United States

Department of

Agriculture

Animal and

Plant Health

Inspection Service

Veterinary

Services

National

Animal Health

Monitoring

System

February 2012

Beef 2007–08

Antimicrobial Drug Use and Antimicrobial

Resistance on U.S. Cow-calf Operations,

2007–08
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USDA–APHIS–VS–CEAH

NRRC Building B, M.S. 2E7

2150 Centre Avenue

Fort Collins, CO 80526-8117

(970) 494–7000

Email: NAHMS@aphis.usda.gov

http://nahms.aphis.usda.gov

#577.0212

Cover photo courtesy of Dr. Dave Dargatz
USDA APHIS VS / i

Items of N ems of Note

Organisms resistance to antimicrobial drugs,

such as antiviral products, anthelmintics, and

antibacterials, is a growing global concern.

Much of this concern stems from the potential

impacts on human health associated with

resistant organisms, which is not to say that

there is a lack of concern about the potential

impact of resistant organisms on animal health

and wellbeing. However, data on animal disease

associated with resistant organisms are very

limited.

There is also concern about antimicrobial drug

use in animals and the impact such use could

have on humans. People can be exposed to

bacteria from animals in a number of ways,

including direct contact and by foodborne

transmission. In some cases, zoonotic bacteria

can be resistant to antimicrobial drugs, which

may complicate treatment of people, should they

become ill, or lead to more severe

consequences. For these reasons, there is

growing interest about how antimicrobial drugs

are used in farm environments and the potential

impacts of such use on animal-source

organisms, particularly those resident in the

gastrointestinal tract of animals. This

information is and will be critical to meaningful

risk assessments and decision making at all

levels, from on-farm use of antimicrobial drugs

to policy making.

Less than 20 percent of cow-calf operations in

the 24 States that participated in the NAHMS

Beef 2007–08 study used antibiotics with or

without decoquinate/ionophores in the feed of

any animals to prevent disease or promote

growth. The relatively low use of these products

in feed is likely a reflection of the way the

animals are managed, i.e., generally without

supplemental feeding of mixed concentrates.

Grazed or harvested forages account for the

majority of feed consumed by cattle in this

production setting, and when supplementation is

required, protein or energy source is used, but

not generally as a mixed diet. Furthermore, the

youngest animals on the operations (calves) are

generally suckling their dams and are often not

provided with supplemental (creep) feed. The

next older group, including replacement heifers

and other calves, are managed to achieve

appropriate growth to facilitate reproduction at

the appropriate time in the production calendar,

and most of this growth is achieved through

forage consumption rather than the consumption

of concentrates. Only 4.1 percent of operations

incorporated antibiotics with or without

decoquinate/ionophores in feed to promote

growth in replacement heifers (5.3 percent of

operations did so for other calves). Finally, cows

have already achieved their full growth potential

and are managed to maintain condition and

support the growth of their fetuses. Depending

on the environmental conditions, some

supplementation may be required, but, as stated

above, supplementation usually consists of

protein supplements and forage with or without

some energy supplementation.

Antibiotics are also used to treat various disease

conditions on cow-calf operations. Unweaned

calves have the highest occurrence of disease,

followed by weaned calves, and finally cows.

Consequently, a declining proportion of animals

are treated with antibiotics with increasing age.

Although 68.0 percent of operations had used
ii / Beef 2007-08

oral or injectable antibiotics to treat disease,

only 7.2 percent of unweaned calves,

6.0 percent of weaned replacements, and

1.9 percent of cows were treated at least once

with oral or injectable antibiotics. The

proportion of sick animals treated with an

antibiotic depends on the illness; some diseases

are not amenable to treatment with antibiotics.

In the Beef 2007–08 study, operation antibiotic

use practices were not associated with the

likelihood of isolating various enteric bacteria

from fecal samples collected on the operations.

Because of the relatively low frequency of

antibiotic use on the cow-calf operations, such

use would have to have profound impacts on the

gut flora to be evident in the culture results. In

addition, few of the bacteria cultured from feces

on the operations were resistant to antibiotics in

the susceptibility test panels. Again, given the

relatively low frequency of use on these

operations, that use would have to have

profound and sustained effects on the enteric

organisms to be detected by the testing carried

out in this study.

Continued efforts by the cattle industry,

veterinary profession, and others to encourage

judicious use of antibiotics in cow-calf

operations and other livestock and poultry

production settings is warranted to sustain both

animal and public health.
USDA APHIS VS / iii

Selected Highlights ed Highlights

This report provides an in-depth look at

antimicrobial use practices on U.S. beef cowcalf operations participating in the NAHMS

Beef 2007–08 study. The report also describes

the occurrence of antimicrobial resistance in

Salmonella, Campylobacter, Enterococcus,

Clostridium difficile, and non-type specific

Escherichia coli on a subset of operations

participating in the study.

Here are a few highlights from the report:

• More than 8 of 10 operations (81.3 percent)

did not use antibiotics or decoquinate/

ionophores in the feed of any animals to prevent

disease or promote growth.

• For weaned calves, 4.1 and 5.3 percent of

operations used antibiotics in feed to promote

growth in replacement heifers and other weaned

calves, respectively. Similarly, 9.8 and 11.9

percent of operations used antibiotics in feed to

prevent respiratory disease in replacement

heifers and other weaned calves.

• Operations reported that 7.2 percent of

unweaned calves, 6.0 percent of weaned

replacement heifers not yet calved, and 1.9

percent of cows were treated at least once with

oral or injectable antibiotics.

• Use of oral, injectable, or in-feed antibiotics

was not associated with recovery of Salmonella,

Campylobacter, Enterococcus, or non-type

specific E. coli on the operations participating in

testing for these organisms.

• Of the Salmonella isolates identified in the

Beef 2007–08 study, none was resistant to any

of the 15 antimicrobials in the test panel.

• Over half of the C. jejuni isolates

(56.2 percent) were susceptible to all nine

antimicrobials tested. Ciprofloxacin and

erythromycin are most often used to treat

Campylobacter infections in humans, and 6.6

and 0.4 percent, respectively, of Campylobacter

isolates were resistant to these antimicrobials.

• Vancomycin is commonly used to treat

humans with enterococcal infections but has not

been used in animal production in the United

States. One of the 1,180 Enterococcus isolates

was resistant to vancomycin, but this finding

was determined to be an intrinsic resistance.

Synercid® is commonly used to treat

vancomycin-resistant infections, and less than

1 percent of the isolates were resistant to

Synercid (excluding E. faecalis isolates which

exhibit intrinsic resistance to Synercid).

• Only 16.6 percent of non-type specific

E. coli isolates were resistant to any

antimicrobials. No resistance to ceftriaxone or

ciprofloxacin was observed among E. coli

isolates.

• When treatment is used for human cases of

C. difficile-associated disease, vancomycin and

metronidazole are the antimicrobials most

commonly used. None of the C. difficile isolates

was resistant to vancomycin and 0.5 percent of

isolates were resistant to metronidazole.
iv / Beef 2007-08

Acknowledgments ledgments

This report was a cooperative effort of the U.S. Department of Agriculture’s (USDA) National

Agricultural Statistics Service (NASS), Animal and Plant Health Inspection Service (APHIS), and

Agricultural Research Service (ARS).

We want to thank the NASS enumerators who contacted beef producers and collected data for the

Beef 2007-08 study. Their hard work and dedication were invaluable. The roles of the producers,

area veterinarians in charge, NAHMS coordinators, veterinary medical officers, and animal health

technicians were critical in providing quality data for the Beef 2007–08 reports. Recognition also

goes to the personnel at the USDA–APHIS–Veterinary Services’ Centers for Epidemiology and

Animal Health for their efforts in generating and distributing this report.

Additional biological sampling and testing for the Beef 2007–08 study were afforded by the

generous contributions of collaborators, including:

• USDA–ARS

 –Bovine Functional Genomics Laboratory, Beltsville, MD

 –Bacterial Epidemiology and Antimicrobial Resistance Research Unit, Athens, GA

 –Environmental Microbial Safety Laboratory, Beltsville, MD

 –Virus and Prion Research Unit, Ames, IA

• USDA–APHIS–VS National Veterinary Services Laboratories, Ames, IA

• IDEXX Laboratories, Inc., Westbrook, ME

All participants are to be commended, particularly the producers whose voluntary efforts made the

Beef 2007–08 study possible.

Larry M. Granger

Director

Centers for Epidemiology and Animal Health
USDA APHIS VS / v

Suggested bibliographic citation for this report:

USDA. 201. Beef 2007–08, Antimicrobial Drug Use and Antimicrobial Resistance on

U.S. Cow-calf Operations, 2007–08

USDA-APHIS-VS-CEAH-NAHMS. Fort Collins, CO

#577.0212

Contacts for further information:

Questions or comments on data analysis: Dr. David Dargatz (970) 494–7000

Information on reprints or other reports: Ms. Abby Fienhold (970) 494–7000

Email: NAHMS@aphis.usda.gov

Feedback

Feedback, comments, and suggestions regarding Beef 2007–08 study reports are welcomed. Please

forward correspondence via email at: NAHMS@aphis.usda.gov, or you may submit feedback via

online survey at: http://nahms.aphis.usda.gov (Click on “FEEDBACK on NAHMS reports.”)
vi / Beef 2007-08

Table of Cont able of Contents

Introduction 1

Terms Used in This Report 3

Section I: Antimicrobial Drug Use and Resistance 6

A. Antimicrobial Drug Use 6

1. Definitions of antimicrobials 6

2. How antimicrobials work 6

3. Why antimicrobials are used 7

B. Antimicrobial Resistance 8

1. Intrinsic versus acquired resistance 8

2. Transferrable drug resistance 9

3. Assessing antimicrobial susceptibility 10

4. Why antimicrobial resistance is a concern 12

5. Foodborne illness 16

6. Complexity of antimicrobial resistance 16

Section II: Population Estimates 17

Antimicrobial Drug Use 17

1. Antibiotics and decoquinate/ionophores in feed 17

2. Use of oral or injectable antibiotics for disease treatment 26

Section III: Fecal Sample Evaluations 42

A. Study Methods for Biological Sampling and Testing for Enteric

Bacteria 42

1. Sample collection 42

2. Culture methods 42

3. Antimicrobial resistance evaluation 44

4. Comparison of operations by whether samples were submitted 49

B. Sample Testing Results 50

1. Salmonella 50

2. Campylobacter 55
USDA APHIS VS / vii

3. Enterococcus 61

4. Escherichia coli 66

5. Clostridium difficile 69

Section IV: Methodology 75

A. Needs Assessment 75

B. Sampling and Estimation 76

1. State selection 76

2. Operation selection 76

3. Population selection 76

C. Data and Sample Collection 77

1. Data collectors and data collection periods 77

2. Biological sample collection, culturing, and testing for antimicrobial

resistance 77

D. Data Analysis 78

1. Phase I: Validation—General Beef Management Report 78

2. Phase II: Validation—Initial and Second Visit Questionnaires 78

E. Sample Evaluation 78

1. Phase I: General Beef Management Report 79

2. Phase II: VS Initial Visit 80

3. Phase II: VS Second Visit 81

Appendix I: Sample Profile—Responding Operations 82

Appendix II: Organism Overviews 83

Appendix III: Number of Beef Cows, by Region 86

Appendix IV: American Veterinary Medical Association Judicious

Use Principles 87

Appendix V: AABP Revised Prudent Drug Usage Guidelines 88

Appendix VI: References 90
USDA APHIS VS / 1

Introduction

Introduction oduction

The National Animal Health Monitoring System

(NAHMS) is a nonregulatory program of the

U.S. Department of Agriculture’s (USDA)

Animal and Plant Health Inspection Service.

NAHMS is designed to help meet the Nation’s

animal health information needs and has

collected data on cattle health and management

practices on cow-calf operations through two

previous studies, the 1992–93 Cow-calf Health

and Productivity Audit and Beef ’97.

The Beef 2007–08 study was conducted in the

24 States (see map next page)that had the largest

beef cow populations and provides participants,

stakeholders, and the industry as a whole with

valuable information representing 79.6 percent

of U.S. cow-calf operations and 87.8 percent of

U.S. beef cows. Parts I and II of the study

contain information from the 2,159 cow-calf

operations that participated in Phase I of the

Beef 2007–08 study. Part III provides

comparisons among population estimates from

all three NAHMS beef studies, Beef 2007–08,

Beef ’97, and the 1992–93 Cow-calf Health and

Productivity Audit.

