United States Department of Agriculture 

Antimicrobial Resistance 

ACTION PLAN 
United States Department of Agriculture 

As the Co-Chairs of the USDA One Health Joint Working Group, we are pleased to present the 

USDA Antimicrobial Resistance (AMR) Action Plan. This plan takes advantage of the strengths of 

our existing activities. In addition, it describes an approach that will allow us to address recognized 

knowledge gaps and develop effective, practical mitigation strategies that will help prolong the effectiveness of antibiotics to treat both people and animals. The action plan describes how the USDA 

proposes to obtain and disseminate science-based, actionable, information about antibiotic drug 

use, its potential role in the development of antibiotic resistance in food-producing animals, and the 

relationship of drug use and resistance patterns to livestock management practices. 

Throughout our action plan, we emphasize the integration of activities across the USDA. Our 

current work in AMR has made important contributions to our understanding of AMR. However, 

these activities are best described as “patchwork,” and their lack of integration has limited the overall results of our investments. To achieve the greatest impact, we recognize that resources must be 

coordinated and expertise leveraged across USDA agencies. We also acknowledge that implementing 

these activities will require the help of our Federal, industry, and academic partners. 

We will continue to perform our existing activities using currently available funding and resources. 

However, the new activities we propose for the future cannot be accomplished within the constraints 

of existing funding levels. A limitation in our ability to fully implement this action plan is the deficiency of dedicated, long-term funding for these activities. We will continue to seek additional funds 

to enact these new policies. 

This USDA Antimicrobial Resistance Action Plan outlines our current activities and proposes a 

comprehensive, integrated approach for future surveillance; research and development; and education, extension, and outreach activities. By fully funding and implementing this plan, the USDA will 

continue to play a major role in addressing recognized knowledge gaps and in developing effective, 

practical mitigation strategies for use in animal agriculture that will help to prolong the effectiveness 

of antibiotics to treat both people and animals. 

We look forward to working with you to implement this action plan. 

John Clifford 

Deputy Administrator 

Animal and Plant Health 

Inspection Service 

Steven Kappes 

Deputy Administrator 

Agricultural Research Service 

David Goldman 

Assistant Administrator 

Food Safety and 

Inspection Service 

An Equal Opportunity Employer 

2 
Contents
 

Executive Summary............................................................................................................................................................... 1
 

Introduction .......................................................................................................................................................................... 3
 

Challenges to Addressing AMR.................................................................................................................... 3
 

Role of the USDA and Partner Agencies in Addressing AMR ............................................................................................ 3
 

USDA’s Action Plan to Address Antimicrobial Resistance ................................................................................................... 5
 

Current Activities.................................................................................................................................................................. 5
 

Surveillance........................................................................................................................................................................ 5
 

Intramural and Extramural Research and Development.................................................................................................... 8
 

Education, Extension, and Outreach.................................................................................................................................. 9
 

Proposed Initiatives ............................................................................................................................................................... 9
 

Surveillance........................................................................................................................................................................ 9 


Intramural and Extramural Research and Development.................................................................................................. 11
 

Education, Extension, and Outreach ............................................................................................................................... 12
 

Conclusion .......................................................................................................................................................................... 13
 

FIGURE 

Figure 1:


USDA’s current and proposed surveillance, research and development, and education, extension,


and outreach activities by objective................................................................................................................................. 7
 

APPENDICES

 Appendix 1: USDA Antimicrobial Resistance Action Plan Committee .......................................................................... 14


 Appendix 2: Abbreviations and Acronyms ....................................................................................................................... 15


 Appendix 3: Figures Demonstrating the Complexity of AMR.............................................................................. 16


 Appendix 4: USDA Agencies’ Roles in Antimicrobial Resistance Mitigation Efforts ..................................................... 20 


 Appendix 5: Strengths and Weaknesses of Current Objective Projects............................................................................ 21
 

3 
4
 
Executive Summary
 

Antimicrobial resistance is considered one of the most serious health threats to both animals 

and humans. The One Health concept recognizes that the health of humans and animals is 

irrevocably linked and closely connected to the environment. Antimicrobial resistance (AMR) 

is an issue that requires a One Health approach. It is a multi-faceted issue that everyone has a 

shared responsibility in limiting its impact. 

Even though the United States Department of Agriculture (USDA) is not the lead regulatory 

agency with respect to antibiotic use and AMR, USDA is an important part of the solution 

to address this challenge. For nearly two decades, the USDA has been actively involved in 

surveillance, basic and applied research, and education and outreach to assess levels of AMR,

develop effective mitigation strategies for AMR, and assist animal producers to implement 

these strategies. USDA activities have made important contributions to understanding the 

role of animal production in AMR and to reducing its development and spread. However,

considerable work remains, and there is a growing sense of urgency to address this problem. 

This action plan describes how USDA proposes to obtain and disseminate science-based,

actionable, quantitative antibiotic drug use information coupled with the development of resistance in food-producing animals and to relate this to livestock management practices. With 

the help of Federal, industry, commodity, and academic partners, USDA proposes to address 

recognized knowledge gaps and develop effective, practical mitigation strategies that will help 

to prolong the effectiveness of antibiotics to treat both people and animals. 

This action plan outlines USDA’s current activities and proposes a voluntary comprehensive,

integrated approach for future surveillance; research and development; and education, extension, and outreach activities that span three objectives: 

Objective 1: Determine and/or model patterns, purposes, and impacts of antibiotic use in 

food-producing animals. 

Objective 2: Monitor antibiotic drug susceptibilities of selected bacterial organisms in 

food-producing animals, production environments, and meat and poultry. 

Objective 3: Identify feasible management practices, alternatives to antibiotic use, and 

other mitigations to reduce AMR associated with food-producing animals and their 

production environments. 

USDA possesses in-depth knowledge of the management practices and technologies associated with animal health, welfare, productivity, and food safety. As such, USDA is uniquely 

positioned to contribute to the body of scientific knowledge about AMR, specifically about 

the role of antimicrobial use in livestock. The successful execution of this action plan would 

provide and disseminate science-based information to the veterinary and animal agricultural 

communities so they can implement effective mitigation strategies that will help to prolong 

the effectiveness of antibiotics for use in both animals and people. 

1 
2
 
Introduction
 

The One Health concept recognizes that the health of 

humans, animals, and the environment is intimately connected. Antimicrobial resistance (AMR) is an example of a 

challenge that will require a One Health approach. Simply 

stated, there is concern that bacteria that cause disease in 

both people and animals are developing more resistance to 

the antibiotics1 used for treatment. Some believe that the 

use of antimicrobial drugs in agriculture is one of the primary 

drivers for the emergence of AMR. In reality, our understanding of the factors that contribute to levels of AMR in 

various settings and the specific role of antimicrobial use in 

agriculture in the selection for AMR bacteria is incomplete. 

1

 In this plan, the terms antimicrobial drug and antibiotic are used interchangeably; however, antimicrobial drugs are a broader category 

since they have activity against more than just bacteria and include 

synthetic medications such as sulfonamides. 

The public health and veterinary communities have implemented actions to encourage the judicious use of antimicrobials in people and animals. Judicious use of antibiotics is an 

integral part of good veterinary and production practices. It 

is an approach that maximizes therapeutic efficacy and minimizes selection of resistant microorganisms. The Food and 

Drug Administration’s (FDA) guidance for antibiotic use is 

provided in “Judicious Use of Medically Important Antimicrobial Drugs in Food-Producing Animals” (FDA Guidance 

#209). However, FDA’s efforts to support good antimicrobial drug stewardship in agriculture have been hampered by 

a lack of science-based data on antimicrobial use linked to 

observed AMR in animals. 

Challenges to Addressing AMR 

The ecology of antimicrobial resistance is extremely complex. This impacts our ability to understand and prevent the 

selection and spread of AMR. The development and spread 

of AMR does not just involve the use of antimicrobial drugs 

in humans or food-producing animals. 

The ecology of antimicrobial resistance is extremely complex. 

This impacts our ability to understand and prevent the selection and spread of AMR. Simple solutions are not sufficient to 

address such a complex problem. 

Since the beginning of time, the soil microbiome has 

produced natural antimicrobials, and bacteria have developed unique mechanisms (i.e., resistance genes) to resist 

their inhibitory or killing effects. This natural exposure and 

continual evolution of resistance continues today in the 

ecological system. Not only is the environment intimately 

linked with both humans and food-producing animals, but 

also our activities, such as disposal and transport of human 

sewage and animal waste, impact soil and water and, in turn,

the ecology of antimicrobial resistance (See figures A and B 

in Appendix 3). 

