKY
NEW YORK
COLORADO
UTAH
OKLAHOMA
VIRGINIA
SOUTH DAKOTA
OREGON
MARYLAND
LOUISIANA
TENNESSEE
NEWJERSEY
WEST VIRGINIA
HAWAII
MONTANA
VERMONT
NEW HAMPSHIRE
MASSACHUSETTS
NORTH DAKOTA
RHODE ISLAND
WYOMING
NEVADA
ALASKA
ARIZONA
CONNECTICUT
DELAWARE
IDAHO
KANSAS
MAINE
NEW MEXICO
U.S. TOTAL
Total Layer
AUs
215,175
108,280
96,954
87,930
84,367
77,093
76,467
55,911
50,993
47,151
42,386
41,950
38,497
36,137
28,998
24,948
23,143
21,142
19,495
18,857
18,338
15,812
15,612
14,339
13,295
12,836
11,683
10,946
10,651
7,968
6,854
6,241
4,881
1,473
1,421
894
842
559
437
183
65
23
14
D
D
D
D
D
D
D
1,351,241
Percent of
Total Layer
AUs
15.92%
8.01%
7.18%
6.51%
6.24%
5.71%
5.66%
4.14%
3.77%
3.49%
3.14%
3.10%
2.85%
2.67%
2.15%
1.85%
1.71%
1.56%
1.44%
1.40%
1.36%
1.17%
1.16%
1.06%
0.98%
0.95%
0.86%
0.81%
0.79%
0.59%
0.51%
0.46%
0.36%
0.11%
0.11%
0.07%
0.06%
0.04%
0.03%
0.01%
0%
0%
0%
Total Tons
Manure
2,463,752
1,239,811
1,110,124
1,006,794
965,997
882,712
875,545
640,183
583,871
539,879
485,323
480,326
440,791
413,773
332,023
285,652
264,983
242,080
223,214
215,917
209,972
181,046
178,755
164,183
152,230
146,968
133,773
125,330
121,953
91,231
78,473
71,456
55,889
16,865
16,269
10,241
9,635
6,401
5,008
2,099
744
268
166
15,471,706
"D" signifies that the data wen not disclosed (because there were too few producers in the category to protect confidentiality).
USDA 2009a.
Page 115 of 125
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EPA-OW
Literature Review of Livestock and Poultry Manure
EPA 820-R-l 3-002
July 2013
Table A-7. Total animal units and estimated tons of manure produced for turkeys, as well as all
poultry (broilers, layers, and turkeys combined) in 2007.
National
Rank
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
State
MINNESOTA
NORTH CAROLINA
ARKANSAS
MISSOURI
CALIFORNIA
VIRGINIA
INDIANA
SOUTH CAROLINA
IOWA
WISCONSIN
PENNSYLVANIA
SOUTH DAKOTA
UTAH
OHIO
TEXAS
MICHIGAN
WEST VIRGINIA
ILLINOIS
NEBRASKA
KANSAS
NORTH DAKOTA
MARYLAND
NEW YORK
KENTUCKY
NEW JERSEY
MASSACHUSETTS
MONTANA
FLORIDA
ALABAMA
NEW MEXICO
VERMONT
WASHINGTON
CONNECTICUT
TENNESSEE
MAINE
OREGON
NEW HAMPSHIRE
GEORGIA
RHODE ISLAND
MISSISSIPPI
IDAHO
ARIZONA
LOUISIANA
ALASKA
DELAWARE
WYOMING
NEVADA
HAWAII
COLORADO
OKLAHOMA
U.S. TOTAL
Total Turkey
A Us
273,109
266,655
140,853
128,421
100,048
94,492
89,128
81,854
59,733
55,010
52,799
33,322
32,676
30,966
29,654
29,535
24,494
12,626
11,362
8,380
6,631
3,332
1,483
459
275
261
243
206
131
92
86
57
53
52
46
45
38
30
29
21
19
13
12
11
10
7
2
1
D
D
1,568,762
Percent of
Total Turkey
AUs
17.41%
17.00%
8.98%
8.19%
6.38%
6.02%
5.68%
5.22%