Of the 2,159 operations participating in Phase I

of the Beef 2007–08 study, 1,033 consented to

be contacted by a veterinary medical officer

regarding participation in Phase II of the study.

Of these 1,033 operations, 567 completed the

Phase II initial visit questionnaire. Data from the

initial visit questionnaire are reported in Part IV

of the Beef 2007–08 study. Of the 567

operations that completed the initial visit

questionnaire, 470 agreed to continue in Phase

II of the study and completed the second visit

questionnaire, data from which are reported in

Part V of the study.

To assess the prevalence of five types of enteric

bacteria (Salmonella, Campylobacter,

Enterococcus, Escherichia coli, and

Clostridium difficile), 173 operations were

selected for sample collection from the 567

operations enrolled in Phase II of the study.

Section I of this report provides an overview of

antimicrobial drug use and antimicrobial

resistance. Section II contains population

estimates from management data collected

during Phase I and Phase II and provides

population inferences on general antimicrobial

drug use practices. Section III provides test

results from 173 operations on which fecal

samples were collected for culturing and

bacterial isolate characterization. Data in

Section III are not weighted to represent the

U.S. beef population. Rather, they describe the

management and testing results from 173

operations.
2 /Beef 2007–08

Introduction
USDA APHIS VS / 3

Introduction

Terms Used in This Report

Antibiotic: A substance produced by a

microorganism that at low concentrations

inhibits or kills other microorganisms.

Antimicrobial: Any substance of natural,

semisynthetic, or synthetic origin that kills or

inhibits the growth of a microorganism but

causes little or no damage to the host.

Antimicrobial resistance: A property of

microorganisms that confers the ability to

inactivate or elude antimicrobials or a

mechanism that blocks the inhibitory or killing

effects of antimicrobials.

Antimicrobial susceptibility testing: Tests that

determine an organism’s susceptibility to

specific antimicrobials. There are many types of

susceptibility tests, but all use inhibition of the

organism (rather than killing) as the end point.

Qualitative results are usually reported as

susceptible, intermediate, or resistant.

Quantitative results are usually reported as

minimal inhibitory concentrations (MIC)

in ìg/mL.

Beef cow: Female bovine that has calved at

least once.

Beef heifer: Female bovine that has not yet

calved.

Break point: The zones of inhibition or MICs

at which an organism is considered to be

susceptible, intermediate, or resistant.

Broad spectrum antimicrobial: A type of

antimicrobial effective against a large number of

bacterial genera; generally describes

antimicrobials effective against both grampositive bacteria and gram-negative bacteria.

Chromosome: A single piece of DNA that

contains many genes and is contained within the

nucleus of a cell.

Extra-label drug use: Actual use or intended

use of a drug, under veterinary direction, in a

manner not in accordance with the approved

labeling. Includes deviation from the label,

including use in nonlisted species, use for

nonlisted durations, alternate dosing levels or

frequencies, use by routes other than listed, and

use of different withdrawal times than listed.

Gene: A segment of DNA that is a unit of

heredity. Changes in the DNA sequence

constitute mutations, which add to the diversity

of a species and could confer antimicrobial

resistance.

Gram-negative bacteria: Bacteria decolorized

by alcohol in Gram’s staining protocol.

Compared with Gram-positive bacteria, Gramnegative bacteria have a thinner layer of

peptidoglycan in the cell wall.

Gram-positive bacteria: Bacteria that resist

decolorization in Gram’s staining protocol, thus

retaining the crystal violet-iodine complex; a

characteristic of bacteria with a thick layer of

peptidoglycan and teichoic acid in the cell wall.
4 /Beef 2007–08

Introduction

Gram’s stain: Staining procedure in which

bacteria are stained with crystal violet, treated

with a solution of iodine, decolorized with

alcohol, and counterstained with a contrasting

dye. Organisms that retain the stain are deep

purple in color and are classified as Grampositive; organisms that lose crystal violet stain

are red in color and classified as Gramnegative.

Herd size: Herd size is based on October 1,

2007, cow inventory. If there were no cows on

October 1, 2007, then July 1, 2007, cow

inventory was used.

Horizontal gene transfer: The passage of

genes between unrelated organisms via mobile

genetic elements, such as plasmids.

Intestinal microflora: Microorganisms that

maintain a constant presence in the intestine of

animals. These organisms help to prevent the

overgrowth of pathogenic bacteria.

Microbe: A collective name given to bacteria,

viruses, fungi, and parasites.

Minimum inhibitory concentration (MIC):

The minimum concentration of an antimicrobial

necessary to completely inhibit growth of the

organism tested.

Minimum bactericidal concentration (MBC):

The minimum concentration of an antimicrobial

necessary to kill the organism tested.

Narrow spectrum antimicrobial: A type of

antimicrobial effective against a limited number

of bacterial genera; an antimicrobial active

against specific families of bacteria.

Operation: Premises with at least one beef cow

on October 1, 2007, or July 1, 2007.

Operation average: The average value for all

operations; a single value for each operation is

summed over all operations reporting divided by

the number of operations reporting. For

example, operation average number of days that

antibiotics or decoquinate/ionophores were used

(p 23) is calculated by summing reported dollars

per head over all operations divided by the

number of operations.

Pathogen: Any disease-producing organism.

Plasmid: A piece of DNA not part of the

chromosome that is self-replicating and not

essential for bacterial survival. Typically they

carry genes that confer some selective advantage

to the host bacterium, such as antimicrobial

resistance.

Polymerase chain reaction (PCR): The

amplification of a specific DNA sequence (or

target sequence) that is present in a complex

mixture. At the end of the amplification, the

target sequence can be detected.
USDA APHIS VS / 5

Introduction

Population estimates: The estimates in this

report make inference to all of the operations in

the target population (see Methodology). Data

from the operations responding to the survey are

weighted to reflect their probability of selection

during sampling and to account for any survey

nonresponse.

Precision of population estimates:

Estimates in this report are provided

with a measure of precision called

the standard error. A 95-percent

confidence interval can be created

with bounds equal to the estimate

plus or minus two standard errors.

If the only error is sampling error,

the confidence intervals created in

this manner will contain the true

population mean 95 out of 100

times. In the example to the left, an

estimate of 7.5 with a standard error

of 1.0 results in limits of 5.5 to 9.5

(two times the standard error above

and below the estimate). The second estimate of

3.4 shows a standard error of 0.3 and results in

limits of 2.8 and 4.0. Alternatively, the 90-

percent confidence interval would be created by

multiplying the standard error by 1.65 instead of

2. Most estimates in this report are rounded to

the nearest tenth. If rounded to 0, the standard

error was reported (0.0). If there were no reports

of the event, no standard error was

reported (—).

Regions:

West: California, Colorado, Idaho, Montana,

New Mexico, Oregon, Wyoming

Central: Iowa, Kansas, Missouri, Nebraska,

North Dakota, South Dakota

Southeast: Alabama, Arkansas, Florida,

Georgia, Kentucky, Louisiana, Mississippi,

Oklahoma, Tennessee, Texas, Virginia

Sample profile: Information that describes

characteristics of the operations from which

Beef 2007–08 data were collected.

Vertical gene transfer: Genes passed from one

generation to the next through bacterial

replication.

Standard Errors

(1.0)

10

9

8

7

6

5

4

3

2

1

0

(0.3)

Examples of a 95% Confidence Interval

95% Confidence 

Intervals
6 / Beef 2007–08

Section I: Antimcrobial Drug Use and Resistance—A. Antimicrobial Drug Use

Section I: Antimicr Section I: Antimicrobial

Drug Use and R ug Use and Resistance

A. Antimicrobial Drug Use

1. Definitions of

antimicrobials

Although the terms antibiotic and antimicrobial

are often used interchangeably, technically they

are not the same. An antibiotic is a substance

produced by a microorganism that at low

concentrations inhibits the growth of or kills

other microorganisms (Prescott et al., 2000,

ch 1). One example of an antibiotic is penicillin,

which is produced from Penicillium mold and

can be used to kill some types of bacteria. An

antimicrobial is any substance of natural,

semisynthetic, or synthetic origin that inhibits

the growth of or kills a microorganism while

causing little or no damage to the host.

Examples of synthetic antimicrobials include

sulfonamides and fluoroquinolones.

Antimicrobials are not limited to antibacterial

drugs, as antifungals, antivirals, and

antiparasitics are also considered antimicrobial

drugs. However, for the remainder of this report,

the terms antibiotic and antimicrobial will be

used interchangeably and will refer only to

antibacterials, unless stated otherwise.

Some drugs, such as ionophores (e.g.,

monensin), which are used to control coccidiosis

in food animals, have activity against protozoa

and bacteria, specifically gram-positive bacteria

(Prescott et al., 2000, ch 16).

2. How

antimicrobials

work

Antimicrobials work in a variety of ways and

can be administered orally, topically, by

infusion, or by injection. Some antimicrobials

are bacteriocidal; they kill the organism. Others

are bacteriostatic; they inhibit the growth and

replication of the organism, allowing the body’s

own immune response to clear the infection.

There are six main mechanisms by which

antimicrobials work to inhibit or kill the

bacterium (Prescott, 2000, ch 1, 16; Mascaretti,

2003, ch 6):

1. Inhibition of cell wall synthesis.

Antimicrobials such as penicillin,

cephalosporins, and avoparcin inhibit synthesis

of the bacterial cell wall. The cell wall is an

essential component of the organism and if it

cannot be synthesized the organism dies.

2. Inhibition of protein synthesis. Tetracyclines,

aminoglycosides and chloramphenicol (among

others) inhibit protein synthesis within the

bacterial cell. Proteins are essential for the

organism because the cellular structures and

enzymes are generally made of proteins.

3. Inhibition of nucleic acid synthesis. Nucleic

acid (DNA and RNA) synthesis is vital for

survival of the bacterial cell. Without DNA

synthesis the cell cannot replicate, and without

RNA synthesis gene expression and protein

synthesis are not possible. Quinolones and

novobiocin inhibit DNA synthesis, while

rifampin blocks RNA synthesis.

4. Inhibition of metabolic pathways.

Sulfonamides and trimethoprim block folic acid

synthesis, indirectly inhibiting nucleic acid

synthesis.
USDA APHIS VS / 7

Section I: Antimcrobial Drug Use and Resistance—A. Antimicrobial Drug Use

5. DNA destruction. Antimicrobials such as

metronidazole and nitrofurans act directly on

bacterial DNA by breaking it down, inhibiting

survival of the organism.

6. Increase in cell wall permeability.

Polypeptides such as polymyxins act by

increasing the permeability of the cell

membrane. This causes small molecules to leak

out of the bacterial cell, leading to cell death.

Antimicrobials are used to treat or prevent

(prophylaxis) disease or disorders caused by

bacteria and to improve growth rate and

efficiency (National Research Council, 1999,

ch 2). One form of prevention is metaphylaxis,

which is the timely mass medication of a group

of animals to prevent or minimize an expected

outbreak of disease.

When using antimicrobials to treat or prevent

disease caused by bacteria, selection of the drug

depends on (Prescott et al., 2000, ch 5):

1. Susceptibility of the suspected (or laboratory

confirmed) pathogen(s)

2. Factors that affect drug concentration at the

site of infection

3. Potential drug toxicities

4. Cost of the treatment

5. Regulations of antimicrobial use and

withdrawal times

3. Why

antimicrobials are

used

Antimicrobials are also used to increase

production performance by increasing the

efficiency of the feed consumed by the animal

for growth, product output, or by modifying the

nutrient composition of an animal product.

Almost as soon as antibiotics were introduced, it

was recognized that adding low concentrations

of antimicrobials to the feed could promote

growth. The discovery was made when pigs and

poultry were fed fungal waste derived from

antibiotic production. The waste was intended as

a source of vitamins and protein. Today, it is still

uncertain how antimicrobial drugs improve feed

efficiency and growth rates. One thought is that

low levels of antimicrobials may have an

inhibitory or metabolic effect on some grampositive intestinal microflora.
8 / Beef 2007–08

Section I: Antimcrobial Drug Use and Resistance—B. Antimicrobial Resistance

B. Antimicrobial Resistance

Note: A bacterial strain is defined as resistant to a specific antimicrobial if it continues to grow in the presence of higher

concentrations of that drug compared with related susceptible strains that are inhibited (susceptible).