At the same time, other species also interact with the environment and contribute to the transmission of antimicrobial 

resistance. Domestic and wild animals, birds, fish, and insects 

can transport bacteria, including resistant strains, to other locations. This movement creates opportunities for animals or 

people to acquire bacteria. There are many pathways among 

people, animals, and the environment connecting resident 

bacterial populations in one population or setting to those in 

other populations or settings. This continuum is constant on 

the global scale. Indeed, no place on Earth is excluded from 

this cycle as recent studies have demonstrated the presence of 

bacteria caught in wind streams at 30,000 feet, which likely 

moves bacteria across the globe. 

The ability of bacteria to move from one setting to another,

sometimes over large geographic distances and among the 

different populations, makes it difficult to know with certainty where resistant strains of bacteria originated. Adding 

even more complexity, bacteria also have the ability to share 

their genetic material with other bacteria in a variety of ways.

Resistance genes can be inherited by the next generation of 

bacteria resulting from cell division or they can be shared 

horizontally among bacteria in close physical proximity. This 

further complicates our ability to understand the ecology of 

AMR (See figures C and D in Appendix 3). 

Clearly, simple solutions are not sufficient to address such 

a complex problem. As the example in figure D illustrates,

antibiotic resistance is a multi-faceted issue. Everyone 

involved in animal production or public health, and even the 

consumer, has a shared responsibility to limit the impact of 

antimicrobial resistance. 

Role of the USDA and Partner Agencies in 

Addressing AMR 

The United States Department of Agriculture plays a dual 

role in the protection of animal production and public health.

As such, USDA is a key partner in establishing the One 

Health concept, particularly concerning AMR. USDA is 

responsible for performing residue testing at slaughter but 

has no other regulatory authority pertaining to antibiotic use 

in animal production. 

3 
The Food and Drug Administration is the primary regulatory 

agency for antibiotic use in animals. The FDA determines 

which antibiotics are safe for use in livestock and poultry and 

establishes appropriate conditions of use. However, USDA 

and FDA work together closely to identify and mitigate 

emerging threats to America’s food supply. For example, under the U.S. National Residue Program, USDA’s Food Safety 

and Inspection Service (FSIS) samples meat, poultry, and egg 

products for antibiotic residues, and FDA takes enforcement 

actions on FSIS-determined violations. USDA has collaborated and provided recommendations to FDA on “Guidance 

for Industry #213,” the most recent guidance regarding the 

judicious use of medically important antibiotics and proposed 

revisions to the veterinary feed directives. Perhaps most 

significantly, the FDA relies on the science-based information that USDA generates about antibiotic drug use, AMR 

patterns, and livestock and poultry management practices to 

inform its policy and regulatory decisions. FDA also taps 

into USDA’s extensive network of collaborative relationships 

with producers and animal agriculture industry organizations 

as part of its outreach. 

Although USDA is not the lead regulatory agency with 

respect to antibiotic use and AMR, USDA is a part of the 

solution to address these challenges through partnerships 

with stakeholders and via the missions of several key agencies. Each USDA agency—the Agricultural Research Service (ARS), the Animal and Plant Health Inspection Service 

(APHIS), the Economic Research Service (ERS), the FSIS,

the National Agricultural Statistics Service (NASS), and the 

National Institute of Food and Agriculture (NIFA)—plays 

a different role in addressing AMR,and these actions are 

described in Appendix 4. USDA employees possess in-depth 

knowledge of the management practices and technologies 

associated with animal health, welfare, productivity, and 

food safety. 

For nearly two decades, USDA has been actively involved 

in surveillance, basic and applied research, and education 

and outreach to assess levels of AMR, to develop effective 

mitigation strategies for AMR, and to assist animal producers to implement these strategies. These activities have made 

important individual agency contributions to understanding 

the role of animal agriculture in AMR and to minimizing its 

selection and spread. However, these efforts lacked integration and prioritization at the departmental level. This has 

ultimately limited their overall impact. USDA recognizes 

that considerable work remains, and there is a growing sense 

of urgency to address this problem. Through this action plan,

USDA describes a roadmap for a comprehensive, integrated 

approach to develop effective, practical mitigation strategies 

for animal agriculture to help prolong the effectiveness of 

antibiotics used to treat people and animals. 

Beyond partnerships within USDA and with the FDA, the 

Department also regularly collaborates with other Federal 

agencies, such as the U.S. Department of Health and Human 

Services’ Centers for Disease Control and Prevention (CDC) 

and the National Institutes of Health (NIH). USDA is a 

member of the Interagency Task Force on Antimicrobial Resistance (ITFAR), which was created in 1999 and is 

co-chaired by the CDC, FDA, and NIH, and includes a 

broad range of Federal partners. The Task Force developed 

a comprehensive document, A Public Health Action Plan to 

Combat Antimicrobial Resistance, which reflects a broadbased consensus by Federal agencies on actions needed to 

address antimicrobial resistance (available at www.cdc.gov/

drugresistance/actionplan/actionplan.html). This action 

plan provides a blueprint for specific, coordinated actions to 

address antimicrobial resistance. USDA also played a major 

role in establishing the National Antimicrobial Resistance 

Monitoring System (NARMS) with the FDA and CDC and 

remains an active collaborator in the program. The USDA 

also partners with academic institutions, as well as international universities, government agencies, and industry. These 

global connections ensure harmonization of methods and 

access to information of emerging trends prior to their arrival 

in the United States. 

In May 2012, USDA sponsored a workshop2

 with stakeholders, Federal partners, and USDA agency staff to review 

current antibiotic use and resistance monitoring, management practices to reduce antibiotic resistance, and alternatives to the use of antibiotics to treat and prevent diseases 

or to enhance production in food-producing animals. This 

workshop identified important knowledge and data gaps,

and participants encouraged USDA to develop an integrated,

strategic plan to address them. 

2 Documents from this workshop can be found online at: www.ars. 

usda.gov/research/programs/programs.htm?np_code=103&docid=17547. 

4 
USDA’s Action Plan to Address Antimicrobial Resistance
 

This action plan describes how USDA proposes to obtain 

and disseminate science-based, actionable, quantitative information about antibiotic drug use and the development of 

resistance in food-producing animals and their relationship 

to livestock management practices. With the help of our 

industry and academic partners, USDA proposes to address 

recognized knowledge gaps and develop effective, practical 

mitigation strategies that will help to prolong the effectiveness of antibiotics to treat both people and animals. In fact,

this action plan aligns well with the ITFAR Public Health 

Action Plan. 

This action plan outlines USDA’s current activities and 

proposes a comprehensive, integrated approach for future 

surveillance; research and development; and education,

extension, and outreach activities that span three objectives 

(See also Figure 1): 

Objective 1: Determine and/or model patterns, purposes, and 

impacts of antibiotic use in food-producing animals. 

Objective 2: Monitor antibiotic drug susceptibilities of 

selected bacterial organisms in food-producing animals,

production environments, and meat and poultry. 

Objective 3: Identify feasible management practices, alternatives to antibiotic use, and other mitigations to reduce AMR 

associated with food-producing animals and their production 

environments. 

Activity Areas 

Surveillance: Ongoing voluntary monitoring of antibiotic 

use, AMR patterns, and management practices associated 

with food-producing animals and their environments at multiple points from the farm through slaughter and processing 

is essential. By describing the current state and evaluating 

changes over time, USDA can identify and respond to 

emerging resistance patterns or strains and objectively evaluate the effectiveness of policies and mitigation strategies that 

are implemented to reduce the selection of AMR. USDA 

possesses expertise in the design, implementation, and analysis of animal health surveillance systems, including AMR. 

USDA’s goal is to obtain and disseminate science-based 

information about antibiotic drug use, the development of 

resistance in food-producing animals, and their relationship to 

livestock management practices to develop effective, practical 

mitigation strategies that will help to prolong the effectiveness 

of antibiotics to treat both people and animals. 

Research and Development: Basic and applied research is 

needed to better understand the ecology and mechanisms 

of AMR in response to antibiotic administration and use 

of management technologies for food-producing animals.

Insufficient attention has been given to identifying management practices that reduce antibiotic use, implementing 

intervention strategies to reduce the development of AMR,

and developing new antibiotics or alternatives to antibiotics 

for livestock and poultry. USDA is uniquely positioned to 

contribute to the body of scientific knowledge about AMR,

specifically about the role of antimicrobial use in livestock,

and leads the U.S. Government’s research efforts in this area. 