3.81%
3.51%
3.37%
2.12%
2.08%
1.97%
1.89%
1.88%
1.56%
0.80%
0.72%
0.53%
0.42%
0.21%
0.09%
0.03%
0.02%
0.02%
0.02%
0.01%
0.01%
0.01%
0.01%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%
Total Tons
Manure
2,234,033
2,181,239
1,152,181
1,050,486
818,394
772,944
729,064
669,564
488,616
449,979
431,894
272,574
267,293
253,305
242,569
241,599
200,364
103,284
92,938
68,551
54,241
27,254
12,128
3,759
2,247
2,137
1,990
1,682
1,073
752
702
463
435
425
378
369
309
242
233
170
152
105
98
88
86
54
18
12
12,832,472
National
Rank
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
State
NORTH CAROLINA
ARKANSAS
GEORGIA
ALABAMA
TEXAS
MISSISSIPPI
MINNESOTA
CALIFORNIA
IOWA
MISSOURI
VIRGINIA
SOUTH CAROLINA
PENNSYLVANIA
INDIANA
OHIO
MARYLAND
KENTUCKY
DELAWARE
OKLAHOMA
TENNESSEE
WISCONSIN
LOUISIANA
FLORIDA
MICHIGAN
WEST VIRGINIA
NEBRASKA
UTAH
SOUTH DAKOTA
ILLINOIS
WASHINGTON
OREGON
NEW YORK
COLORADO
KANSAS
NORTH DAKOTA
NEW JERSEY
MONTANA
HAWAII
VERMONT
NEW HAMPSHIRE
MASSACHUSETTS
CONNECTICUT
RHODE ISLAND
NEW MEXICO
MAINE
WYOMING
IDAHO
ALASKA
NEVADA
ARIZONA
U.S. TOTAL
Total
Poultry AUs
647,147
641,595
594,486
430,581
366,807
355,951
334,506
281,962
278,871
259,956
203,470
201,354
201,187
198,251
161,273
157,947
128,197
112,302
110,690
97,104
90,022
87,729
78,398
67,172
57,537
55,010
47,021
45,230
34,008
33,413
19,795
18,325
15,636
8,423
7,103
6,555
1,901
1,479
1,074
933
820
274
212
117
79
75
36
30
26
17
6,442,085
Percent of
Total Poultry
AUs
10.05%
9.96%
9.23%
6.68 /o
5.69%
5.53%
5.19%
4.38%
4.33%
4.04%
3.16%
3.13%
3.12%
3.08%
2.50%
2.45%
1.99%
1.74%
1.72%
1.51%
1.40%
1.36%
1.22%
1.04%
0.89%
0.85%
0.73%
0.70%
0.53%
0.52%
0.31%
0.28%
0.24%
0.13%
0.11%
0.10%
0.03%
0.02%
0.02%
0.01%
0.01%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%
Total Tons
Manure
7,697,703
8,451,469
8,627,880
6,309,404
5,020,588
5,240,622
3,003,937
3,244,681
3,011,703
2,917,493
2,359,159
2,392,098
2,343,756
2,021,359
1,822,849
2,304,346
1,851,437
1,681,085
1,610,230
1,429,169
905,486
1,285,179
1,006,247
677,820
677,834
598,696
431,561
409,710
348,948
418,344
257,497
208,603
179,119
69,194
59,769
74,293
21,811
16,947
12,341
10,741
8,538
3,743
2,332
1,121
867
848
412
323
296
171
81,029,754
"D " signifies that the data were not disclosed (because there were too few producers in the category to protect confidentiality).
USD A 2009 a.
Page 116 of 125
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Literature Review of Livestock and Poultry Manure
EPA 820-R-l 3-002
July 2013
Table A-8. Livestock (cattle, swine, and poultry) animal units as a total
and per acre of farmland in 2007.