1. Intrinsic versus

acquired resistance

Groups of bacteria can be naturally resistant to

an antimicrobial if they possess a structural or

functional trait that allows for tolerance of a

particular antimicrobial or class of

antimicrobial. Natural resistance is also known

as intrinsic resistance and should be thought of

as insensitivity, since it occurs in groups of

bacteria that were never sensitive to the drug

(Prescott et al., 2000, ch 3; Mascaretti, 2003,

ch 5).

Bacteria that are naturally susceptible can

become resistant. Resistance can be the result of

a specific nonfatal genetic mutation that happens

rarely, or can be the result of acquiring genes

encoding resistance from another bacterium.

Acquired resistance is a threat to both animal

and human health because the resistance of

normally susceptible bacteria, which often

occurs by genetic change in a normally

susceptible organism, can spread, leading to

treatment failure (Prescott et al., 2000, ch 3;

Mascaretti, 2003, ch 5). Acquired resistance is

associated with only some strains of a bacterial

genus or species (unlike intrinsic resistance,

which affects an entire bacterial group). When

the antimicrobial resistance confers a survival

advantage to the organism, the resistance

becomes more prevalent. The ability of the

bacterium to resist the effects of antimicrobials

occurs through one or more of the following

mechanisms (Prescott et al, 2000, ch 3):

1. Enzymatic inactivation. Some bacteria are

able to produce enzymes that inactivate certain

antimicrobials. One clinically important enzyme

is beta-lactamase, which renders penicillin

inactive for inhibiting cell wall synthesis.

2. Decreased cell wall permeability. Decreased

bacterial cell wall permeability for

antimicrobials can occur with a loss or

decreased expression of porins, which allow

access through the bacterial cell wall. Reduced

uptake of antimicrobials is clinically important

for beta-lactams and fluoroquinolones against

gram-negative bacteria, especially Pseudomonas

aeruginosa and Enterobacteriaceae.

3. Efflux. Active drug export, or efflux, is an

energy-dependent mechanism used by bacteria

to reduce the concentration of the antimicrobial

in the cell. Some efflux pumps act on specific

drugs (specific-drug-resistance, or SDR pumps),

while others are active against multiple drugs

(multiple-drug-resistance or MDR pumps). SDR

pumps are the most important resistance

mechanism against tetracyclines.

4. Alteration in target receptors. The drug target

receptor can be altered such that the

antimicrobial is no longer able to attach and

exert its activity on the bacteria. For methicillinresistant Staphylococcus aureus (MRSA), the

drug target receptor has been altered.

5. Alteration of metabolic pathways.

Development of alternative biochemical

pathways to bypass the effect of the drug. Some

antimicrobials (e.g., sulfonimides) target

enzymes used by the bacteria. If the target

enzyme mutates or is modified, the bacteria

become resistant.
USDA APHIS VS / 9

Section I: Antimcrobial Drug Use and Resistance—B. Antimicrobial Resistance

2. Transferrable

drug resistance

Plasmids are mobile genetic elements that can

transfer antibiotic-resistance genes from one

bacterium to another (Prescott et al., 2000, ch 3;

Mascaretti, 2003, ch 5). Plasmids are extrachromosomal circular DNA and are not required

for the survival of the bacterial cell. They

replicate independently, but synchronously with

chromosomal DNA. Plasmids can subsequently

be transferred to the cell’s offspring (vertical

transmission) or neighboring bacterial cells

(horizontal transmission).

Plasmids are capable of coding for resistance to

one or more different antimicrobials. By treating

with any one of the antibiotics for which the

plasmid has a resistance gene, maintenance of

the entire plasmid is being enhanced. However,

the issue of bacterial fitness is very complex.

Some research has suggested resistance to a

single antimicrobial, such as tetracycline, may

have a greater fitness advantage in the presence

of tetracycline compared to resistance to

multiple antimicrobials.

Transposons, also known as jumping genes, are

short sequences of DNA that can contain

antimicrobial resistance genes (Prescott et al.,

2000, ch 3; Mascaretti, 2003, ch 5).

Transposons can move quickly between

plasmids within a cell, or between the plasmid

and the chromosomal DNA.

Integrons are also mobile genetic elements that

are often found on plasmids or transposons

(Prescott et al., 2000, ch 3; Mascaretti, 2003,

ch 5). Integrons contain collections of genes

called gene cassettes. The gene cassettes contain

a single antimicrobial resistance gene, but

integrons with multiple gene cassettes can

develop. Furthermore, genes in the integron can

code for resistance to heavy metals and

disinfectants. These tightly linked cassettes of

resistance genes tend to be transferred or

inherited together. Again, use of any of the

products for which there are resistance genes in

the integron will tend to select for resistance to

all of the products. This is called co-selection.

Genes that code for antimicrobial resistance can

be transferred horizontally by three different

mechanisms. Transduction occurs when the

plasmid DNA becomes incorporated into

bacteriophage, or bacterial virus, and is

transferred to another bacterium (Prescott et al.,

2000, ch 3). Bacteriophages are very specific, so

this mechanism is of less importance than the

others. Transformation is the mechanism by

which naked DNA or a DNA fragment is taken

up by a cell and incorporated into the recipient’s

chromosome (Prescott et al., 2000, ch 3). The

transfer usually happens between related

bacteria and can lead to development of new

forms of resistance genes. Transformation is an

important source of emergence of antimicrobial

resistance.

Conjugation is a common process of gene

transfer that involves direct transfer of DNA

from one cell to another (Prescott et al., 2000,

ch 3). During conjugation, a donor bacterium

has direct contact with a recipient cell and

transfers copies of plasmid-mediated resistance

genes. The donor also retains copies of the

plasmid, and the recipient becomes a new

potential donor. The transfer of genes can occur

between both closely related and unrelated

bacteria, such as those of a different genus and

species.
10 / Beef 2007–08

Section I: Antimcrobial Drug Use and Resistance—B. Antimicrobial Resistance

There are several in vitro methods for testing

antimicrobial susceptibility of an organism. All

of the methods use inhibition of growth of the

bacterium as the endpoint, and test results can

be reported either quantitatively or qualitatively.

Qualitative results report the organism as

susceptible, intermediate, or resistant to the

antimicrobial(s) in question. When a laboratory

reports that an organism is susceptible, it implies

that the recommended dosage of the

antimicrobial agent will reach blood or tissue

concentrations in the host that are sufficient to

inhibit growth of the organism. These reported

results are based on predetermined breakpoints

that classify the organism as susceptible,

intermediate, or resistant to a particular drug.

Many times, these breakpoints are determined in

human medicine and then carried over into

veterinary medicine, and may even be applied to

unrelated organisms. The actual organism tested

may behave differently than the organism for

which the breakpoint was developed.

Quantitative results are reported as minimal

inhibitory concentrations (MIC) in ìg/mL. The

MIC is the minimum concentration of an

antimicrobial necessary to completely inhibit

growth of the organism tested. The results of

quantitative tests are often collapsed and

interpreted qualitatively (for example, the MIC

below a certain level for a specific drug is

deemed “susceptible”).

3. Assessing

antimicrobial

susceptibility

The disk diffusion test is based on the diffusion

of an antimicrobial agent from a commercially

prepared disk that results in a concentration

gradient that declines with increasing distance

from the disk (Prescott et al., 2000, ch 2). The

disk is placed on culture medium that has been

seeded with a pure culture of the organism to be

tested. A zone of inhibition is formed around the

disk, with the border of the zone being the point

at which the antimicrobial concentration

becomes too low to inhibit growth of the

bacterium. The larger the zone of inhibition, the

smaller the concentration of that drug needed to

inhibit the bacterium. It is important to note that

the zone of inhibition for one drug cannot be

compared to that of another drug. The zone of

inhibition for one drug may be relatively small

(compared to other drugs), but is still classified

as susceptible. Conversely, another drug may

have a relatively large zone of inhibition, but the

organism may be considered resistant. The

organism can only be classified as susceptible,

intermediate, or resistant to a specific drug

based upon previously determined breakpoints

for that drug. Disk diffusion is the antimicrobial

susceptibility test most widely used in veterinary

medicine. The disadvantage is that the results

can usually only be reported qualitatively, and

the specific drug concentrations that are

necessary to inhibit growth cannot be

determined with this test.
USDA APHIS VS / 11

Section I: Antimcrobial Drug Use and Resistance—B. Antimicrobial Resistance

Agar dilution uses agar growth medium that is

produced with a known concentration of

antimicrobial drug in it (Prescott et al., 2000,

ch 2). A series of agar plates with known

dilutions are used to determine at what

concentration of antimicrobial drug the bacterial

growth will be inhibited.

Broth microdilution is also a quantitative test,

and is being used more frequently in veterinary

laboratories (Prescott et al., 2000, ch 2). The

test uses microdilution plates with

antimicrobials of known concentration in twofold dilutions. The isolated bacterium is

suspended in broth or saline and diluted to a

known concentration and then added to all of

the wells. The microdilution plates are then

incubated for 16 to 20 hours and the MIC is

determined by the lowest concentration of

antimicrobial needed to inhibit growth of the

bacterium.

DNA-based techniques such as polymerase

chain reaction (PCR) are now able to detect

resistance genes within bacterial populations

(Mascaretti, 2003, ch 5). Since this technique is

still being developed and is quite expensive, it is

not yet widely used. Microarrays are also being

used to screen bacteria for a number of genes,

including those coding for antimicrobial

resistance.

In vitro tests may not always be able to predict

the susceptibility of an organism in vivo. In vivo,

many conditions play a role in whether a strain

is considered susceptible or resistant. The

location of the infection, the dosage and mode

of administration of the drug, tissue distribution

of the drug, and the state of the immune system

of the individual animal being treated must all

be considered. This is why clinical in vivo

studies must be combined with in vitro

susceptibility tests to predict the efficacy of

antimicrobials in the host. After the appropriate

antimicrobial has been determined, the ultimate

test is the host’s response to treatment. If the

host is not responding, the course of treatment

must be reevaluated.
12 / Beef 2007–08

Section I: Antimcrobial Drug Use and Resistance—B. Antimicrobial Resistance

4. Why

antimicrobial

resistance is a

concern

The short generation times of bacterial

organisms, combined with their ability to

mutate and transfer genetics, can lead to rapid

production of resistant populations. Until

recently, antimicrobial resistance could

generally be overcome with the development of

new antimicrobials. Unfortunately, the

development of new antimicrobials has slowed

due to the tremendous expense of research,

development, and long-term clinical trials.

In 1998, the American Veterinary Medical

Association (AVMA) approved the Judicious

Use of Antimicrobial Therapy policy (AVMA,

2008). The goal of this policy is to preserve the

therapeutic efficacy of antimicrobials and to

ensure the current and future availability of

veterinary antimicrobials. The AVMA

recognized the need for improved monitoring

and feedback systems for antimicrobial use and

resistance patterns as well as more research to

improve scientifically based therapeutic

practices. Many of the veterinary species

specialty groups have also developed judicious

use guidelines and distributed them to their

members. For example, “A Beef Producers

Guide for Judicious Use of Antimicrobials in

Cattle” provides the following guidelines:*

1. Prevent Problems: Emphasize appropriate

husbandry and hygiene, routine health

examinations, and vaccinations.

2. Select and Use Antibiotics Carefully: Consult

with the herd veterinarian on the selection and

use of antibiotics. Have a valid reason to use an

antibiotic. Therapeutic alternatives should be

considered prior to using antimicrobial therapy.

3. Avoid Using Antibiotics Important In Human

Medicine As First Line Therapy: Avoid using as

the first antibiotic those medications that are

important to treating strategic human or animal

infections.

4. Use the Laboratory to Help You Select

Antibiotics: Cultures and susceptibility test

results should be used to aid in the selection of

antimicrobials, whenever possible.

5. Combination Antibiotic Therapy Is

Discouraged Unless There Is Clear Evidence

The Specific Practice Is Beneficial: select and

dose an antibiotic to affect a cure.