Education, Extension, and Outreach: Targeted education,

extension, and outreach activities will help transfer the 

information USDA generates about AMR through voluntary surveillance and research to the agricultural community 

and the public to promote the judicious use of antimicrobial 

drugs in food-producing animals. Education is defined here 

as training delivered through formal classroom lectures and 

laboratory courses, while extension and outreach refer to 

the delivery of science-based education and training in 

non-formal settings to a variety of people. USDA has a 

long history of educating the animal agricultural community 

and the public. 

Current Activities 

USDA’s current activities are foundational to efforts to address key knowledge gaps about AMR in animal production.

USDA plans to continue these activities and has proposed 

enhancements for several. A review of the strengths and 

weaknesses of the current work is included in Appendix 5. 

Current Surveillance: 

1. National Animal Health Monitoring System (NAHMS) 

(APHIS, ARS, and NASS). NAHMS commodity studies 

involve the use of questionnaires administered to U.S. livestock, poultry, and aquaculture farmers to establish nationally representative estimates of management practices and 

operation/animal characteristics. NAHMS performs a study 

in each major commodity at 5- to 7-year intervals. With 

regard to AMR, NAHMS studies usually gather information 

about general farm policy and management practices related 

to reasons for use, antimicrobial class, and delivery route. All 

surveys are voluntary. Information is protected by Title 7,

U.S. Code, Section 2276 and the Confidential Information 

Protection and Statistical Efficiency Act which prohibit public disclosure of individual information. In addition, personal 

information, including reported data, is protected from legal 

subpoena and Freedom of Information Act requests. In some 

instances, data are collected on individual animals. 

5 
NAHMS studies typically incorporate collection of onfarm biological samples. For many years, fecal samples were 

collected to isolate important pathogens and commensal 

bacteria and to determine the presence of antibiotic resistance. The repeated nature of NAHMS studies has allowed 

an examination of patterns over time. Finally, NAHMS 

studies explore actions related to preserving the health of animals on farms. These activities may reduce the need to use 

antibiotic drugs to prevent, control, or treat disease. Furthermore, the data allow direct evaluation of associations between 

management practices (including antibiotic drug use) and 

AMR observed in the farm setting. Such information will 

be important in identifying potential mitigation strategies.

(Objectives 1, 2, and 3) 

2. Agricultural Resource Management Survey (ARMS) (ERS, 

NASS, and APHIS). ARMS is an annual farm-level survey 

jointly administered by ERS and NASS with consultation 

from APHIS. All surveys are voluntary. Information is 

protected by Title 7, U.S. Code, Section 2276 and the Confidential Information Protection and Statistical Efficiency 

Act prohibit public disclosure of individual information. In 

addition, personal information, including reported data, is 

protected from legal subpoena and Freedom of Information Act requests. The survey focuses on farm finances, but 

includes detailed questions aimed at commercial producers 

of certain livestock species on production practices, including 

antibiotic drug use. ERS obtained data on antimicrobial use 

during 2004 and 2009 for hogs, and during 2006 and 2011 

for broilers. These data provide estimates of antibiotic drugs 

used, the purpose of their use, stage of production, and type 

of farm. (Objectives 1 and 3) 

3. FSIS sampling in slaughter plants (FSIS). Two monitoring 

streams are used: (1) sampling of the contents of the large 

intestine from a random sample of animals through the 

NARMS program; and (2) product sampling through Salmonella Pathogen Reduction: Hazard Analysis and Critical 

Control Points (PR/HACCP) verification sampling. Large 

intestine contents of swine (market hogs and sows), cattle 

(beef and dairy), and poultry (young chickens and turkeys),

and product samples from young chicken, young turkey,

and ground beef are being collected at slaughter establishments. Large intestine sampling, in partnership with FDANARMS, monitors year-to-year trends in prevalence of 

Salmonella and other bacteria of interest (e.g., Campylobacter, 

Escherichia coli, Enterococcus) in the gut of animals at slaughter

with particular emphasis on their antibiotic susceptibility and 

genetic relatedness. (Objective 2) 

4. The U.S. National Residue Program (NRP), administered 

by FSIS since 1967, is an interagency program designed to 

identify, rank, and test for chemical contaminants (including 

antibiotics) in meat, poultry, and egg products. Chemical 

compounds tested in the program include approved and 

unapproved veterinary drugs, pesticides, and environmental 

compounds. (Objective 1) 

5. Assessment of the presence of emerging AMR organisms of

public health and zoonotic potential such as methicillin-resistant Staphylococcus aureus (MRSA) and Clostridium difficile,

among food-producing animals, retail products, and humans 

in the United States (ARS, APHIS, CDC, FDA, and universities). Several preliminary surveys have been conducted to 

determine the prevalence of MRSA in swine and C. difficile 

in swine, cattle, humans, and retail products. One C. difficile 

study is a collaborative project between ARS and university 

scientists to assess incidence in a closed population (prison 

system) that raises pigs and consumes the pork. Previous 

NAHMS studies in swine and dairy and beef cattle have also 

included surveillance for C. difficile. (Objective 2) 

6 
 Current

 Proposed 

Figure 1: 


USDA’s current and proposed surveillance; research and development; and education, extension, and outreach 


activities by objective. 

USDA will provide science-based information relating to: 

Objective 1: 

Antibiotic use in food 

producing animals 

Objective 2: 

Antibiotic drug 

Susceptibility in food 

animals and meat and poultry 

Objective 3: 

Mitigations to reduce AMR 

associated with food 

producing animals and their 

production environments 

Surveillance 

1. National Animal Health Monitoring System (NAHMS) 

2. Agricultural Resource 

Management Survey (ARMS) 

2. Agricultural Resource Management 

Survey (ARMS) 

3. FSIS sampling in 

slaughter plants (NARMS 

and HACCP) 

4. National Residue 

Program (NRP) 

5. Emerging AMR organisims of public health and 

zoonotic potential. 

1. Ongoing longitudinal studies 

2. Enhanced NASS and ARMS 

survey questionnaires 

2. Enhanced NASS and ARMS survey 

questionnaires 

3. Antibiotic susceptibility 

testing of selected animal 

pathogens 

4. Targeted on-farm and in-plant sampling 

Research and 

Development 

6. On-farm pilot studies 

7. Economic effects of the use of 

growth-promoting antimicrobials 

8. Alternatives to antibiotics

 9. Intramural research 

10. Extramural research 

5. Intra- and extramural research on microbial ecology 

6. Intra- and extramural research on alternatives to antibiotics 

Education and 

Outreach 11. Judicious use 

on-line training module 

for veterinarians 

11. Judicious use on-line training module 

for veterinarians 

12. Educational content funded by NIFA 

13. Food Animal Residue 

Avoidance Database (FARAD) 

13. Food Animal Residue 

Avoidance Database (FARAD) 

7. Judicious use training 7. Judicious use training 

8. Online extension training 

9. Education and extension component of Food Safety Challenge Area 

7 
Current Intramural and Extramural Research 

and Development: 

6. On-farm sample collection with linkage to slaughter from 

swine, dairy, beef, and poultry (broiler and turkeys) (ARS). 

These pilot studies are evaluating potential methods for establishing a sustainable program for collecting samples from 

animals on farms and at slaughter for bacterial isolation and 

AMR testing. The project includes the collection of samples 

from a cohort of animals for bacterial isolation and resistance 

testing from farm through slaughter. These data will provide 

information on differences in resistance prevalence at each 

sampling location. Minimal antibiotic use data are being 

collected in this study. (Objective 2) 

7. Economic effects of the use of growth-promoting antimicrobials on livestock production and costs of production (ERS 

and NASS). Using ARMS data, ERS assessed the impact of 

antibiotic use for growth promotion on output and production costs in hog finishing and broiler grow-out operations.

The focused studies also assessed alternative practices in place 

on farms that use growth-promoting antibiotics. Current 

research explores the market effects on the use of certain 

antibiotic drugs for production purposes (i.e., growth promotion) in livestock. The research will provide estimates of the 

impacts on livestock production and prices, wholesale and 

retail meat prices and sales, and feed prices and production.