Rank Total
AUs
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
State
TEXAS
IOWA
NEBRASKA
CALIFORNIA
KANSAS
OKLAHOMA
MISSOURI
MINNESOTA
WISCONSIN
SOUTH DAKOTA
NORTH CAROLINA
COLORADO
MONTANA
ARKANSAS
KENTUCKY
IDAHO
TENNESSEE
PENNSYLVANIA
ILLINOIS
GEORGIA
FLORIDA
VIRGINIA
NORTH DAKOTA
OHIO
ALABAMA
INDIANA
NEW YORK
NEW MEXICO
OREGON
MISSISSIPPI
MICHIGAN
WYOMING
WASHINGTON
LOUISIANA
ARIZONA
UTAH
SOUTH CAROLINA
WEST VIRGINIA
NEVADA
MARYLAND
VERMONT
DELAWARE
HAWAII
MAINE
CONNECTICUT
MASSACHUSETTS
NEW JERSEY
NEW HAMPSHIRE
ALASKA
RHODE ISLAND
U.S. TOTAL
AUs
11,109,770
5,586,515
5,235,899
5,235,439
4,932,902
4,571,012
4,178,962
3,268,570
3,213,092
3,179,772
2,704,347
2,183,438
2,172,114
2,164,456
2,143,425
1,934,024
1,901,829
1,801,172
1,623,316
1,582,445
1,572,198
1,540,785
1,511,460
1,486,479
1,446,018
1,426,494
1,405,612
1,369,823
1,182,494
1,171,555
1,136,740
1,101,102
980,293
840,534
813,626
760,972
586,368
394,816
380,843
333,955
268,767
132,875
130,823
82,780
48,862
45,418
41,652
36,402
11,903
5,364
92,969,509
RankAUs/Acre
Farmland
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
State
NORTH CAROLINA
DELAWARE
PENNSYLVANIA
VERMONT
WISCONSIN
CALIFORNIA
NEW YORK
VIRGINIA
IOWA
TENNESSEE
FLORIDA
IDAHO
MARYLAND
ALABAMA
ARKANSAS
GEORGIA
KENTUCKY
MISSOURI
OKLAHOMA
MINNESOTA
CONNECTICUT
SOUTH CAROLINA
HAWAII
NEBRASKA
MICHIGAN
WEST VIRGINIA
OHIO
KANSAS
LOUISIANA
MISSISSIPPI
INDIANA
MASSACHUSETTS
TEXAS
RHODE ISLAND
NEW HAMPSHIRE
SOUTH DAKOTA
OREGON
COLORADO
UTAH
WASHINGTON
NEVADA
MAINE
ILLINOIS
NEW JERSEY
NORTH DAKOTA
WYOMING
MONTANA
NEW MEXICO
ARIZONA
ALASKA
U.S. AVERAGE
AUs/Acre
Farmland
0.32
0.26
0.23
0.22
0.21
0.21
0.20
0.19
0.18
0.17
0.17
0.17
0.16
0.16
0.16
0.16
0.15
0.14
0.13
0.12
0.12
0.12
0.12
0.12
0.11
0.11
0.11
0.11
0.10
0.10
0.10
0.09
0.09
0.08
0.08
0.07
0.07
0.07
0.07
0.07
0.06
0.06
0.06
0.06
0.04
0.04
0.04
0.03
0.03
0.01
0.12
USDA 2009a.
Page 117 of 125
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EPA-OW
Literature Review of Livestock and Poultry Manure
EPA 820-R-l 3-002
July 2013
Table A-9. Total estimated livestock and poultry (cattle, swine, and
poultry) manure and estimated tons of manure per acre of farmland in
2007.