6. Avoid Inappropriate Antibiotic Use: Confine

therapeutic antimicrobial use to proven clinical

indications, avoiding inappropriate uses such as

for viral infections without bacterial

complication.

7. Treatment Programs Should Reflect Best Use

Principles: Regimens for therapeutic

antimicrobial use should be optimized using

current pharmacological information and

principles.

8. Treat the Fewest Number of Animals

Possible: Limit antibiotic use to sick or at-risk

animals.

*

 NCBA BQA Train the Trainer Manual. Available at

http://www.bqa.org.
USDA APHIS VS / 13

Section I: Antimcrobial Drug Use and Resistance—B. Antimicrobial Resistance

9. Treat for the Recommended Time Period: To

minimize the potential for bacteria to become

resistant to antimicrobials.

10. Avoid Environmental Contamination with

Antibiotics: Steps should be taken to minimize

antimicrobials reaching the environment through

spillage, contaminated ground runoff or

aerosolization.

11. Keep Records of Antibiotic Use: Accurate

records of treatment and outcome should be

used to evaluate therapeutic regimens and

always follow proper withdrawal times.

12. Follow Label Directions: Follow label

instructions and never use antibiotics other than

as labeled without a valid veterinary

prescription.

13. Extra-label Antibiotic Use Must follow FDA

Regulations: Prescriptions, including extra-label

use of medications must meet the Animal

Medicinal Drug Use Clarification Act

(AMDUCA) amendments to the Food, Drug,

and Cosmetic Act and its regulations. This

includes having a Veterinary/Client/Patient

Relationship.

14. Subtherapeutic Antibiotic Use Is

Discouraged: Antibiotic use should be limited to

prevent or control disease and should not be

used if the principle intent is to improve

performance.

Antibiotic use guidelines

1. Strictly follow all recommendations and

guidelines from herd veterinarian for selection

of products.

2. Follow label directions for use of product.

Use product at recommended dosage for

required time period. Treatment regimens must

comply with label directions unless otherwise

prescribed by a veterinarian. If drugs are to be

used in an extra-label manner, that must be done

under the prescription or direct supervision of a

licensed veterinarian. All cattle treated in an

extra-label manner must comply with prescribed

withdrawal times, which have been set by a herd

veterinarian under the guidelines of a

Veterinarian-Client-Patient Relationship

(VCPR).*

The BQA program does not support/recommend

extra-label drug use (ELDU) for injectable

aminoglycosides (such as neomycin, gentamicin

or kanamycin) because of the potential violative

residues related to extremely long withdrawal

times. Some studies have shown withdrawal

times on these types of products could be as

long as 18 months.

3. Accurately calculate dose requirements based

on the animal’s weight and the specific health

problem being treated. Providing the same drug

simultaneously by injection, feed or water may

result in overdosing and, thereby, create a

residue problem.

*A valid VCPR is defined as one in which:

1. A veterinarian has assumed the responsibility for making medical judgments regarding the health of (an) animal(s) and the need for medical

treatment, and the client (the owner of the animal or animals or other caretaker) has agreed to follow the instructions of the veterinarian;

2. There is sufficient knowledge of the animal(s) by the veterinarian to initiate at least a general or preliminary diagnosis of the medical condition

of the animal(s); and

3. The practicing veterinarian is readily available for follow-up in case of adverse reactions or failure of the regimen of therapy.

Such a relationship can exist only when the veterinarian has recently seen and is personally acquainted with the keeping and care of the animal(s)

by virtue of examination of the animal(s), and/or by medically appropriate and timely visits to the premises where the animal(s) are kept.
14 / Beef 2007–08

Section I: Antimcrobial Drug Use and Resistance—B. Antimicrobial Resistance

4. When administering injectable products,

follow the Best Management Practices for

Injections.

5. Never administer more than 10 cc per IM

injection site. Exceeding this amount will

increase tissue damage, alter withdrawal time

and may require testing before cattle are

marketed for consumption.

6. Do not mix products prior to administration.

This practice of using “Bloody Mary” mixes is

compounding use and will result in

undetermined withdrawal periods.

7. All animals treated for problems unique to the

individual animal should be recorded by the

animal’s ID, treatment date, drug and dose

administered product serial/lot number,

approximate weight of animal, route and

location of administration, and the earliest date

the animal would clear the prescribed or labeled

withdrawal period. You can record treatments

either by individually identifying each animal in

your herd and/or individually identifying each

animal when or if they are treated. The ID

number should be unique to that animal and tie

it to the group from which it came.

8. A special note for producers who do not

individually identify animals: Identifying each

animal individually is not required to participate

in this program. Cattle can be identified by

group. However, if treated cattle are not

individually identified, then the entire group

must be managed together until the appropriate

withdrawal times have elapsed for every animal

in the group. The withdrawal time applies to the

entire group of animals.

For example, let’s say several calves develop

scours and numerous calves are treated within a

10-day period. The entire group of calves would

receive a withdrawal date based on the last date

of administration of the product (to any

individual animal) with the longest withdrawal

period. The complete history of product use

should be available for transfer when the group

of cattle is sold or moved to the next production

unit within an operation.

Otherwise, the buyer (or the foreman of the

other unit) will not be aware of when those

calves can safely enter the marketing chain. For

example, when a stocker operator culls his

nonperforming steers any time during the course

of a grazing period, those animals could

potentially be sent to a packer. If the stocker

operator is unaware that the prior owner treated

the animal with an antibiotic whose withdrawal

time has not expired, he might have

unknowingly contributed to a violative residue

problem.

9. All animals treated as part of a group will be

identified by group or lot with treatment

information recorded. Records should include

the animal lot or group identification,

processing/treatment date, product serial/lot

number, product and dose administered, route

and location of administration, name of person

who administered it and withdrawal information.

Recording animals under this system assumes

that every animal in the lot or group received the

treatment.
USDA APHIS VS / 15

Section I: Antimcrobial Drug Use and Resistance—B. Antimicrobial Resistance

10. All cattle marketed from the operation can

potentially go directly to harvest. Therefore,

records for any cattle to be marketed should be

checked by personnel to ensure that treated

animals will meet or exceed label withdrawal

times for all products administered. A release

slip should be signed and dated by the person

who checks records prior to shipping cattle from

the operation. The examination should include

processing records, feeding records, treatment

records and all other records that may apply.

11. Extended withdrawal times should be

expected for emaciated or severely debilitated

animals. All cattle sold that are not typical of the

herd (medicated market cows/bulls and realizer

cattle) may be subject to verification of drug

withdrawal. (Realizers are animals with a health

problem that get culled because they never

recover.) Should there be any question about

withdrawal period, the veterinarian will evaluate

the treatment history against information

provided by the Food Animal Residue

Avoidance Databank and the animal may have

to pass a residue screening test, such as the Live

Animal Swab Test (LAST), which tests for

antibiotic residues. Residue screening will be

performed by qualified personnel under the

supervision of a veterinarian. The results will

determine whether the animals can be released

for shipment, but cannot be used to shorten the

labeled withdrawal time. Attempting to salvage

sick animals by treatment and prompt harvest

requires an accurate diagnosis and careful

selection of drugs.

12. Make sure that all employees are aware of

the proper use and administration of antibiotics

and withdrawal times, and they have the ability

to check appropriate withdrawal restrictions

before moving cattle to market. For example,

provide employees with charts or software to

help them track withdrawal dates.
16 / Beef 2007–08

Section I: Antimcrobial Drug Use and Resistance—B. Antimicrobial Resistance

5. Foodborne

illness

Foodborne illnesses are defined as diseases

caused by agents that enter the body through the

ingestion of food. It has been reported that up to

30 percent of the human population in

industrialized nations suffers from foodborne

illness each year. It is estimated that each year in

the United States there are 47.8 million cases of

foodborne illness, resulting in 127,839

hospitalizations and 3,037 deaths (Scallan,

2011a, 2011b). Norovirus, nontyphoidal

Salmonella spp., Clostridium perfringins,

Campylobacter spp., and Staphylococcus aureus

account for over 90 percent of domestically

acquired foodborne illness cases in the United

States (Scallan, 2011b). The health-related cost

of foodborne illness in the United States is

estimated to be $152 billion annually (Scharff,

2010).

Salmonella, Campylobacter, and E. coli are

three of the bacterial organisms that most

commonly cause foodborne illness. If bacteria

with resistance genes are present in farm

animals, it is possible these may get transferred

to humans through food consumption (by meat

contaminated during slaughter) or direct contact.

If organisms can survive and be transferred from

farm animals to the human gastrointestinal tract,

the resistance genes contained by the organism

can also be transferred.

6. Complexity of

antimicrobial

resistance

Antimicrobial resistance is a complex issue.

There are many factors that can affect the

frequency of occurrence of bacterial organisms

with resistance determinants among bacterial

populations. These factors include exposure to

antimicrobial drugs and exposure to metals,

disinfectants, and other environmental

conditions that affect the fitness of certain

strains of bacteria that may also possess

resistance genes. Furthermore, bacterial

populations resistant to antimicrobial drugs may

reside in a number of different subpopulations.

Bacteria can be transferred among these

subpopulations through any number of routes,

eventually ending up in other subpopulations

either transiently or established for the long

term.
USDA APHIS VS / 17

Section II: Population Estimates—Antimicrobial Resistance

Section II: P Section II: Population opulation

Estimates*

*Note: Estimates in Section II are based on producer responses to questionnaires completed during both Phase I and Phase II of the study. These responses were weighted to reflect

the inference population for which they were selected. Additional details are presented in Section IV.

Antimicrobial Drug Use

1. Antibiotics and

decoquinate/

ionophores in feed

Antibiotics may be incorporated into cattle feed

at rates specified by the U.S. Food and Drug

Administration to control, prevent, or treat

disease. These specified rates are determined

during the approval process, prior to marketing

the antibiotic. Subsequently, feed mills and

producers are required to use the products as

indicated on their labels.

Decoquinate is used in feed to prevent or treat

coccidiosis. Ionophores such as monensin and

lasalocid are used in feed to prevent coccidiosis

and improve feed efficiency.1 Again, these

products can be used only according to the

specifications on the products’ labels.

Overall, the majority of operations

(81.3 percent) did not use antibiotics or

decoquinate/ionophores in cattle feed to prevent

disease or promote growth. A higher percentage

of operations with 1 to 49 beef cows

(86.2 percent) did not use either type of additive

in feed compared with operations with 200 or

more beef cows (57.8 percent).

a. Percentage of operations that used the following additives in cattle feed to 

prevent disease and/or promote growth, by herd size 

Percent Operations 

Herd Size (number of beef cows)

1–49 50–99 100–199 200 or more 

All 

operations 

and all 

classes of 

cattle 

Additives 

in feed used Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error 

Antibiotics with 

or without 

decoquinate or 

ionophores 

11.9 (2.7) 22.1 (4.7) 24.9 (4.5) 31.6 (4.7) 15.8 (2.1) 

Decoquinate/ 

ionophores only 1.9 (1.0) 4.4 (1.9) 3.5 (1.8) 10.6 (2.9) 2.9 (0.8) 

Neither 86.2 (2.8) 73.5 (5.0) 71.6 (4.8) 57.8 (5.0) 81.3 (2.2) 

Total 100.0 100.0 100.0 100.0 100.0 

1

1

In collecting the data for this section, producers were asked about their use of “antibiotics in feed to prevent disease and/or promote growth.” Data collectors were instructed to

include products such as decoquinate or ionophores under the general term “antibiotics” for this question. However, it is possible that some producers may not have reported use of

decoquinate or ionophores, even though they were used, because many do not consider these products to be true antibiotics. (Ionophores are antibiotics; however, decoquinate is not

an antibiotic but was considered an antibiotic for the purpose of this question.)
18 / Beef 2007–08

Section II: Population Estimates—Antimicrobial Drug Use

In the West region, 94.6 percent of operations

did not use antibiotics or decoquinate/

ionophores in cattle feed to treat disease or

b. Percentage of operations that used the following additives in cattle feed to 

prevent disease and/or promote growth, by region 

Percent Operations 

Region 

West Central Southeast 

Additives 

in feed used Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error 

Antibiotics with or 

without decoquinate 

or ionophores 

4.1 (1.4) 28.0 (4.2) 12.8 (2.6) 

Decoquinate/ 

ionophores only 1.3 (0.6) 6.7 (2.3) 1.7 (0.8) 

Neither 94.6 (1.6) 65.3 (4.5) 85.5 (2.7) 

Total 100.0 100.0 100.0 

promote growth. Use of one or the other product

was most common in the Central region, where

34.7 percent of operations used one or both

types.