(Objective 3) 

8. Ongoing research on alternatives to antibiotics (ARS and 

NIFA). “Alternatives to antibiotics” are broadly defined as any 

substance that can prevent the need for or be substituted 

for the therapeutic use of antimicrobial drugs. ARS held 

an international symposium in cooperation with the World 

Organization for Animal Health in Paris, France, September 

25–28, 2012, to highlight promising research results and 

novel technologies that could potentially lead to the development of alternatives to conventional antibiotics (www.ars. 

usda.gov/alternativestoantibiotics/). Numerous alternative 

strategies are proposed, including vaccines, prebiotics, probiotics, bacteriophages, bacteriophage gene products, bioactive 

phytochemicals, essential oils, naturally occurring bacterial 

lytic enzymes, animal-derived antimicrobial peptides, small 

interfering ribonucleic acids, immune enhancers, and recombinant and hyperimmune therapeutic antibodies. Through 

competitive and capacity funds, NIFA is supporting projects 

that target effective interventions, including alternatives to 

antibiotics, in food-producing animals. (Objective 3) 

9. Intramural research to generate science-based data about 

mechanisms of antimicrobial resistance and strategies to reduce AMR in food-producing animals and their environments 

(ARS). (Objectives 1, 2, and 3) 

a. Studies to better understand the mechanisms of how 

foodborne pathogens acquire, maintain, and transmit 

genes for AMR and virulence. One project investigates 

and characterizes plasmid maintenance, transferability,

gene content, and evolution in a diverse set of Salmonella 

serotypes isolated from cattle and poultry from production 

to harvest environments. Understanding the diversity 

of plasmids and their role in a diverse set of Salmonella 

and E. coli (including non-O157) strains is important in 

establishing their role in AMR. 

b. Studies to better understand the role of animal production environments in AMR. Several ongoing studies 

provide information on the distribution and frequency 

of AMR bacteria and their genes in the environment.

For example, one study is determining the presence of 

AMR-related genes or cassettes for commonly administered agricultural antibiotics such as tetracycline, penicillin, and aminoglycosides in samples from cattle, poultry,

and swine manure and manure-impacted areas. Gene 

transfer, both horizontal and vertical, selection via plasmid 

or resistance cassettes of indigenous soil bacteria, and 

their possible transfer into pathogens are being studied.

Another project investigates the role of biofilms in the 

development of resistant microorganisms and transfer and 

persistence of resistance genes in poultry and produce. It 

compares the capability of Shigatoxigenic groups of 

E. coli (STEC) O157:H7 and non-O157 STEC strains 

and serotypes to form biofilms on food contact surfaces 

and the resultant bacterial dissemination. 

c. Studies to better understand factors that reduce pathogens and improve animal health to reduce the use of antibiotics. ARS conducts research on actions that reduce the 

level of important animal and food safety pathogens for 

all food-producing livestock species. These studies investigate the effectiveness of new and innovative management 

practices to reduce pathogen load and transmission of 

foodborne pathogens to meat and poultry products. This 

includes management practices, vaccination strategies, and 

nutritional supplements to improve and maintain animal 

health as well as minimize the pathogens persisting in the 

animal and the environment. In addition, other important 

research is identifying animals that shed higher levels of 

foodborne pathogens and developing strategies to reduce 

their shedding and thus transmission of the pathogens. 

10. Extramural integrated research, education, and/or extension grants that generate science-based data about antimicrobial use, mechanisms of antimicrobial resistance, and 

mitigations to reduce AMR in food-producing animals and 

their environments (NIFA). (Objectives 1, 2, and 3) 

a. Since 2008, NIFA has awarded approximately $9 

million in competitive awards to study AMR through 

programs in both its Food Production and Sustainability 

8 
and Food Safety and Nutrition Institutes. Funded research has addressed how resistance develops and spreads 

in animals and food supply systems. The research identified critical control points and practices for mitigating 

the emergence, spread, and persistence of AMR in the 

preharvest or postharvest food environment, in products,

and/or in host and environmental ecosystems. 

b. NIFA has funded a project that is identifying critical on-farm control points in dairy production that will 

decrease antimicrobial-resistant salmonellae. In addition,

grant funds through the Agriculture and Food Research 

Initiative (AFRI) of $2 million to $4 million are available 

to support systematic studies that identify intervention 

strategies for effective mitigation of AMR throughout the 

food chain. 

c. In the combined 2012/2013 request for applications,

the AFRI Food Safety Challenge (integrated) area made 

up to $2.8 million available to address effective AMR 

mitigation strategies. In 2013, NIFA funded two research 

grants to three universities and one conference for a total 

of $1.6 million. Specific award information can be found 

at http://cris.nifa.usda.gov. 

Current Education, Extension, and Outreach: 

11. Judicious use online training module for veterinarians. 

The National Veterinary Accreditation Program (APHIS,

academic partners, FDA, and CDC) requires supplemental 

training every 3 years for renewal of accreditation, which allows private veterinarians to engage in regulatory work, such 

as writing health certificates for export or the submission 

of tests for diseases of regulatory importance. A module on 

judicious use of antimicrobials has been added to the menu 

of online, supplemental training modules. Such education 

of veterinary practitioners will support efforts to avoid both 

the selection of AMR and residues in animal products. The 

module will require periodic updates on the basis of new 

information gleaned from surveillance efforts and as policy related to antimicrobial drug use is implemented. For 

example, the FDA Guidance #213 calls for greater veterinary 

oversight of medically important antimicrobials used in feed 

or water. When the Veterinary Feed Directive is fully implemented, there will be a need to further educate veterinarians 

on the proper use of the directive. (Objectives 1 and 3) 

12. Educational content through NIFA. NIFA provides 

principal Federal support for the Cooperative Extension 

System which serves as a national resource to disseminate 

validated scientific information to the private sector within every county in the United States. In recent years, the 

Web site www.eXtension.org was launched to provide even 

more efficient online methods to share high-quality, reliable 

information within and between States. Considerable Web 

content relating to AMR already exists within the eXtension 

system. Education is also part of NIFA’s mission. NIFA 

administers curriculum development grant programs such as 

the Higher Education Challenge Grant program. Although

formal educational development projects specifically relating 

to AMR have not been funded recently, these NIFA grant 

programs are available for institutions of higher education to 

apply to develop innovative teaching methods and curricula 

relating to specific areas of study. (Objectives 1, 2, and 3) 

13. Food Animal Residue Avoidance Database (FARAD). 

(NIFA) This program is a resource to the food-producing 

industry and supports the production of safe foods of animal 

origin through the prevention and mitigation of violative 

chemical residues (i.e., drugs, antibiotics, pesticides, natural 

toxins, and environmental contaminants) in food animal 

products. FARAD (www.farad.org) is funded through NIFA 

and is operated by a consortium of four university laboratories (University of California–Davis, Kansas State University,

University of Florida, and North Carolina State University).

(Objectives 1 and 3) 

Proposed Initiatives 

Despite USDA’s long history of activities, partnerships,

and investments in AMR, considerable work remains to fill 

existing knowledge gaps and strengthen current, ongoing 

activities. This action plan proposes several initiatives that 

will enable USDA to use its collective expertise and strengths 

to develop effective, practical strategies for animal agriculture 

to prolong the effectiveness of antibiotics to treat people and 

animals. To achieve the greatest impact, these initiatives 

would build upon existing activities and be integrated across 

USDA agencies. Because all of these proposed activities are 

voluntary, collaborations with stakeholders and producers 

will be needed to leverage expertise and resources in the most 

efficient and effective ways 

Proposed Surveillance: 

1. Ongoing longitudinal studies that collect quantitative data on 

antimicrobial drug use and management practices along with 

biological samples at various points and locations from the farm 

and at slaughter. (Objectives 1, 2, and 3) 

Description: Detailed data and biological samples could be 

collected from a limited number of cooperating operations 

that volunteer to participate over time. Initially, feedlot 

cattle, swine, and poultry (broilers) operations would be 

surveyed with dairy cattle and other commodities to follow.

Questionnaires would be used to measure antimicrobial 

drug use (including the specific drugs, delivery system, and 

purpose of use) and related production practices by livestock 

9 
and poultry producers. Ongoing monitoring of antimicrobial drug susceptibilities for common animal and foodborne 

pathogens would directly link temporal changes in these 

AMR patterns with on-farm antimicrobial use and other 

management practices. Various biological samples could also 

be collected at slaughter and cultured for multiple bacteria 

(i.e., Salmonella, Campylobacter, generic E. coli, and Enterococcus). Isolates would be tested for antimicrobial drug susceptibility. Changes in microbial and resistance status in the 

slaughter plant could then be evaluated in light of contemporary on-farm antimicrobial use and management practices. 