Rank Total
Manure
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
State
TEXAS
CALIFORNIA
IOWA
NEBRASKA
KANSAS
OKLAHOMA
MISSOURI
WISCONSIN
MINNESOTA
SOUTH DAKOTA
NORTH CAROLINA
ARKANSAS
KENTUCKY
COLORADO
MONTANA
IDAHO
PENNSYLVANIA
TENNESSEE
GEORGIA
ILLINOIS
NEW YORK
FLORIDA
OHIO
VIRGINIA
ALABAMA
INDIANA
NORTH DAKOTA
NEW MEXICO
MICHIGAN
MISSISSIPPI
OREGON
WYOMING
WASHINGTON
ARIZONA
LOUISIANA
UTAH
SOUTH CAROLINA
MARYLAND
WEST VIRGINIA
NEVADA
VERMONT
DELAWARE
HAWAII
MAINE
CONNECTICUT
MASSACHUSETTS
NEW JERSEY
NEW HAMPSHIRE
ALASKA
RHODE ISLAND
U.S. TOTAL
Tons Manure
128,048,896
68,496,143
68,360,493
59,100,556
55,792,510
52,036,892
48,070,611
42,531,594
39,816,914
36,358,712
32,620,857
25,665,769
25,117,706
25,022,958
24,709,841
24,532,956
23,359,900
22,209,901
20,202,017
19,190,293
19,084,031
18,563,926
18,460,395
18,029,169
17,902,968
17,368,868
17,175,740
17,173,686
14,628,016
14,583,109
13,989,238
12,472,771
12,340,841
10,074,405
9,968,209
8,938,890
6,895,155
4,578,248
4,548,748
4,459,013
3,757,488
1,944,044
1,490,546
1,100,800
658,068
588,513
521,513
486,181
137,131
67,158
1,113,232,385
Rank Tons
Manure/Acre
Farmland
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
State
NORTH CAROLINA
DELAWARE
VERMONT
PENNSYLVANIA
WISCONSIN
CALIFORNIA
NEW YORK
MARYLAND
VIRGINIA
IOWA
IDAHO
TENNESSEE
FLORIDA
GEORGIA
ALABAMA
ARKANSAS
KENTUCKY
MISSOURI
CONNECTICUT
OKLAHOMA
MINNESOTA
MICHIGAN
SOUTH CAROLINA
HAWAII
OHIO
NEBRASKA
MISSISSIPPI
WEST VIRGINIA
LOUISIANA
KANSAS
INDIANA
MASSACHUSETTS
NEW HAMPSHIRE
RHODE ISLAND
TEXAS
OREGON
SOUTH DAKOTA
WASHINGTON
MAINE
UTAH
COLORADO
NEVADA
ILLINOIS
NEW JERSEY
NORTH DAKOTA
WYOMING
MONTANA
NEW MEXICO
ARIZONA
ALASKA
U.S. AVERAGE
Tons
Manure/Acre
Farmland
3.85
3.81
3.05
2.99
2.80
2.70
2.66
2.23
2.22
2.22
2.13
2.02
2.01
1.99
1.98
1.85
1.80
1.66
1.62
1.48
1.48
1.46
1.41
1.33
1.32
1.30
1.27
1.23
1.23
1.20
1.18
1.14
1.03
0.99
0.98
0.85
0.83
0.82
0.82
0.81
0.79
0.76
0.72
0.71
0.43
0.41
0.40
0.40
0.39
0.16
1.50
USDA 2009a.
Page 118 of 125
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Literature Review of Livestock and Poultry Manure
EPA 820-R-l 3-002
July 2013
Table A-10. Freshwater and saltwater aquaculture farms
in the U.S. during 2005.