Photograph courtesy of Anson Eaglin.
USDA APHIS VS / 19

Section II: Population Estimates—Antimicrobial Drug Use

Producers were asked whether antibiotics with

or without decoquinate/ionophores were used in

feed to prevent respiratory diseases, promote

growth, or for other reasons. Overall, 10.7, 10.7,

and 13.0 percent of operations used antibiotics

in feed for any reason in preweaned calves,

weaned replacement heifers, and other weaned

calves, respectively. For weaned calves,

4.1 percent and 5.3 percent of all operations

used antibiotics in feed to promote growth in

replacement heifers and other weaned calves,

respectively.

c. Percentage of operations that used antibiotics with or without decoquinate/ 

ionophores or that used decoquinate/ionophores only in the feed of the 

following cattle classes, by primary purpose of use and by herd size 

Percent Operations 

Herd Size (number of beef cows)

1-49 50-99 100-199 200 or more 

All 

operations 

Primary 

purpose Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error 

Preweaned calves 

Prevent 

respiratory 

disease 

9.1 (2.4) 10.1 (3.2) 8.5 (3.0) 5.3 (2.0) 9.0 (1.7) 

Other 1.4 (0.9) 5.1 (2.3) 4.5 (1.9) 5.0 (1.7) 2.5 (0.7) 

Any 10.0 (2.4) 14.0 (3.8) 10.8 (3.2) 9.1 (2.5) 10.7 (1.8) 

Replacement heifers weaned but not yet calved 

Prevent 

respiratory 

disease 7.7 (2.1) 12.4 (3.8) 15.5 (3.5) 19.8 (4.4) 9.8 (1.6) 

Promote 

growth 2.8 (1.4) 5.3 (2.4) 5.6 (1.8) 15.8 (4.0) 4.1 (1.1) 

Other 0.0 (0.0) 0.1 (0.1) 2.7 (1.4) 3.6 (1.1) 0.5 (0.1) 

Any 7.7 (2.1) 13.9 (3.9) 17.5 (3.6) 27.6 (4.6) 10.7 (1.6) 

Other calves weaned but not yet shipped for feeding or sold as breeding stock 

Prevent 

respiratory 

disease 7.7 (2.0) 21.5 (4.7) 16.9 (3.7) 29.5 (4.8) 11.9 (1.7) 

Promote 

growth 3.2 (1.5) 7.3 (2.7) 8.3 (2.7) 21.3 (4.5) 5.3 (1.2) 

Other 0.0 (0.0) 1.5 (1.0) 1.4 (1.4) 5.6 (1.6) 0.7 (0.2) 

Any 7.9 (2.0) 23.6 (4.8) 19.3 (4.0) 36.0 (4.9) 13.0 (1.7) 
20 / Beef 2007–08

Section II: Population Estimates—Antimicrobial Drug Use

Of the 15.8 percent of operations that used

antibiotics with or without decoquinate/

ionophores in cattle feed to prevent disease and/

or promote growth (see Section II, table 1.a.),

50.9 percent used them in the feed of any

preweaned calves to prevent respiratory disease.

A higher percentage of small operations with 1

to 49 beef cows used antibiotics in the feed of

preweaned calves to prevent respiratory disease

compared with operations with 200 or more beef

cows. Nearly two-thirds of operations (61.0

percent) used antibiotics in the feed of any

replacement heifers weaned but not yet calved

to prevent respiratory disease. For other weaned

calves not yet shipped, nearly three of four

operations (73.5 percent) used antibiotics in

feed to prevent respiratory disease.

d. For the 15.8 percent of operations that used antibiotics with or without 

decoquinate/ionophores in cattle feed, percentage of operations that used 

antibiotics for the following cattle classes, by primary purpose of use and by 

herd size 

Percent Operations* 

Herd Size (number of beef cows)

1-49 50-99 100-199 200 or more 

All 

operations 

Primary 

purpose Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error 

Preweaned calves 

Prevent 

respiratory 

disease 

69.4 (10.6) 37.5 (11.2) 34.0 (9.4) 11.7 (4.7) 50.9 (6.8) 

Other 7.3 (5.3) 4.6 (3.2) 10.0 (5.5) 8.3 (4.2) 7.2 (3.0) 

Any 71.9 (10.5) 40.0 (11.3) 35.1 (9.3) 18.7 (6.1) 53.7 (6.7) 

Replacement heifers weaned but not yet calved 

Prevent 

respiratory 

disease 

65.8 (11.5) 56.2 (11.5) 59.0 (9.2) 52.5 (9.1) 61.0 (6.6) 

Promote 

growth 21.2 (10.8) 12.3 (6.3) 6.5 (3.7) 16.7 (8.6) 16.3 (5.8) 

Other 0.0 (—) 0.7 (0.7) 9.4 (5.3) 4.9 (2.3) 2.1 (0.9) 

Any 65.8 (11.5) 59.4 (11.4) 62.1 (9.2) 55.5 (8.9) 62.6 (6.5) 

Other calves weaned but not yet shipped for feeding or sold as breeding stock 

Prevent 

respiratory 

disease 

65.6 (11.7) 92.8 (4.7) 61.4 (9.4) 83.5 (5.8) 73.5 (6.4) 

Promote 

growth 22.9 (10.9) 17.0 (7.4) 13.9 (6.9) 34.5 (9.9) 21.4 (6.0) 

Other 0.0 (—) 0.0 (—) 5.6 (5.4) 6.8 (2.9) 1.6 (0.9) 

Any 65.6 (11.7) 95.3 (4.0) 65.0 (9.2) 85.1 (5.6) 74.8 (6.4) 

*Note that due to the small number of reports estimates are associated with large standard errors. 
USDA APHIS VS / 21

Section II: Population Estimates—Antimicrobial Drug Use

As shown in Section II, table 1.a., only 2.9

percent of operations used only decoquinate/

ionophores as a feed additive to prevent disease

and/or promote growth. Of these operations,

27.9, 19.5, and 28.6 percent used decoquinate/

ionophores to prevent respiratory disease in

preweaned calves, weaned replacement heifers,

and other weaned calves, respectively.

e. For the 2.9 percent of operations that used only decoquinate/ionophores in 

cattle feed, percentage of operations that used decoquinate/ionophores for the 

following cattle classes, by primary purpose of use and by herd size 

Percent Operations 

Herd Size (number of beef cows)

1-49 50-99 100-199 200 or more 

All 

operations 

Primary 

purpose Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error 

Preweaned calves 

Prevent 

respiratory 

disease 

32.7 (25.7) 41.8 (23.2) 0.0 (—) 14.8 (11.1) 27.9 (13.6) 

Other 29.6 (24.4) 52.1 (22.9) 12.3 (12.3) 14.6 (7.1) 30.3 (12.7) 

Any 62.3 (24.0) 76.8 (19.8) 12.3 (12.3) 29.4 (12.3) 54.0 (13.3) 

Replacement heifers weaned but not yet calved 

Prevent 

respiratory 

disease 

24.6 (21.7) 0.0 (—) 23.6 (21.1) 29.9 (15.4) 19.5 (10.9) 

Promote 

growth 24.6 (21.7) 16.7 (15.7) 36.0 (23.6) 72.1 (10.8) 32.9 (11.9) 

Other 0.0 (—) 0.0 (—) 0.0 (—) 16.5 (8.2) 3.1 (1.7) 

Any 24.6 (21.7) 16.7 (15.7) 36.0 (23.6) 83.9 (8.6) 35.2 (12.1) 

Other calves weaned but not yet shipped for feeding or sold as breeding stock 

Prevent 

respiratory 

disease 

24.6 (21.7) 23.2 (19.8) 54.0 (26.2) 29.9 (15.4) 28.6 (11.9) 

Promote 

growth 37.6 (24.0) 39.9 (22.2) 69.6 (24.8) 65.7 (13.2) 47.1 (13.5) 

Other 0.0 (—) 18.3 (17.0) 0.0 (—) 23.4 (10.4) 8.9 (5.1) 

Any 37.6 (24.0) 58.2 (23.2) 100.0 (—) 76.8 (11.6) 57.0 (14.3) 
22 / Beef 2007–08

Section II: Population Estimates—Antimicrobial Drug Use

Across all cattle classes, nearly 9 of 10

operations did not use any of the following

primary feed additives for any purpose. For both

preweaned calves and replacement heifers,

f. Percentage of operations in which additives were used in the feed of the following cattle 

classes, by primary purpose of use and by primary additive 

Percent Operations 

Primary Additive 

Tetracyclines Peptides 

Combinations/ 

other 

Decoquinates/ 

ionophores 

Fed but 

unknown 

type None fed 

Primary 

purpose Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Total 

Preweaned calves 

Prevent 

respiratory 

disease

6.5 (1.4) 0.7 (0.7) 0.7 (0.5) 1.0 (0.5) 0.1 (0.1) 91.0 (1.7) 100.0 

Other 0.8 (0.4) 0.0 (—) 0.2 (0.2) 1.4 (0.5) 0.1 (0.1) 97.5 (0.7) 100.0 

Any 6.7 (1.4) 0.7 (0.7) 0.9 (0.5) 2.2 (0.7) 0.1 (0.1) 89.3 (1.8) 

Replacement heifers weaned but not yet calved 

Prevent 

respiratory 

disease 

7.6 (1.4) 0.0 (—) 0.9 (0.3) 0.6 (0.4) 0.7 (0.7) 90.2 (1.6) 100.0 

Promote 

growth 1.7 (0.7) 0.0 (—) 0.0 (0.0) 1.7 (0.5) 0.8 (0.7) 95.8 (1.1) 100.0 

Other 0.3 (0.1) 0.0 (—) 0.0 (—) 0.1 (0.1) 0.1 (0.1) 99.5 (0.1) 100.0 

Any 7.7 (1.4) 0.0 (—) 0.9 (0.3) 1.7 (0.5) 0.8 (0.7) 89.3 (1.8) 

Other calves weaned but not yet shipped for feeding or sold as breeding stock 

Prevent 

respiratory 

disease 

8.7 (1.4) 0.0 (—) 1.6 (0.5) 0.8 (0.4) 0.8 (0.7) 88.1 (1.7) 100.0 

Promote 

growth 2.1 (0.7) 0.0 (—) 0.4 (0.2) 2.1 (0.6) 0.7 (0.7) 94.7 (1.2) 100.0 

Other 0.1 (0.0) 0.1 (0.1) 0.0 (0.0) 0.4 (0.2) 0.0 (0.0) 99.4 (0.2) 100.0 

Any 8.8 (1.4) 0.1 (0.1) 1.7 (0.5) 2.5 (0.6) 0.8 (0.7) 87.0 (1.7) 

87.3 percent of operations did not feed any

feed additives for any purpose. Similarly,

87.0 percent did not use feed additives for

other calves for any purpose.
USDA APHIS VS / 23

Section II: Population Estimates—Antimicrobial Drug Use

The 9.0 percent of operations that used

antibiotics in the feed of preweaned calves to

prevent respiratory disease (see Section II, table

1.c.) included the antibiotics in the feed for an

average of 127.4 days. A similar average

duration (119.4 days) was used among the

9.8 percent of operations that included

antibiotics in the feed of weaned replacement

heifers to prevent respiratory disease. For

prevention of respiratory disease in other

weaned calves, the average duration of inclusion

for the 11.9 percent of operations using this

practice was 92.5 days. While there are

numerical differences in the duration of

inclusion of antibiotics in the feed for different

purposes by type of cattle, these differences are

not significantly different based on statistical

analysis.

g. For operations that used antibiotics with or without decoquinate/ionophores or 

only decoquinate/ionophores in cattle feed, operation average number of days 

that antibiotics or decoquinate/ionophores were used for the following cattle 

classes, by primary purpose of use 

Operation Average Number of Days1

Antibiotics2 Decoquinate/ionophores only 

Primary purpose Number Std. error Number Std. error 

Preweaned calves 

Prevent respiratory disease 127.4 (29.8) 125.9 (48.6) 

Other 106.1 (30.6) 102.5 (9.8) 

Replacement heifers weaned but not yet calved 

Prevent respiratory disease 119.4 (29.3) 146.5 (98.9) 

Promote growth 76.1 (32.0) 140.8 (32.0) 

Other 28.2 (15.6) 86.0 (32.4) 

Other calves weaned but not yet shipped for feeding or sold as breeding stock 

Prevent respiratory disease 92.5 (24.2) 109.1 (60.8) 

Promote growth 53.6 (15.0) 172.2 (45.2) 

Other 62.4 (17.1) 140.9 (67.7) 

1

Note: Due to the relatively low number of operations reporting the use of these practices and the wide 

variation in the reported values for duration of inclusion in feed, the estimates in this table are associated 

with large standard error values. The effect is a lack of precision for the estimates that are reported here.