Outcomes: These studies would provide quantitative data 

about antibiotic use, AMR patterns, and management practices on farms, their relationships, and trends over time. The 

ability to monitor temporal trends will be particularly useful 

to measure the effectiveness of policies and interventions in 

reducing AMR. For example, USDA could quantify changes 

in antimicrobial drug use on these farms after the new FDA 

guidelines and regulations are implemented. USDA could 

also produce better estimates of the quantities of antibiotics 

used in animal agriculture. 

Ongoing monitoring of microbial and resistance status at 

various points in the slaughter process would help in understanding microbial flow through the system and identify 

points where changes in microbial load or microbial ability 

to adapt to the processing environment may be occurring 

or where interventions may be most effective to reduce 

microbial loads. Resulting data could be used to formulate 

guidelines for processors and potentially in developing new 

inspection strategies to prevent pathogens and other hazards 

from contaminating meat and poultry products. The data 

could inform risk analysis and provide a transparent, scientific basis for regulatory decisionmaking. 

Integration: The FDA will use these data to evaluate antibiotic use by U.S. livestock and poultry producers. Producers 

can implement evidence-based strategies to reduce AMR 

that are identified through this surveillance. Finally, multiple USDA agencies and university partners will use the data 

to identify critical areas for further focused, collaborative 

research and education/outreach activities. 

2. Enhanced NASS and ARMS survey questionnaires with new 

and expanded questions about antibiotic drug use and related 

production practices. (Objectives 1 and 3) 

Description: Questions about antibiotic drug use will be added to existing and proposed NASS livestock surveys so that 

national estimates of antibiotic drug use can be determined 

for feedlot cattle, swine, and poultry. All surveys are voluntary. Information is protected by Title 7, U.S. Code, Section 

2276 and the Confidential Information Protection and 

Statistical Efficiency Act which prohibit public disclosure 

of individual information. In addition, personal information, 

including reported data, is protected from legal subpoena and 

Freedom of Information Act requests.

 Doing so will provide monitoring of trends in antimicrobial 

drug use over time. Similarly, new ARMS survey questionnaires with detailed coverage of antimicrobial use and 

related production practices will be introduced for swine and 

broilers. The surveys would track producer behavior before 

and after the finalization of the FDA Guidance #213 and the 

accompanying changes to the Veterinary Feed Directive rule 

to measure their effect, and the effect of retailer requirements 

pertaining to antimicrobial use on farm productivity, costs,

and production practices. The survey would extend the scope 

of the current research that investigates the likely impact of 

the loss of growth-promoting drugs on outputs and production costs at the farm level and would track adoption of 

production practices meant to replace antimicrobial use for 

growth promotion. 

Outcomes: These surveys will provide national data about 

antibiotic use and management practices on farms, their relationships, and how these change over time for three major 

livestock commodities. Further, data from both of these 

surveys would supplement ongoing surveillance conducted 

through NAHMS. The ability to monitor temporal trends 

would be particularly useful to measure the effectiveness 

of policies and interventions in changing antimicrobial 

use practices and reducing AMR. It would also better 

enable estimation of the quantities of antibiotics used in 

animal agriculture. 

Integration: The results from these studies will provide the 

FDA with valuable information regarding the impacts of 

its guidance. Retailers and processors may potentially use 

the data to inform procurement policies that address the use 

of antimicrobials in livestock. Many stakeholders and the 

general public will be interested in more accurate estimates 

of antimicrobial use in livestock and poultry. The results of 

these surveys would be integrated with ongoing NAHMS 

information to further coordinate on-farm commodity 

studies. Finally, multiple USDA agencies and university 

partners will be able to use the data to identify critical areas 

for further focused, collaborative research and education/

outreach activities. 

3. Implement routine antibiotic susceptibility testing of selected 

animal pathogens and collate and report data across veterinary 

diagnostic laboratories. (Objective 2) 

Description: State veterinary diagnostic laboratories test 

samples from clinically ill animals to identify the pathogens 

responsible for causing disease. AMR testing is conducted 

on some of these isolated pathogens. Veterinarians use this 

information to guide treatment for the ill animals and other 

animals in close contact or in the local area. However, these 

data on AMR patterns are rarely collated and reported at the 

10 
laboratory level or across multiple laboratories. Developing 

a voluntary data system that links AMR testing data across 

State veterinary diagnostic laboratories and reports resistance 

trends over time for animal pathogens will help inform veterinarians’ and producers’ for judicious treatment decisions and 

promote the judicious use of antibiotics in animals. 

State veterinary diagnostic laboratories routinely submit Salmonella isolates to the NVSL for serotyping. These isolates 

are typically associated with higher than expected morbidity 

and mortality, more severe disease, or more persistent disease 

conditions in groups, herds, or flocks. AMR testing is not

currently performed on these isolates. However, this action 

plan proposes to reinitiate AMR testing on these Salmonella 

isolates. This would create a surveillance stream to identify 

newly emerging strains with increased resistance to multiple 

antimicrobial drugs or specific antimicrobial drugs of high 

interest (e.g., those critically important to public health).

Veterinarians and producers would gain knowledge about 

emerging threats to animal health and information to guide 

treatment decisions. The public health community would 

benefit from a possible early warning system for potential 

future foodborne illness. 

Outcomes: Developing this surveillance stream for monitoring AMR profiles in animal pathogens would be important 

to maintain animal health and encourage the judicious use 

of antibiotics. Specifically, this surveillance would allow veterinarians and producers to make more informed treatment 

decisions by using the AMR data to judge the likelihood of 

success of a specific antibiotic drug, to monitor the continued 

usefulness of a particular antibiotic, and to identify whether 

a new or different antimicrobial product is needed over the 

course of treatment. Further, it would provide information 

related to the unintended consequences of resistance developing in non-target pathogens if access to the production 

facility was granted and additional studies were initiated. 

Integration: In addition to its value to the veterinary and 

animal agricultural communities, this newly tapped surveillance stream would provide the FDA, CDC, and public 

health communities with important information about AMR 

patterns observed in pathogens that cause disease in animals 

and that can potentially result in foodborne illness in people. 

4. Targeted on-farm and in-plant sampling to supplement 

ongoing NAHMS studies and case investigations. (Objectives 

1, 2, and 3) 

Description: Detailed epidemiological investigations could be 

conducted when clusters of AMR pathogens are identified 

on farms as part of NAHMS, in slaughter plants through 

FSIS Salmonella HACCP verification testing, or as outbreaks of human illnesses through PulseNet. USDA would 

collaborate with the producers, slaughter establishments,

and public health officials (as appropriate) on a voluntary 

basis to conduct targeted on-farm and/or in-plant biological 

sampling and complete questionnaires about antimicrobial 

use and management practices to determine the source of the 

pathogen and to identify mitigation strategies. Information is 

protected by Title 7, U.S. Code, Section 2276 and the Confidential Information Protection and Statistical Efficiency Act 

which prohibit public disclosure of individual information.

In addition, personal information, including reported data, is 

protected from legal subpoena and Freedom of Information 

Act requests. 

Outcomes: These in-depth studies would allow a more 

complete understanding of factors associated with specific 

incidents of AMR pathogens associated with food-producing 

animals. They could allow for a comparison of management 

practices on those affected operations with control (not 

affected) operations in an effort to identify and mitigate risk 

factors for the selection and spread of AMR both on farms 

and in slaughter plants. Additionally, they would allow 

for study and in-depth characterization of both target and 

non-target pathogens/bacteria that may or may not develop 

resistance when approved antibiotics are used. 

Proposed Intramural and Extramural Research 

and Development: 

5. Research on understanding the microbial ecology associated 

with feeding antibiotics or antimicrobials at therapeutic, preventive, and production levels. (Objectives 1, 2, and 3) 

Description: Preliminary data have shown that the microbiome of the gastrointestinal system changes in response to numerous factors, including management and feeding practices,

environment, transport, and the administration of antimicrobials. Expanded research is needed to better understand 

the causes and conditions that induce increased development 

of AMR in production animals. This information is critical 

for developing strategies to minimize the level of AMR in 

production animals. The programs would include a systems 

science approach with strong multi-disciplinary and a One 

Health emphasis. This research would be broad spectrum 

and collaborative between Federal agencies and colleges. In 

addition, education and outreach would be integrated into 

each project. 

Outcomes: The results from this research would aid in understanding the role microbial ecology plays in the development 

of AMR. This information is critical in understanding the 

mechanisms and results from administration of antimicrobials and from various management strategies. Anticipated 

outcomes include not only new system-compatible integrated 

strategies for control and mitigation of AMR, but the overall 

holistic, judicious (risk-benefit balanced) use of antibiotics 

throughout the food chain from “farm to fork.” An addi11 
tional benefit will be support to ensure a pipeline of the next 

generation of scientists and educators. The resulting data will 

be coordinated with surveillance data to provide answers 

to help minimize the development of AMR and to develop 

alternative strategies to reduce AMR in production animals. 