Geographic Area
Louisiana
Mississippi
Florida
Alabama
Arkansas
Washington
North Carolina
Massachusetts
Virginia
California
Texas
New Jersey
Maryland
South Carolina
Wisconsin
Georgia
Minnesota
Kentucky
Hawaii
Pennsylvania
Ohio
New York
Maine
Oregon
Illinois
Tennessee
Missouri
Idaho
Michigan
Connecticut
Nebraska
Alaska
Iowa
West Virginia
Oklahoma
Indiana
Colorado
Kansas
Rhode Island
Utah
Arizona
New Hampshire
Vermont
Montana
South Dakota
Wyoming
New Mexico
Delaware
North Dakota
Nevada
United States
Rank
Farms
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
24
26
27
27
29
30
31
31
33
33
35
36
37
38
38
40
40
42
43
44
45
45
47
47
49
50
Freshwater
Farms
738
403
196
213
211
21
129
18
28
96
79
17
11
43
84
78
77
65
33
56
55
41
10
26
47
45
35
35
34
3
26
1
21
21
20
17
15
12
2
11
11
5
9
8
7
7
3
3
1
-
3,127
Saltwater
Farms
135
1
163
2
-
175
57
140
122
22
19
70
75
45
-
1
-
-
30
-
-
13
40
21
1
-
-
-
1
27
-
25
-
-
-
1
-
-
11
-
-
6
-
-
-
-
-
-
-
-
1,203
Total
Farms
873
403
359
215
211
194
186
157
147
118
95
87
86
85
84
79
77
65
59
56
55
54
50
47
47
45
35
35
34
30
26
26
21
21
20
18
15
12
12
11
11
10
9
8
7
7
3
3
1
-
4,309
USDA 2006.
Page 119 of 125
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Literature Review of Livestock and Poultry Manure
EPA 820-R-l 3-002
July 2013
Table A-11. Aquaculture in the U.S. presented as total acres and sales.
Geographic Area
Louisiana
Mississippi
Connecticut
Arkansas
Minnesota
Alabama
Washington
Virginia
California
Texas
NewJersey
North Carolina
Florida
Missouri
Oregon
South Carolina
Wisconsin
Georgia
Massachusetts
South Dakota
Illinois
Ohio
Tennessee
Pennsylvania
Kentucky
Maine
Iowa
Kansas
Oklahoma
Nebraska
Indiana
Michigan
Maryland
New York
Hawaii
Idaho
Alaska
Colorado
New Hampshire
Rhode Island
West Virginia
Utah
Wyoming
Arizona
Montana
Vermont
New Mexico
Delaware
North Dakota
Nevada
United States
Rank
Acres
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
-
-
-
Freshwater
Acres
104,645
102,898
D
61,135
41,023
25,351
209
143
3,338
4,651
51
3,463
2,292
2,689
101
683
1,977
1,914
60
1,066
805
759
707
626
624
32
594
590
557
503
443
429
155
385
75
151
D
85
10
D
48
38
37
31
13
11
1
D
D
-
365,566
Saltwater
Acres
215,770
D
62,959
-
D
13,269
12,412
6,002
2,432
4,466
707
718
-
2,425
1,531
-
D
1,108
-
D
-
-
-
-
585
-
-
-
-
D
D
238
D
254
-
148
-
70
51
-
-
-
-
-
-
-
-
-
-
327,487
Total
Acres
320,415
102,898
62,959
61,135
41,023
25,351
13,478
12,555
9,340
7,083
4,517
4,170
3,010
2,689
2,526
2,214
1,977
1,914
1,168
1,066
805
759
707
626
624
617
594
590
557
503
443
429
393
385
329
151
148
85
80
51
48
38
37
31
13
11
1
-
-
693,053
Total Sales
(1,000s of S)
$101,314
$249,704
$12,902
$110,542
$8,412
$102,796
$93,203
$40,939
$69,607
$35,359
$3,714
$24,725
$57,406
$7,144
$12,478
$4,773
$7,025
$7,502
$9,342
$484
$3,176
$3,185
$1,286
$8,951
$2,341
$25,580
$1,469
$342
$1,958
$1,750
D
$2,398
$7,292
$8,913
$13,761
$37,685
$826
$3,349
$1,054
$840
$1,145
$559
$209
$562
$302
$80
D
$1,870
D
-
$1,092,386
Rank
S
4
1
14
2
19
3
5
8
6
10
25
12
7
22
15
24
23
20
16
42
28
27
35
17
30
11
34
43
31
33
-
29
21
18
13
9
39
26
37
38
36
41
45
40
44
46
32
-
"D" signifies that the data were not disclosed (because there were too few
producers in the category to protect confidentiality).