2

With or without decoquinate. 
24 / Beef 2007–08

Section II: Population Estimates—Antimicrobial Drug Use

The 18.7 percent of operations that used

antibiotics with or without decoquinate/

ionophores or only decoquinate/ionophores in

feed to prevent disease and/or promote growth

(see Section II, table 1.a.) reported a variety of

influences when deciding which additives to

use. Similar percentages of operations cited

local veterinary practitioners, suppliers other

than veterinarians, trade journals, and other

producers as primary influences on additive use

for prevention of respiratory disease or growth

promotion. Few operations reported that

consulting or second-opinion veterinarian was

the primary influence on additive choice. This

finding is likely due to the relatively low use of

consulting veterinarians on beef cow-calf

operations compared with the use of local

private veterinary practitioners.

h. For the 18.7 percent of operations that used antibiotics with or without decoquinate/ionophores 

or only decoquinate/ionophores in feed to prevent disease and/or promote growth, percentage of 

operations that used them in the following cattle classes, by primary purpose of use and by 

primary influence on decision about which to use 

Percent Operations 

Primary Influence 

Trade 

journals 

Other 

producers 

Local 

veterinary 

practitioner 

Consulting 

or secondopinion 

veterinarian 

Supplier of 

antibiotics 

other than 

veterinarian Other 

No other 

influence 

Primary 

purpose Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Total 

Preweaned calves 

Prevent 

respiratory 

disease 

9.8 (6.0) 14.6 (6.7) 32.1 (9.9) 0.1 (0.1) 37.2 (9.6) 0.0 (—) 6.2 (3.1) 100.0 

Other 0.0 (—) 0.0 (—) 12.6 (5.8) 0.0 (—) 66.2 (13.7) 0.0 (—) 21.2 (13.6) 100.0 

Replacement heifers weaned but not yet calved 

Prevent 

respiratory 

disease 

13.1 (6.2) 11.2 (5.6) 34.5 (8.4) 1.4 (0.9) 21.9 (5.9) 9.0 (5.4) 8.9 (3.6) 100.0 

Promote 

growth 10.3 (9.9) 2.9 (1.8) 27.9 (14.2) 2.3 (2.0) 31.6 (10.4) 18.7 (11.9) 6.3 (4.0) 100.0 

Other 0.0 (—) 0.0 (—) 43.4 (15.0) 0.0 (—) 36.8 (17.9) 9.5 (6.9) 10.3 (6.7) 100.0 

Other calves weaned but not yet shipped for feeding or sold as breeding stock 

Prevent 

respiratory 

disease 

8.4 (4.4) 12.0 (5.1) 32.0 (7.3) 2.3 (1.3) 25.1 (5.5) 7.5 (4.5) 12.7 (3.6) 100.0 

Promote 

growth 9.3 (7.8) 4.2 (2.6) 33.7 (11.5) 4.2 (2.9) 26.8 (8.2) 14.3 (9.4) 7.5 (3.6) 100.0 

Other 0.0 (—) 1.6 (1.7) 38.9 (16.7) 0.0 (—) 48.0 (17.3) 1.7 (1.8) 9.8 (5.8) 100.0 
USDA APHIS VS / 25

Section II: Population Estimates—Antimicrobial Drug Use

Of the 18.7 percent of operations that used

antibiotics with or without decoquinate/

ionophores or only decoquinate/ ionophores in

feed to prevent disease and/or promote growth

(see Section II, table 1.a.), the highest

percentage used tetracyclines as the primary

additive to prevent respiratory disease across all

cattle classes. Similar percentages of operations

used decoquinate/ionophores or tetracyclines as

the primary additives used for growth

promotion.

i. For the 18.7 percent of operations that used antibiotics with or without 

decoquinate/ionophores or only decoquinate/ionophores in feed to prevent disease and/or 

promote growth, percentage of operations that used them in the following cattle classes, by 

primary purpose of use and by primary additive 

Percent Operations 

Primary Additive 

Tetracyclines Peptides 

Combinations/ 

other 

Decoquinates/ 

ionophores 

Fed but 

unknown type 

Primary 

purpose Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Total 

Preweaned calves 

Prevent 

respiratory 

disease

72.3 (9.4) 8.0 (7.5) 7.9 (5.5) 10.9 (5.5) 0.9 (0.8) 100.0 

Other 33.9 (13.9) 0.0 (—) 9.0 (8.0) 54.6 (14.5) 2.5 (2.5) 100.0 

Replacement heifers weaned but not yet calved 

Prevent 

respiratory 

disease 

77.0 (7.7) 0.0 (—) 9.6 (3.5) 5.8 (3.5) 7.6 (7.1) 100.0 

Promote 

growth 40.5 (13.0) 0.0 (—) 0.3 (0.3) 40.2 (12.1) 19.0 (15.1) 100.0 

Other 55.6 (15.4) 0.0 (—) 0.0 (—) 29.4 (12.3) 15.0 (10.5) 100.0 

Other calves weaned but not yet shipped for feeding or sold as breeding stock 

Prevent 

respiratory 

disease 

72.9 (6.8) 0.0 (—) 13.4 (3.9) 7.0 (3.3) 6.7 (5.9) 100.0 

Promote 

growth 39.7 (10.7) 0.0 (—) 7.1 (3.9) 39.2 (10.1) 14.0 (12.3) 100.0 

Other 8.6 (5.4) 21.1 (16.4) 3.3 (3.3) 63.5 (16.5) 3.5 (3.5) 100.0 
26 / Beef 2007–08

Section II: Population Estimates—Antimicrobial Drug Use

2. Use of oral or

injectable

antibiotics for

disease treatment

Antibiotics are used to both prevent and treat

disease. Antibiotics used to treat disease can be

administered orally (in feed, water, or directly to

individual animals, e.g., boluses) or injected.

More than two of three operations

(68.0 percent) used oral or injectable antibiotics

to treat disease in any cattle or calves.

Operations with 1 to 49 beef cows were less

likely to use oral or injectable antibiotics to treat

any cattle or calves than operations with 50 or

more beef cows. This difference could be a

reflection of the decreased likelihood of disease

occurrence when fewer animals are present,

thereby decreasing the indication for antibiotic

use for treatment.

a. Percentage of operations that used oral or injectable antibiotics to treat 

disease, by herd size 

Percent Operations 

Herd Size (number of beef cows)

1–49 50–99 100–199 200 or more 

All 

operations 

Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error 

58.2 (4.4) 89.1 (3.6) 90.8 (3.0) 92.4 (3.2) 68.0 (3.2) 

The Southeast region had a lower percentage of

operations that used oral or injectable antibiotics

to treat disease compared with the Central

region.

b. Percentage of operations that used oral or injectable antibiotics to treat 

disease, by region 

Percent Operations 

Region 

West Central Southeast 

Percent Std. error Percent Std. error Percent Std. error 

76.3 (5.0) 86.1 (3.9) 60.2 (4.5) 
USDA APHIS VS / 27

Section II: Population Estimates—Antimicrobial Drug Use

In unweaned calves, a higher percentage of

operations with 50 or more beef cows than

operations with 1 to 49 beef cows used

antibiotics to treat pinkeye and respiratory and

digestive diseases in unweaned calves.

c. Percentage of operations that treated unweaned calves and replacement 

heifers weaned but not yet calved with oral or injectable antibiotics, by disease 

treated and by herd size 

Percent Operations 

Herd Size (number of beef cows)

1-49 50-99 100-199 200 or more 

All 

operations 

Disease Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error 

Unweaned calves 

Pinkeye 24.4 (3.7) 45.5 (6.2) 43.8 (5.8) 49.0 (5.4) 30.9 (2.9) 

Respiratory 

disease 31.6 (4.0) 69.2 (5.8) 70.9 (6.1) 79.6 (4.2) 43.8 (3.2) 

Digestive 

disease 20.8 (3.7) 46.5 (6.3) 41.4 (5.6) 57.8 (5.4) 28.8 (2.8) 

Other 5.2 (1.7) 10.6 (3.4) 5.5 (2.0) 13.1 (3.6) 6.5 (1.3) 

Replacement heifers weaned but not yet calved 

Pinkeye 17.6 (3.2) 28.9 (5.4) 33.9 (5.4) 37.6 (5.3) 22.0 (2.5) 

Respiratory 

disease 21.4 (3.5) 42.0 (6.4) 41.5 (5.7) 58.1 (5.2) 28.5 (2.8) 

Other 4.0 (1.5) 11.5 (4.1) 11.0 (3.0) 14.6 (3.0) 6.4 (1.3) 

Similarly, operations with 50 or more beef cows

were more likely than operations with 1 to 49

beef cows to use oral or injectable antibiotics to

treat replacement heifers for respiratory disease.
Section II: Population Estimates—Antimicrobial Drug Use

28 / Beef 2007-08
USDA APHIS VS / 29

Section II: Population Estimates—Antimicrobial Drug Use

A higher percentage of operations in the Central

region used antibiotics to treat respiratory

disease in unweaned calves compared with

operations in the other two regions.

d. Percentage of operations that treated unweaned calves and replacement 

heifers weaned but not yet calved with oral or injectable antibiotics, by disease 

treated and by region 

Percent Operations 

Region 

West Central Southeast 

Disease Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error 

Unweaned calves 

Pinkeye 30.2 (6.3) 44.7 (5.0) 25.8 (3.7) 

Respiratory disease 39.4 (6.5) 66.9 (5.0) 35.8 (4.2) 

Digestive disease 33.4 (6.1) 47.3 (5.0) 21.3 (3.6) 

Other 10.3 (4.3) 8.7 (2.3) 5.1 (1.7) 

Replacement heifers weaned but not yet calved 

Pinkeye 23.9 (5.7) 29.2 (4.6) 19.1 (3.2) 

Respiratory disease 32.5 (6.0) 38.3 (4.9) 24.3 (3.6) 

Other 6.7 (2.0) 8.9 (2.5) 5.4 (1.7) 
30 / Beef 2007–08

Section II: Population Estimates—Antimicrobial Drug Use

Of operations that used oral or injectable

antibiotics to treat specific diseases, the highest

percentage cited the local veterinary practitioner

as the primary influence when deciding which

antibiotics to use.

e. For operations that used oral or injectable antibiotics to treat unweaned calves and 

replacement heifers weaned but not yet calved, percentage of operations by disease treated 

and by primary influence on decision about which antibiotics to use 

Percent Operations 

Primary Influence 

Trade 

journals 

Other 

producers 

Local 

veterinary 

practitioner 

Consulting or 

secondopinion 

veterinarian 

Supplier of 

antibiotics 

other than 

veterinarian Other 

No other 

influence 

Disease Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Total 

Unweaned calves 

Pinkeye 0.1 (0.1) 3.1 (1.5) 63.9 (5.1) 3.0 (1.5) 13.2 (4.0) 3.9 (1.7) 12.8 (3.8) 100.0 

Respiratory 

disease 0.1 (0.1) 4.4 (1.4) 66.1 (4.3) 4.5 (2.0) 11.2 (3.0) 2.4 (1.0) 11.3 (3.1) 100.0 

Digestive 

disease 0.1 (0.1) 9.3 (4.9) 65.1 (5.7) 4.7 (1.9) 10.0 (3.2) 2.4 (1.1) 8.4 (3.5) 100.0 

Other 0.0 (—) 3.3 (2.9) 56.3 (10.6) 5.6 (5.0) 14.1 (9.2) 1.5 (1.2) 19.2 (7.4) 100.0 