6. Develop innovative antimicrobials to provide alternatives to 

conventional antibiotics. (Objectives 1, 2, and 3) 

Description: Development of specific alternatives to antibiotics, such as prebiotics and probiotics, novel antimicrobial 

molecules, and immune enhancement products through intramural and extramural research projects, is critically needed.

Alternatives to antibiotic strategies include, but would not be 

limited to, the following: antimicrobial peptides; prebiotics;

probiotics; bacteriophage; modulators of innate and adaptive 

immunity; immune modulation (including vaccines); novel 

approaches based on gut microbiome and host interactions;

or genetic resistance to disease, including classical animal 

breeding. Proposals for research, education, and extension 

activities leading to innovative experimental methods and 

tools for the study of AMR and new knowledge and strategies aimed at improving animal management and husbandry 

methods would also be eligible for funding. This program 

will address AMR control in the context of the concomitant 

obligation to protect animal health and well-being and to 

support adequate (profitable) animal production efficiency. 

Outcomes: There is a critical need to develop novel antibiotics and alternative strategies for preventing and treating 

infectious diseases not just to safeguard the use of currently 

available antibiotics, but also to meet the challenges of AMR.

Paramount is establishing partnerships between academic 

and government researchers and the feed and pharmaceutical 

industries and their regulators to enable the development of 

effective and safe alternatives to antibiotics. Integrating nutrition, health, and disease research will drive new technological advances and the application of the “omic” fields. These 

technological advances will include new research tools and 

opportunities that afford scientists a hitherto unprecedented 

ability to discern the mechanisms by which alternatives to 

antibiotics can be effectively used to treat and prevent animal 

diseases. Working in partnership with stakeholders, funding 

organizations, public and private research institutions, and 

Federal partners will harness the resources needed to develop 

technologies more resilient to AMR and alternative strategies to enhance the health and welfare of animals 

and humans. 

Proposed Education, Extension, and Outreach 

7. Education and outreach for producers on judicious antimicrobial use. (Objective 2) 

USDA proposes to partner with the CDC to reinitiate the 

“Get Smart: Know When Antibiotics Work on the Farm” 

(www.cdc.gov/narms/get-smart.html). USDA, in collaboration with a number of other stakeholders, proposes to reinitiate this outreach that was recently discontinued by the CDC 

to agricultural industries and the veterinary community. 

8. Develop an online informational/educational tool to promote 

judicious antibiotic use in animal agriculture (www.extension. 

org/search?q=antimicrobial). (Objectives 1, 2, and 3) 

The project will use the Cooperative Extension Service,

including the network of local extension agents, to provide 

science-based information about the appropriate use of 

antibiotics to maximize animal health while minimizing the 

development of AMR. In addition to sharing new information obtained through the surveillance and research and 

development activities described previously, this effort will 

integrate concepts from existing quality assurance programs 

already in place in many animal agriculture industries. 

9. The 2014 Food Safety Challenge area will make up to $6 million available for integrated projects that address AMR through 

a combination of research, education, and extension. (Objectives 

1, 2, and 3) 

NIFA released a request for applications on January 29, 2014.

Applicants must address one or more criteria that directly include research, education, and/or extension/outreach.

Specified extension and education-related criteria include 

the following: 

Develop novel systems approaches to investigate the ecology 

of microbial resistance gene reservoirs in the environment 

(i.e., soil, water, air, storage environments), in animals, in food 

products, and in farm-raised aquaculture products. 

a. The design of effective training, education, and outreach 

materials and resources (including Web-based resources) 

that can be easily customized to meet the unique needs 

of various users across the food chain from farm to fork,

including, but not limited to, policymakers, producers,

processors, retailers, and consumers. 

b. The design and execution of studies that evaluate the 

impact and efficacy of proposed research, education,

and extension/outreach interventions on AMR from

farm to fork. 

12 
Conclusion
 

USDA possesses in-depth knowledge of the management 

practices and technologies associated with animal health,

welfare, productivity, and food safety. As such, USDA is 

uniquely positioned to contribute to the body of scientific 

knowledge about AMR, specifically about the role of antimicrobial use in livestock. 

This action plan is a roadmap to guide USDA’s future activities to address AMR. It describes how USDA proposes 

to provide science-based, quantitative information about 

antibiotic drug use and resistance in food-producing animals 

and their relationship to livestock management practices. It 

outlines USDA’s current activities and proposes a comprehensive, integrated approach for future activities that includes 

surveillance; research and development; and education,

extension, and outreach. 

The successful execution of this action plan would provide 

and disseminate science-based information for the veterinary 

and animal agricultural communities so they can implement 

effective mitigation strategies to prolong the effectiveness of 

antibiotics for use in both animals and people. Because the 

proposed activities are voluntary, USDA must closely cooperate with Federal, industry, commodity, and academic partners 

to implement this plan. 

13 
APPENDIX 1
 

USDA Antimicrobial Resistance Action Plan Committee 

Eileen Thacker, ARS—Chair 

Cyril Gay, ARS 

Paula Cray, ARS 

David Dargatz, APHIS 

Bruce Wagner, APHIS 

Eva Ring, APHIS 

James MacDonald, ERS 

Stacy Sneeringer, ERS 

Pat Basu, FSIS 

Neena Anandaraman, FSIS 

Dan Kerestes, NASS 

Gary Sherman, NIFA 

Mervalin Morant, NIFA 

Alecia Naugle, Office of the Chief Scientist 

Sponsors 

Steven Kappes, ARS 

John Clifford, APHIS 

David Goldman, FSIS 

14 
APPENDIX 2
 

Abbreviations and Acronyms 

AALPI Antimicrobial Alternatives for Livestock Production Research Initiative 

AFRI Agricultural Food Research Initiative 

APHIS Animal and Plant Health Inspection Service 

AMR Antimicrobial resistance 

ARMS Agricultural Resource Management Survey 

ARS Agricultural Research Service 

CDC Centers for Disease Control and Prevention 

CES Cooperative Extension System 

CRIS Current Research Information System 

EEI Element Ecology Research Initiative 

EPA Environmental Protection Agency 

ERS Economic Research Service 

FARAD Food Animal Residue Avoidance Database 

FDA Food and Drug Administration 

FSIS Food Safety and Inspection Service 

ITFAR Interagency Task Force on Antimicrobial Resistance 

MRSA Methicillin-resistant Staphylococcus aureus 

NAHMS National Animal Health Monitoring System 

NARMS National Antibiotic Resistance Monitoring System 

NASS National Agricultural Statistics Service 

NIFA National Institute of Food and Agriculture 

NIFSI National Integrated Food Safety Initiative 

NIH National Institutes of Health 

NRP National Residue Program 

NVSL National Veterinary Services Laboratories 

PR/HACCP Pathogen Reduction: Hazard Analysis and Critical Control Points 

USDA U.S. Department of Agriculture 

15 
1930 1940 1950 1960 1970 1980 1990 2000 2010

APPENDIX 3
 

Timeline of Class and Antimicrobial First Marketed for Use
 

4 million old bacteria resistant to modern antimicrobials 

Continual exposure to “natural antibiotics” from soil bacteria and fungi globally 

FIGURE A 

Figure A depicts the timeline of antimicrobial exposure available to humans, animals, and, by default, the ecosystem/environment. The timeline starting in 1935 describes the early development and marketing of the major classes and first antimicrobial within the class. Antimicrobials were largely introduced for human use with the exception of Chlortetracycline in 1948, 

which was and is still used in veterinary medicine. Resistance to all classes of antimicrobials emerged in human medicine 

after introduction, primarily among target pathogens. Veterinary applications for some classes of antimicrobials have been 

approved for use against veterinary pathogens. As observed in human medicine, resistance also emerges in target pathogens. Ancillary resistance also appears in both human and veterinary non-target commensal and foodborne bacteria. 