USDA 2006.
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Literature Review of Livestock and Poultry Manure
EPA 820-R-l 3-002
July 2013
Appendix 2. Animal Life Stages
Table A-12. Livestock animal type and life stages definitions.
Animal Type
?
&
•S
01
CD
01
1
(J
01
c
1
Poultry (Broilers,
Layers, and Turkeys)
Term
Bovine
Dairy Cow
Heifer
Beef Cattle
Steer
Calf
Preweaned Calf
Weaned Heifer
Replacement Heifer
Lactating
Non-Lactating
Cow-Calf Operation
Growing
Feedlot
Hog
Sow
Farrow
Preweaned
Nursery (Weaned)
Breeder
Grower/Feeder/Finisher/Market
Broiler
Layer
Pullet
Grower/Finisher
Breeder
Definition
General term for cattle
A female cow that produces milk for human consumption, or raises
replacement heifers
A female cow that has not yet had her first calf. Typically less than
three years of age
Cattle raised for meat production
A castrated bovine male
A male or female bovine under one year of age
Calves that are nursing from their mother or a dam (i.e., a female
parent in pedigree)
Heifers that are no longer nursing
Cows raised to replace those currently in the herd
A cow that is producing milk
A cow that is dry (i.e., not secreting milk). Cows are typically provided a
dry period between lactations to allow the cow's udders an
opportunity to regenerate secretory tissue
A facility that maintains breeding bovine and produces weaned calves
A cattle grown to market weight
Beef cattle in confined, outdoor pens and fed a high-energy ration of
grains and other concentrates
General term for growing swine
A female after she has borne a litter
The life stage between birth and weaning
Pigs that are still nursing and have not yet been removed from the sow
Pigs that are no longer nursing and have been removed from the sow
Swine that produce offspring
Swine that are fed until they reach market weight and are ready for
slaughter
A chicken utilized for meat production
A chicken utilized for egg production
A laying hen prior to laying its first egg
Birds grown to market weight and sent to slaughter
A bird that produces offspring
MacDonald andMcBride 2009 and USEPA 2009c.
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Appendix 3. Additional Technical Resources for Manure Management
This appendix includes a sampling of on-line resources that are available to help planners and producers with
manure management. It is intended to illustrate the breadth of information available and identify the agencies
and organizations that are working actively to provide information to planners and producers.
World Health Organization
• Animal Waste. Water Quality and Human Health- This website provides links to resources published by
WHO on water sanitation and health including a book which contains relevant information, in
connection with pathogens, on: the scope of domestic animal manure discharged into the environment;
the fate and transport of the discharged manure (and the pathogens they may contain); human exposure
to the manure; potential health effects associated with those exposures; and interventions that can limit
human exposures to livestock manure. It also addresses the monitoring, detection and effectiveness of
the best management practices related to these issues.
http://www.who.int/water sanitation health/publications 72012/animal waste/en/
U.S. Department of Agriculture
• USDA's NRCS Technical Standard 590 - Nutrient Management- This website contains the USDA's 590
Nutrient Management Conservation Practice Standard. The standard provides guidance on managing
nutrient applications to meet crop needs and minimize nonpoint source
pollution. http://www.nrcs.usda.gov/Internet/FSE DOCUMENTS/stelprdbl046433.pdf
• NRCS Manure and Nutrient Management Resources- This site contains many helpful resources,
including a guide that provides a complete review of key management practices and methods to minimize
waste production, software that may be used by large livestock and poultry facility operators and owners
to estimate manure generation and production of process water, and training courses on water quality,
waste management, nutrient and pest management, conservation practices and planning, and designing
animal waste containment.
http://go.usa.gov/KoB
• USDA's ERS Manure Management Website- This website is an important resource for publications and
economic research related to animal and manure
production. http://www.ers.usda.gov/Browse/view.aspx?sub)ect=FarmPracticesManagementManureMa
nagement
• USDA's Agricultural Research Service (ARS) Website- The ARS has ongoing efforts designed to enhance
current practices and develop new methods for efficiently and effectively managing manure.