Replacement heifers weaned but not yet calved 

Pinkeye 0.1 (0.1) 4.4 (2.1) 62.2 (5.5) 4.0 (2.2) 12.8 (4.4) 7.6 (3.0) 8.9 (3.2) 100.0 

Respiratory 

disease 1.1 (1.0) 9.0 (4.3) 65.2 (5.3) 4.3 (1.9) 10.8 (3.3) 2.8 (1.2) 6.8 (2.7) 100.0 

Other 0.0 (—) 1.0 (0.8) 71.7 (9.6) 0.5 (0.4) 15.2 (9.2) 0.1 (0.1) 11.5 (4.5) 100.0 
USDA APHIS VS / 31

Section II: Population Estimates—Antimicrobial Drug Use

f. Percentage of operations that treated any cattle or calves in 2007 at least once 

with oral or injectable antibiotics for any diseases or disorders, by cattle class 

and by disease treated 

Disease Percent operations Std. error 

Unweaned calves 

Respiratory 22.3 (2.4) 

Digestive 19.3 (2.5) 

Pinkeye 11.3 (1.9) 

Navel 2.6 (0.6) 

Other 3.3 (0.9) 

Any 40.2 (3.2) 

Weaned replacement 

Respiratory 7.7 (1.6) 

Digestive 1.1 (0.6) 

Pinkeye 3.2 (0.9) 

Lameness 1.4 (0.3) 

Other 0.3 (0.2) 

Any 12.9 (2.0) 

Cows 

Respiratory 6.5 (1.5) 

Digestive 2.0 (1.0) 

Pinkeye 8.3 (1.8) 

Reproductive 4.6 (1.2) 

Abortion 0.3 (0.1) 

Lameness 11.3 (1.8) 

Other 2.7 (1.0) 

Any 28.3 (2.9) 
32 / Beef 2007–08

Section II: Population Estimates—Antimicrobial Drug Use

A higher percentage of younger animals

(unweaned calves and replacement heifers) than

mature cows were treated at least once with oral

or injectable antibiotics.

g. Percentage of cattle or calves 

treated at least once with oral or 

injectable antibiotics for any 

diseases or disorders, by cattle 

class 

Cattle class Percent 

treated* Std. error 

Unweaned 

calves 7.2 (0.7) 

Replacement 

heifers weaned 

but not yet 

calved 

6.0 (1.3) 

Cows 1.9 (0.3) 

*Number of treated animals divided by inventory on 

October 1, 2007, for heifers and cows. For unweaned 

calves, the number treated was divided by the number 

of calves weaned or expected to be weaned in 2007. 

On operations that used oral or injectable

antibiotics in 2007 to treat affected/sick animals

for any disease or disorder, 3.8 percent of

unweaned calves were affected with respiratory

disease, and most of these calves (97.0 percent)

were treated with injectable antibiotics. A higher

percentage of unweaned calves with respiratory

disease and other disease were treated with

injectable antibiotics compared to oral

antibiotics.

h. For operations that treated any affected/sick cattle or calves in 2007 with oral 

or injectable antibiotics, percentage of unweaned calves on these operations 

that were affected/sick and percentage of these affected/sick calves treated 

with oral or injectable antibiotics, by disease treated 

Of the affected/sick 

calves, percent treated by 

administration route2

Percent 

affected/sick 

calves1

Oral 

antibiotic 

Injectable 

antibiotic 

Disease Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error 

Respiratory 3.8 (0.6) 7.6 (2.3) 97.0 (1.5) 

Diarrhea/scours or 

other digestive 3.5 (0.5) 60.6 (7.0) 57.4 (8.2) 

Pinkeye 2.2 (0.5) 20.5 (15.7) 77.5 (15.4) 

Navel infection 0.2 (0.1) 36.7 (19.9) 70.2 (21.5) 

Other 0.2 (0.1) 19.3 (11.4) 94.0 (4.5) 

1

Affected calves as a percentage of calves weaned or expected to be weaned during 2007. 

2

Treated calves as a percentage of calves affected. 
USDA APHIS VS / 33

Section II: Population Estimates—Antimicrobial Drug Use

Relatively few operations (less than 10 percent

for any disease) used oral antibiotics to treat

unweaned calves in 2007. When oral antibiotics

were used, the primary antibiotics used were

generally split equally between tetracyclines and

sulfonamides. The use of oral antibiotics was

more common for treating unweaned calves with

diarrhea or other digestive problems than for

other diseases.

Overall, 20.9 percent of operations used

injectable antibiotics to treat some unweaned

calves for respiratory disease in 2007. In most

cases (8.3 percent of all operations and

39.7 percent of those treating) the primary

antibiotic used was tetracycline. Use of

injectable antibiotics for treatment of diarrhea or

other digestive problems in unweaned calves

occurred on 13.4 percent of operations. Most

commonly, tetracycline was used to treat these

calves (4.7 percent of operations). However, on

an estimated 4.0 percent of operations,

fluoroquinolones were the primary antibiotic

used to treat diarrhea or digestive disease in

unweaned calves, which is an illegal use of

fluoroquinolones. The Food and Drug

Administration has approved the use of

fluoroquinolones in cattle for the treatment of

respiratory disease but has prohibited its use for

other indications. The estimate for use of

fluoroquinolones for the treatment of digestive

disease in beef calves is based on producer

responses to a questionnaire. The actual use of

fluoroquinolones for this indication was not

validated nor was there an attempt to determine

the reasons for this use. Given that only 3.5

percent of unweaned calves experienced clinical

diarrhea or other digestive problems and that

only about half of these calves were treated with

an injectable antibiotic (57.4 percent), the

overall number of calves potentially treated with

a fluoroquinolone for an illegal indication is

very small. Some of these calves may have

experienced concurrent respiratory disease

which would be a legal indication for

fluoroquinolone use. Still, the finding suggests a

need to continue to educate beef producers and

veterinarians on appropriate and approved uses

of antibiotics. Such education has been a

component of the Beef Quality Assurance

guidelines distributed by the National

Cattlemen’s Beef Association (see http://

www.bqa.org). Since producers cite

veterinarians as an important source for

information on all uses of antibiotics, including

the selection of antibiotics to use in unweaned

calves with diarrhea or digestive disease, efforts

by veterinary organizations to educate and

encourage their members to help producers

make appropriate choices of antibiotics will

continue to be important.
34 / Beef 2007–08

Section II: Population Estimates—Antimicrobial Drug Use

i. Percentage of operations that used oral or injectable antibiotics to treat unweaned 

calves in 2007, by primary antibiotic used and by disease treated 

Percent Operations 

Disease 

Respiratory 

Diarrhea/ 

scours or 

other 

digestive Pinkeye 

Navel 

infection Other 

Primary antibiotic Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error 

Oral 

Sulfonamides 0.7 (0.2) 3.6 (0.7) 0.1 (0.0) 0.2 (0.1) 0.2 (0.1) 

Tetracyclines 0.8 (0.5) 2.8 (1.2) 1.0 (0.8) 0.0 (—) 0.0 (0.0) 

Aminoglycosides 0.0 (—) 0.5 (0.3) 0.0 (—) 0.0 (—) 0.0 (—) 

None 98.5 (0.5) 93.1 (1.4) 98.9 (0.8) 99.8 (0.1) 99.8 (0.1) 

Total 100.0 100.0 100.0 100.0 100.0 

Injectable 

Sulfonamides 0.0 (0.0) 0.9 (0.7) 0.0 (—) 0.0 (—) 0.0 (—) 

Noncephalosporin 

beta-lactams 1.5 (0.8) 0.2 (0.1) 1.4 (0.6) 0.9 (0.3) 0.2 (0.1) 

Tetracyclines 8.3 (1.7) 4.7 (1.4) 8.8 (1.7) 1.0 (0.4) 2.3 (0.8) 

Aminoglycosides 0.2 (0.2) 0.4 (0.4) 0.1 (0.1) 0.1 (—) 0.0 (—) 

Macrolides 2.7 (0.6) 0.7 (0.3) 0.1 (0.1) 0.0 (0.0) 0.4 (0.3) 

Cephalosporins 1.0 (0.5) 0.6 (0.2) 0.0 (0.0) 0.0 (0.0) 0.1 (0.0) 

Florfenicol 4.7 (1.1) 1.9 (0.6) 0.0 (0.0) 0.1 (0.1) 0.2 (0.1) 

Fluoroquinolones 2.5 (0.8) 4.0 (1.2) 0.0 (—) 0.1 (0.1) 0.0 (—) 

None 79.1 (2.3) 86.6 (2.1) 89.6 (1.8) 97.8 (0.5) 96.8 (0.9) 

Total 100.0 100.0 100.0 100.0 100.0 
USDA APHIS VS / 35

Section II: Population Estimates—Antimicrobial Drug Use

For operations that used oral or injectable

antibiotics in 2007 to treat affected/sick animals

for any disease or disorder, 3.2 percent of

replacement heifers on these operations were

affected with respiratory disease, and the

majority of these heifers (84.4 percent) were

treated with injectable antibiotics. A higher

percentage of replacement heifers with

respiratory disease and lameness/footrot were

treated with injectable antibiotics than were

treated with oral antibiotics.

j. For operations that treated any affected/sick cattle or calves in 2007 with oral or 

injectable antibiotics, percentage of replacement heifers on these operations 

that were affected/sick and percentage of these affected/sick heifers treated 

with oral or injectable antibiotics, by disease treated 

Percent treated2 with... 

Percent 

affected/sick 

heifers1 

Oral 

antibiotic 

Injectable 

antibiotic 

Disease Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error 

Respiratory 3.2 (0.7) 9.1 (4.3) 84.4 (9.1) 

Diarrhea/other 

digestive 2.5 (1.7) 95.3 (4.1) 44.7 (32.5) 

Pinkeye 2.1 (0.8) 46.7 (19.4) 53.3 (19.4) 

Lameness/footrot 0.6 (0.1) 28.8 (12.3) 90.5 (5.4) 

Other 0.0 (0.0) 5.6 (6.4) 100.0 (—) 

1

Affected heifers as a percentage of beef-cow replacement heifers, weaned or older, on the operations on 

October 1, 2007. 

2

Treated heifers as a percentage of heifers affected. 
36 / Beef 2007–08

Section II: Population Estimates—Antimicrobial Drug Use

Photograph courtesy of Geni Wren “Bovine Veterinarian” magazine.
USDA APHIS VS / 37

Section II: Population Estimates—Antimicrobial Drug Use

Very few operations (less than 1 percent) used

oral antibiotics to treat any disease condition in

replacement heifers in 2007. In addition, less

than 8 percent of operations treated any

replacement heifers with injectable antibiotics

for any individual disease in 2007. The most

common use of antibiotics in this age class of

animals was for treatment of respiratory disease.

When injectable antibiotics were used to treat

replacement heifers for respiratory disease, the

primary antibiotics were tetracycline and betalactams (2.5 and 2.1 percent of operations,

respectively).

k. Percentage of operations that used oral or injectable antibiotics to treat replacement 

heifers in 2007, by primary antibiotic used and by disease treated 

Percent Operations 

Disease 

Respiratory 

Diarrhea or 

other 

digestive Pinkeye 

Lameness/ 

footrot Other 

Primary 

antibiotic class Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error 

Oral 

Sulfonamides 0.2 (0.1) 0.1 (0.0) 0.0 (0.0) 0.2 (0.1) 0.0 (0.0) 

Tetracyclines 0.0 (0.0) 0.0 (0.0) 0.8 (0.7) 0.0 (—) 0.0 (—) 

None 99.8 (0.1) 99.9 (0.0) 99.2 (0.7) 99.8 (0.1) 100.0 (0.0) 

Total 100.0 100.0 100.0 100.0 100.0 

Injectable 

Sulfonamides 0.0 (0.0) 0.0 (—) 0.0 (—) 0.0 (—) 0.0 (—) 

Noncephalosporin

beta-lactams 2.1 (1.2) 0.0 (0.0) 0.3 (0.1) 0.3 (0.2) 0.2 (0.1) 

Tetracyclines 2.5 (0.8) 0.4 (0.3) 1.9 (0.6) 0.8 (0.2) 0.1 (0.1) 

Macrolides 0.7 (0.2) 0.0 (0.0) 0.0 (—) 0.0 (0.0) 0.0 (—) 

Cephalosporins 0.5 (0.4) 0.0 (—) 0.1 (0.1) 0.0 (0.0) 0.0 (—) 

Florfenicol 1.1 (0.5) 0.1 (0.1) 0.0 (0.0) 0.1 (0.1) 0.0 (—) 

Fluoroquinolones 0.7 (0.5) 0.5 (0.4) 0.0 (0.0) 0.0 (—) 0.0 (—) 

None 92.4 (1.6) 99.0 (0.6) 97.7 (0.6) 98.8 (0.3) 99.7 (0.2) 

Total 100.0 100.0 100.0 100.0 100.0 
38 / Beef 2007–08

Section II: Population Estimates—Antimicrobial Drug Use

On operations that treated any cattle or calves

with oral or injectable antibiotics, less than 1 of

100 cows were affected with any specific

disease or disorder. For cows affected, a higher

percentage received injectable antibiotics than

oral antibiotics for all diseases and disorders.

l. For operations that treated any affected/sick cattle or calves in 2007 with oral or 

injectable antibiotics, percentage of cows on these operations that were 

affected/sick and percentage of these affected/sick cows that were treated with 

oral or injectable antibiotics, by disease or disorder treated 

Percent affected/sick cows 

treated with2 . . . 