1935: 

Sulfonamides, 

Prontosil 

1942: 

Penicillin, 

Benzylpenicillin 

1944: 

Aminoglycoside, 

Streptomycin
 

1948:

Tetracycline, 

Chlortetracycline 

1949: 

Amphenicol, 

Chloramphenicol 

1952: 

Macrolide, 

Erythromycin 

1955:

GlycopepLde,


Vancomycin
 

1958: 

Polymyxin, 

Colistin 

1960: Nitroimidazole, 

Metronidazole 

1961: 

Dihydrofolate 

reductase 

inhibitor, 

trimethoprim 

1964: 

Cephalosporin, 

Cefalothin 

1967: 

Quinolone, 

Nalidixic acid 

1968: 

2nd 

Lincosamide,

Clindamycin

1985: 

Carbapenem, 

Imipenem

1987: 

2nd gen 

Fluorquinolone, 

Ciprofloxacin and

Ansamycin, Rifaximin 

2000: Oxazolidone, 

Linezolid 

2001:

Ketolide,

Telithromycin 

2009:

Lincoglycopeptide,

Telavancin 

16 
FIGURE B 

The Collective Antimicrobial Resistance Ecosystem
 

As described in figure A, the available antimicrobial exposure will affect the bacterial populations humans and animals are 

exposed to both in the absence and presence of antimicrobial use within the veterinary and medical disciplines. 

Unlike previous depictions, which typically show a circular continuum with uni- and bi-directional flows of resistant bacteria impacting certain outcomes and in particular humans and animals, this diagram links humans and animals under the 

One Health concept as both are impacted by the available antimicrobial exposure levels as well as the contribution(s) to the 

resistance issue afforded by each surrounding circle. Contributions may consist of direct sources of resistant bacteria or 

resistance genes or indirect sources via vectors that serve to move resistant bacteria or deposit feces containing resistant 

bacteria in distant places. The curved line interconnects each circle as no one source/activity within a circle is independent 

of the other. 

Collectively the human/animal/available antimicrobial exposure level/circular sources and activities of antimicrobial resistance 

comprise the global ecosystem that continues to add and delete antimicrobial resistance attributes over time. 

Crops,fruits, 

and 

vegetables 

Travel-global, 

national 

and local 

Pests 

and 

insects/flies 

Rivers, oceans, 

lakes and 

streams 

Climate, 

weather and 

atmosphere 

Available antimicrobial 

exposure level 

Linked 

Human/Animal 

Interface 

Natural 

antibiotics 

from soil 

bacteria and 

fungi 

Ancient 

resistance 

genes and 

bacteria 

Modern 

antimicrobials 

Wildlife, 

non-bird 

Aquaculture, 

farmed fish 

Litter 

and manure 

Sewage, 

wastewater, 

and industry 

Birds, 

including 

migratory 

Sources and activities of antimicrobial resistance Sources and activities of antimicrobial resistance 

17 
FIGURE C 

An antimicrobial (ABX) is given to treat an infection directed against a target bacteria (tan circle). 

However, the body is replete with hundreds of millions of different types of bacteria, all of which 

are equally exposed to the antimicrobial (represented by other shapes and colors). 

= target bacteria 

= non-target bacteria 

ABX 

ABX R 

Non-targeted bacteria (green) which either harbored or acquired resistance gene(s) were 

able to divide to numbers that potentially either harms the host, are excreted at levels to 

other susceptible hosts, or are transferred by food, vectors or other means to other hosts 

resulting in illness. 

18 
Figure D 

Figure D shows the differences in antimicrobial resistance patterns between four strains of 

Salmonella Kentucky. 

This figure illustrates these differences. Among the group or serotype Kentucky for Salmonella, four 

different strains have been identified by a molecular technique called pulsed field gel electrophoresis. 

These four strains behave very differently. A majority, but not all, of the strains are susceptible to all 

antimicrobials tested. For strain 1, less than 1 percent are susceptible to all antimicrobials tested, 

while 54 percent are resistant to Streptomycin and Tetracycline, two of the earliest antibiotics 

developed for use in human and veterinary medicine. Other differences in resistance are noted. 

Resistance profile 

Strain 1 

JGP01.0003 

(n=1216) 

Strain 2 

JGPX01.0001 

(n=365) 

Strain 3 

JGPX01.0342 

(n=324) 

Strain 4 

JGPX01.0041 

(n=153) 

No Resistance 

0.8% 92.9% 76.5% 87.0% 

Streptomycin/Tetracycline 

54.1% 0.3% 3.9% 1.0% 

Tetracycline 

25.2% 0.6% 0.7% 1.0% 

Amoxicillin-clavulanic acid/Ampicillin/Cefoxitin/ 

Cetiofur/Ceftriaxone/Streptomycin/Tetracycline 10.3% 0.0% 2.0% 1.0% 

Amoxicillin-clavulanic acid/Ampicillin/Cefoitin/ 

Cetiofur/Ceftriaxone/Tetracycline 4.5% 0.3% 0.0% 0.0% 

Amoxicillin-clavulanic acid/Ampicillin/Cefoxitin/ 

Cetiofur/Ceftriaxone/Tetracycline 0.0% 0.0% 6.2% 4.0% 

Gentamicin/Streptomycin/Sulfamethoxazole/ 

Tetracycline 1.7% 0.0% 0.0% 1.0% 

Gentamicin/Sulfamethoxazole 

0.0% 0.0% 0.0% 0.0% 

Gentamicin/Sulfamethoxazole 

0.0% 0.0% 5.6% 0.0% 

Amoxicillin-clavulanic acid/Ampicillin/Cefoxitin/ 

Ceftiofu/Cerftriaxone/Chloramphenicol/Gentamicin/ 

Kanamycin/Streptomycin/Sulfamethoxazole/ 

Tetracycline 

0.0% 4.0% 0.0% 1.0% 

Amoxicillina-clavulanic acid/Ampicillin/Ceftiofur/ 

Ceftriaxone/Tetracycline 0.8% 0.0% 0.7% 0.0% 

19 
APPENDIX 4
 

USDA Agencies’ Roles in Antimicrobial Resistance 

Mitigation Efforts 

The Agricultural Research Service (ARS) is the USDA’s 

intramural research program. ARS research considers AMR 

from perspectives of animal health, food safety, and public 

health. Areas of research include: investigating changes in 

the gut microbiome in response to antibiotics; investigating 

mechanisms of the development of AMR; identifying and 

characterizing resistant bacteria; developing alternatives to 

antibiotics; understanding the effects of antibiotic administration on manure and the environment; and exploring the 

potential for transfer of antimicrobial-resistant foodborne 

pathogens or resistance genes from food animals (or their 

environment) through food processing to consumers. 

The Animal and Plant Health Inspection Service (APHIS) 

conducts monitoring and surveillance activities to characterize health and management of livestock and poultry populations on farms. As a component of those activities, APHIS 

characterizes on-farm use of antibiotic drugs. APHIS collects samples on farms to determine the prevalence of select 

zoonotic pathogens and includes characterizing resistance to 

antimicrobial drugs. APHIS evaluates relationships between 

management practices, use of animal health practices, and 

on-farm antimicrobial use and resistance. The National 

Veterinary Services Laboratories of APHIS is a reference 

laboratory for animal pathogens and helps accurately identify 

and characterize pathogens of animals in support of veterinary diagnostic laboratories and the academic community 

to identify new antibiotic drug resistance mechanisms and 

AMR testing. 

The Economic Research Service (ERS) analyzes the effects 

of production inputs and practices, including antibiotic drugs 

on production, costs, and revenues on farms. In addition,

ERS evaluates the effects of changes in farm-level productivity, costs, and prices on domestic and international markets 

for agricultural commodities and food products. As part of 

that effort, ERS maintains extensive databases on the farm 

sector economy, including the agricultural and food markets. 

The Food Safety and Inspection Service (FSIS) is responsible 

for ensuring that the Nation’s commercial supply of meat,

poultry, and egg products is safe, wholesome, and correctly labeled and packaged, as required by the Federal Meat 

Inspection Act, the Poultry Products Inspection Act, and the 

Egg Products Inspection Act. FSIS monitors antimicrobial 

use and AMR at slaughter and verifies that establishments 

have food safety systems in place to minimize the level of 

pathogens that reach consumers. 

The mission of the National Agricultural Statistics Service 

(NASS) is to provide timely, accurate, and useful statistics 

in service to U.S. agriculture. NASS conducts surveys and 

prepares reports covering virtually every aspect of U.S. agriculture. In partnership with APHIS and ERS, NASS carries 

out surveys and collects information on antimicrobial use 

practices using statistically drawn samples from a maintained 

list of farmers and ranchers in the United States. 

The National Institute of Food and Agriculture (NIFA) is 

USDA’s primary extramural research, education, and extension funding agency. NIFA leads food and agricultural 

sciences by supporting research, education, and extension 

programs in the Land-Grant University System and other 

partner organizations. In recent years, proposals funded 

through NIFA’s Food Production and Sustainability or Food 

Safety and Nutrition institutes have addressed how resistance 

develops and spreads in animals and food supply systems and 

the development of alternatives to antibiotics. NIFA’s Small 

Business Innovation Research program supports innovation 

and product development in many areas, including vaccine 

development and alternatives to antibiotic use. 