http://www.ars.usda.gov/research/programs/programs.htmPNP CODE=214
U.S. Environmental Protection Agency
• The USEPA's Agricultural Center Website- This is the USEPA's primary website for agricultural
planning, management, and news.
http://www.epa.gov/agriculture
• Animal Feeding Operations (AFO) Virtual Information Center- The Animal Feeding Operations (AFO)
Virtual Information Center is a tool to facilitate quick access to livestock and poultry agricultural
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information in the U.S. This site is a single point of reference to obtain links to state regulations, web
sites, permits and policies, nutrient management information, livestock and trade associations, federal
web sites, best management practices and controls, cooperative extension and land grant universities,
research, funding, and information on environmental issues.
http://cfpub.epa.gov/npdes/afo/virtualcenter.cfm
• National Management Measures to Control Nonpoint Source Pollution from Agriculture- This guidance
document contains economically achievable best management practices designed to reduce agricultural
pollution to surface and ground water, http: / Avater.epa.gov/polwaste /nps /agriculture /agmm index.cfm
• The USEPA's Nonpoint Source Pollution Publications & Resources Website- This website provides links
and references to nonpoint source materials for both professionals and the
public, http://water.epa.gov/polwaste/nps/pubs.cfm
• The USEPA's Source Water Protection Program- This website provides information and resources about
protecting surface water and ground water drinking water
sources, http://water.epa.gov/infrastructure/drinkingwater/sourcewater/protection/index.cfm
• Healthy Watersheds Initiative- This website provides information on the concept and benefits of
protecting healthy, unimpaired waters from degradation and also provides information on conservation
approaches and tools.
http://water.epa.gov/polwaste/nps/watershed/index.cfm
• EPA's Nutrient Indicators Dataset- The Dataset consists of a set of nine indicators and associated state-
level data to serve as a regional compendium of information pertaining to documented or potential
nitrogen and phosphorus pollution, impacts of this pollution, and states' efforts to minimize loadings and
adopt numeric criteria.
www.epa.gov/nutrientpollution/dataset
Additional State and University Technical Resources
The list of useful resources available from state and university resources is too lengthy to include in this
report. In addition to the exceptional resources listed below, please contact applicable university extension
services and state agencies responsible for natural resources management and environmental protection for
more information.
• extension- This website provides objective and research-based information and learning opportunities
that help people improve their lives, extension is an educational partnership of 74 universities in the U.S.
http://www.extension.org/animal manure management
• Cornell University's Cornell Dairy Environmental Systems Program - This program provides information
to dairy farmers to help manage their businesses in a way that protects the environment. This program
also focuses on renewable energy (dairy manure-based anaerobic digestion).
http://www.manuremanagement.cornell.edu/
• Ohio State University's Ohio Composting and Manure Management Website- This program researches,
develops, and communicates sustainable strategies for management of animal manure and nutrients.
Resources provided include workshops and literature on topics such as composting, application of liquid
manure, and ammonia emissions and nitrogen conservation.
http://www.oardc.ohio-state.edu/ocamm/t01 pageview/Home.htm
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• The University of Illinois' Manure Central Website- This website directs the reader to a variety of
resources for topics such as composting, manure management plans, a manure exchange program, and
manure management for small farms.
http://web.extension.illinois.edu/manurecentral/
• Wisconsin Manure Management Advisory System- This website provides tools that can be used by
producers to assist with manure spreading decisions that protect water quality. This is one of many
practical tools that incorporate weather forecasts to plan daily hauling activities for specific
locations, http://www.manureadvisorysystem.wi.gov/
• Texas A & M University's Texas Animal Manure Management Issues Website- This is an information
clearinghouse providing educational materials on regulations and policies and up to date research on
animal waste management and air and water quality issues.
http://tammi.tamu.edu/index.html
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