20 
APPENDIX 5 

Strengths and Weaknesses of Current 

Objective Projects 

Current Objective 1 Projects: 

Strengths 

•	 Projects capture nationally representative samples for 

target populations and provide some basic information 

about drug use and current practices with differing levels 

of specificity (e.g., qualitative vs. quantitative, animal level 

vs. farm level). 

•	 Current NAHMS surveys contain detailed information 

on general antibiotic administration practices that encompass number of animals treated, purpose of treatment, and 

delivery method. 

•	 ARMS links estimates of antibiotic usage by stage of production and reason for use with farm production attributes 

(e.g., farm size, contractual relationships, age of facilities) 

and farm financial variables. 

•	 NRP measures drug residues in all animal species to verify 

that approved drugs are used according to FDA regulations. 

Weaknesses 

•	 NAHMS and ARMS identify whether antibiotics are 

used and for what purpose, but they do not estimate quantities used. 

•	 NAHMS surveys are conducted periodically (generally, every 5–7 years), leading to a series of point-in-time 

estimates rather than providing any ongoing real-time 

surveillance of AMR or antimicrobial use during the 

interim periods. 

•	 The surveys do not track the same farms over time, making 

it difficult to identify causal factors associated with patterns of drug use or resistance. 

•	 Lack of integration of ARMS data and coordination 

between APHIS, ERS, and NASS. 

•	 With reduced ARMS funding, antimicrobial drug use 

questions will be eliminated in future livestock versions of 

the survey. 

•	 NRP tests a limited number of animals and may not detect 

the lower levels of antimicrobials typically used for growth 

promotion. It is only a proxy for information about antimicrobial drug use. 

•	 FARAD data are retrospective only. 

Current Objective 2 Projects: 

Strengths 

•	 Pilot on-farm sampling will provide information on 

potential study methods for monitoring the AMR profile 

of organisms present in animals and how consistent a bacterial population is with samples collected at the site where 

those animals are slaughtered. The collaboration between 

Federal agencies and university scientists constitutes a 

valuable consortium of expertise for assessing AMR and 

future research methods. 

•	 NAHMS studies of bacterial isolates are broadly representative of what is observed across the industry. Standard 

methods are used across multiple commodities, which facilitate a consistent measure of prevalence of resistance and 

associations with animal and management factors. NASS 

ensures the confidentiality of data collected by NAHMS. 

•	 The current evaluation of clinical Salmonella isolates by 

the National Veterinary Services Laboratories (NVSL) of 

APHIS provides a picture of the populations of Salmonella serotypes in sick animals. 

•	 Large intestine and cecal content sampling in slaughter 

plants by FSIS has the potential to provide ongoing information on trends in prevalence of resistance among bacterial flora in animals at slaughter. PR/HACCP sampling 

is also providing data on salmonellae in products meant 

for consumers. The PR/HACCP selection of samples is 

risk-based, so more samples are collected at establishments 

with a questionable history of process control, thus potentially increasing the recovery of salmonellae. 

•	 Identification of the impact of AMR bacteria in manure 

and associated with biofilms is important in determining 

the ecological and environmental impacts of the administration of antimicrobials. 

•	 Surveillance data are used by scientists applying for NIFA 

grants to guide hypothesis development and to target 

study focus and design. It is anticipated that data generated by NIFA scientists will in turn complement and inform 

ongoing official surveillance efforts. 

21 
Weaknesses	 

•	 The on-farm/slaughter project is a pilot project with a 

small sample size, and although it provides important 

preliminary information on methods, it will need to be 

repeated and/or expanded. 

•	 The samples collected in current NAHMS studies are 

concentrated on enteric pathogens of importance to public 

health, excludes animal pathogens, and are periodic (every 

5–7 years per species). Sample numbers are limited due 

to laboratory costs and capacity, which precludes precise 

national estimates of resistance prevalence. 

•	 Interpretation of the data on clinical Salmonella isolates 

from NVSL is hampered by the limited data on sources 

and circumstances that accompany the isolates. 

•	 The number of large intestine content samples collected by 

FSIS at slaughter is small, so it may be difficult to detect 

enough salmonellae to determine true prevalence that 

might be reflective of year-to-year trends. Animals are 

not identified, so it is not possible to trace samples back to 

management practices on the farm such as antibiotic drug 

use. Furthermore, large intestine contents could reflect 

microbial status on the farm, at transport, or at holding, so 

it is difficult to infer results from a specific sampling location. PR/HACCP sampling is currently risk-based and 

not random, so it cannot be used to determine year-to-year 

trends in national prevalence. Furthermore, the PR/HACCP program tests only for levels of Salmonella. Neither 

the large intestine content sampling nor PR/HACCP 

programs collect information on management practices 

that may affect changes in microbial profiles, such as the 

use of in-plant antimicrobial interventions. 

•	 Coordination might be improved between NIFA’s process 

of developing requests for applications, NIFA grantees,

and official surveillance data collection to expand and 

enhance the scope, value, and impact of NIFA-supported 

AMR-related science. 

•	 NIFA cannot formally request information generated 

through the conduct of any funded projects beyond the 

required Final Termination Report of the study. Therefore, important follow-on data analyses, resulting scientific 

advances, outcomes, and impacts are not captured in the 

CRIS database. 

Current Objective 3 Projects: 

Strengths 

•	 Large nationally representative samples are available for 

NAHMS and ARMS. 

•	 ARMS contains reliable estimates on annual outputs,

inputs, and costs for economic analyses. 

•	 Research projects assessing alternatives to antibiotics are 

being implemented and new products are in the research 

pipeline. 

•	 Alternatives to antibiotics with defined mechanisms of 

action provide new opportunities for the selection of multiple products that can work synergistically. 

•	 Alternatives to antibiotics that affect the gut microbiome,

such as phytochemicals and immune enhancers, provide 

new opportunities for integrating nutrition, health, and 

disease research. 

•	 Many opportunities exist to seek funding from sources 

that have an interest in both agriculture and public health. 

•	 Partnering can occur between the private sector and stakeholders to seek funding and support. 

•	 NAHMS studies concurrently evaluate AMR, drug use,

and other management practices on farms. 

•	 Collaboration and partnerships (e.g., between USDA and 

FDA) ensures that issues of common interest are being 

addressed across agencies and departments, where appropriate. 

•	 Integration of research, education, and extension efforts 

by NIFA ensures that topics are relevant to stakeholders 

and that subsequent dissemination, communication, and 

application of science-based data and knowledge occurs to 

various end users. 

22 
Weaknesses 

•	 NAHMS studies are periodic and cross-sectional, which 

limits their timeliness and the ability to make causal 

inferences. 

•	 ARMS estimates are based on nonexperimental data (i.e.,

they compare outcomes for users and nonusers). Because 

users and nonusers may differ in several ways, it is more 

difficult to identify causality, even with the use of statistical 

matching techniques. 

•	 ARMS identifies only whether antimicrobial drugs are 

used (there are no quantity measures), and includes only 

two animal species—broilers and swine. 

•	 Lack of clear regulatory pathways for licensing and 

marketing alternatives to antibiotics, including whether 

new molecules will be regulated as a drug, biologic, feed 

additive, or possibly all three. 

•	 Lack of national and international standards to meet 

requirements of efficacy, safety, and quality of alternatives 

to antibiotics. 

•	 Research on finding alternatives to antibiotics are poorly 

funded with a poor success rate in successfully obtaining 

extramural funding. 

• Identifying alternatives to antibiotics that can be used for 

both disease treatment and growth promotion has a low 

success rate. 

• By necessity, NIFA’s funding programs that include AMR 

are limited not only by financial constraints, but also the 

parameters/priorities identified by NIFA on the basis of 

stakeholder input. Only the most outstanding projects are 

selected for funding, and they may be focused on program 

priority topics other than or in addition to those addressing Objective 3. 

23 
USDA is an equal opportunity provider and employer. To file a complaint of discrimination, write: USDA, Office of the 

Assistant Secretary for Civil Rights, Office of Adjudication, 1400 Independence Ave., SW, Washington, DC 20250-9410 or call 

(866) 632-9992 (Toll-free Customer Service), (800) 877-8339 (Local or Federal relay), (866) 377-8642 (Relay voice users). 

June 2014