Percent 

affected/sick cows1 Oral antibiotic Injectable antibiotic 

Disease Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error 

Respiratory 0.4 (0.1) 2.4 (1.6) 99.7 (0.2) 

Diarrhea or other 

digestive 0.1 (0.0) 9.5 (5.5) 86.6 (8.1) 

Pinkeye 0.9 (0.2) 14.0 (11.9) 81.3 (11.9) 

Reproductive 

(retained 

placenta/uterine 

infection) 

0.3 (0.1) 5.3 (2.8) 95.6 (3.0) 

Abortion 0.0 (0.0) 13.5 (12.9) 73.0 (16.2) 

Lameness/footrot 0.8 (0.1) 12.1 (4.4) 95.0 (2.7) 

Other 0.1 (0.0) 0.8 (0.7) 79.9 (15.1) 

1

Affected cows as a percentage of total beef cows on the operations on October 1, 2007. 

2

Treated cows as a percentage of cows affected.
USDA APHIS VS / 39

Section II: Population Estimates—Antimicrobial Drug Use

Very few operations used oral antibiotics to treat

cows for any specific disease condition in 2007.

The most common disease condition prompting

use of an injectable antibiotic was lameness or

footrot in cows, which occurred on 10.1 percent

of operations in 2007. The most common

primary injectable antibiotic used for treatment

of cows with lameness was tetracycline, which

was used on 7.8 percent of operations.

m. Percentage of operations by primary antibiotic used to treat cows in 2007 

Percent Operations 

Disease 

Respira-tory 

Diarrhea/ 

scours or 

other 

digestive Pinkeye 

Reproductive Abortion Lameness/ 

footrot Other 

Primary 

antibiotic Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error 

Oral 

Sulfonamides 0.1 (0.1) 0.1 (0.1) 0.0 (—) 0.1 (0.0) 0.0 (—) 0.7 (0.2) 0.0 (0.0) 

Tetracyclines 0.0 (0.0) 0.0 (0.0) 0.7 (0.7) 0.1 (0.1) 0.0 (0.0) 0.3 (0.3) 0.0 (0.0) 

None 99.9 (0.1) 99.9 (0.1) 99.3 (0.7) 99.8 (0.1) 100.0 (0.0) 99.0 (0.3) 100.0 (0.0) 

Total 100.0 100.0 100.0 100.0 100.0 100.0 100.0 

Injectable 

Sulfonamides 0.0 (—) 0.0 (—) 0.0 (—) 0.0 (—) 0.0 (—) 0.1 (0.1) 0.1 (0.1) 

Noncephalosporin 

beta-lactams 

0.8 (0.5) 0.0 (0.0) 0.8 (0.4) 1.1 (0.4) 0.1 (0.1) 0.3 (0.2) 1.0 (0.7) 

Tetracyclines 4.1 (1.4) 0.3 (0.2) 6.2 (1.5) 2.2 (0.9) 0.1 (0.1) 7.8 (1.6) 1.4 (0.7) 

Aminoglycosides 0.0 (—) 0.0 (—) 0.1 (0.1) 0.6 (0.6) 0.0 (—) 0.0 (--) 0.0 (--) 

Macrolides 0.2 (0.1) 0.2 (0.2) 0.0 (0.0) 0.0 (0.0) 0.0 (—) 0.9 (0.4) 0.2 (0.2) 

Cephalosporins 0.6 (0.4) 0.0 (—) 0.0 (0.0) 0.0 (—) 0.0 (—) 0.1 (0.0) 0.0 (—) 

Florfenicol 0.5 (0.2) 0.6 (0.6) 0.4 (0.4) 0.0 (—) 0.1 (0.1) 0.9 (0.4) 0.0 (—) 

Fluoroquinolones 0.2 (0.1) 0.7 (0.7) 0.0 (—) 0.0 (—) 0.0 (—) 0.0 (—) 0.0 (—) 

None 93.6 (1.5) 98.2 (1.0) 92.5 (1.6) 96.1 (1.1) 99.7 (0.1) 89.9 (1.7) 97.3 (1.0) 

Total 100.0 100.0 100.0 100.0 100.0 100.0 100.0 
40 / Beef 2007–08

Section II: Population Estimates—Antimicrobial Drug Use

About 4 of 10 operations (37.2 percent)

generally treated calves 7 days and older with

antibiotics for diarrhea (scours). The percentage

of operations that gave antibiotics to calves

n. Percentage of operations that generally treated calves 7 days and older with 

antibiotics for diarrhea (scours), by herd size 

Percent Operations 

Herd Size (number of beef cows)

1–49 50–99 100–199 200 or more 

All 

operations 

Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error Pct. 

Std. 

error 

28.0 (5.2) 49.8 (6.8) 46.0 (6.1) 61.1 (4.7) 37.2 (3.5) 

7 days or older for diarrhea ranged from

28.0 percent of operations with 1 to 49 beef

cows to 61.1 percent of operations with 200 or

more beef cows.
USDA APHIS VS / 41

Section II: Population Estimates—Antimicrobial Drug Use

The percentage of operations that generally

treated calves 7 days and older with antibiotics

for diarrhea did not differ substantially across

regions.

o. Percentage of operations that generally treated calves 7 days and older with 

antibiotics for diarrhea (scours), by region 

Percent Operations 

Region 

West Central Southeast 

Percent Std. error Percent Std. error Percent Std. error 

48.5 (6.2) 47.3 (5.5) 29.9 (5.0) 
42 / Beef 2007–08

Section III: Fecal Sample Evaluations—A. Study Methods

Section III: F Section III: Fecal Sam ecal Sample

Evaluations aluations

A. Study Methods for Biological Sampling and Testing for

Enteric Bacteria

1. Sample

collection

Based on laboratory capacity, a total sample size

of 175 operations was set. One-hundred

operations were designated for collections,

which took place from January 14 to April 15,

2008. Another 75 operations were designated

for collection, which took place from July 7 to

August 31, 2008. In both sampling periods the

total number of herds was allocated to the 24

States, roughly in proportion to the number of

beef cows in those States. State coordinators

selected a convenience sample of the operations

for fecal sampling from operations participating

in the NAHMS Beef 2007–08 study that had

agreed to sample collection.

On each operation, 30 to 40 fecal samples from

adult beef cows were collected. The number of

samples collected depended on the number of

cows in the herd. For herds with 1 to 30 cows,

the number of samples collected was equal to

the number of cows in the herd. For herds with

41 to 100 cows, 35 samples were collected. For

herds with 101 or more cows, 40 samples were

collected. Collectors were instructed to collect

only fresh fecal samples off the ground across a

distributed area. Each 10-gram fecal sample was

placed into Whirl-Pak® bags using a clean

tongue depressor. This was done to ensure that

collected samples represented different animals.

Fecal samples were immediately chilled on ice

packs and shipped for overnight delivery to the

laboratory.

2. Culture

methods

All samples were cultured for Salmonella. A

subset of the samples was cultured for

Campylobacter, Enterococcus, Escherichia coli,

and Clostridium difficile. When the samples

were processed for Salmonella, every other

sample was cultured for Campylobacter and

C. difficile and every fourth sample was cultured

for E. coli and Enterococcus.

Salmonella: Feces (1 g) were incubated in

10 mL of GN Hajna (Difco Laboratories,

Detroit, MI) for 18–24 h at 37oC, and

tetrathionate broth (Difco) for 40–48 h at 37oC.

After initial enrichments, aliquots (100 μL) were

transferred to 10 mL of Rappaport-Vassiliadis

R10 broth (Difco) which were incubated for

18–24 h at 37o

C. Ten-μL aliquots of RappaportVassiliadis R10 broth were then streaked onto

Xylose-Lysine-Tergitol-4 (Difco) and BG Sulfa

(Difco) agar. Plates were incubated for 18–24 h

at 37oC. Isolated colonies characteristic of

Salmonella were inoculated into triple sugar

iron and lysine iron agar slants for biochemical

confirmation. Presumptive positive isolates were

serogrouped using serogroup specific antisera

(Difco) and sent to the National Veterinary

Services Laboratories (Ames, IA) for

serotyping.

Campylobacter: Fecal samples were diluted 1:9

(wt/vol) in sterile phosphate-buffered saline

(PBS, 0.1 M, pH 7.2) and 100-μL aliquots were

inoculated onto Campy-Cefex agar plates (Stern

et al., 1992) and into Bolton Broth enrichment

media (1-mL broth enrichments in Falcon

353047 tissue culture plates, 24 wells/ Becton
USDA APHIS VS / 43

Section III: Fecal Sample Evaluations—A. Study Methods

Dickinson Labware, Franklin Lakes, NJ 07417).

Agar plates and enrichment broth were

incubated for 36–48 h at 42oC under

microaerobic conditions (5% O2, 10% CO2 and

85% N2). Presumptive Campylobacter colonies

were selected by observation of cellular

morphology and motility using a wet mount

under phase-contrast microscopy. Isolates were

identified by species using a commercial

multiplex PCR (BAX® PCR, DuPont Qualicon,

Wilmington, DE).

Enterococcus spp.: 100-μL aliquots of fecal

dilutions (1:9 wt/vol, in PBS) were inoculated

into 24 well tissue culture plates (Becton

Dickinson Labware, Franklin Lakes, NJ 07417)

containing 1 mL of Enterococcosel broth

(Becton Dickinson, Sparks MD 21152) per well.

The plates were incubated for 18–24 h at 37o

C,

followed by streaking for isolation onto

Enterococcosel agar (Becton Dickinson).

Isolates were identified by species using a

multiplex PCR [27].

Non-type specific E. coli: 100-μL aliquots of

fecal dilutions (1:9 wt/vol, in PBS) were

streaked for isolation onto CHROMagar EECTM

(Hardy Diagnostics, Santa Maria, CA) plates.

The plates were incubated for 18–24 h at 42o

C,

after which colonies indicative of E. coli were

selected.

C. difficile: Two isolation methods single shock

(SS) and double shock (DS) and two plating

methods (BA and CCFA; Remel, Lenexa, KS)

were employed for the isolation of C. difficile.

All plating media and broth were prereduced in

an anaerobic chamber (5% hydrogen, 5% CO2

,

balanced nitrogen; Bactron Anaerobic, model

BacII, Sheldon Manufacturing, Cornelius, OR)

24 h prior to use. The SS method was performed

as described by Arroyo et al. (2005). The DS

method was performed as follows. In brief, 2 g

of fecal sample was mixed with 6 mL of

absolute ethanol in a 15-mL conical tube and

left at room temperature for 60 min. The sample

was then centrifuged at 3,800 | g for 10 min at

4°C. The resulting pellet was disrupted with a

swab, which was then used to inoculate 9.0 mL

of prereduced TCCFB in screw-capped tubes

and incubated aerobically at 37°C for 7 d. After

incubation, 3.0 mL was transferred into a 15-mL

conical tube, mixed with an equal amount of

absolute ethanol, and left at room temperature

for 60 min, at which time the sample was

centrifuged at 4,600 | g for 30 min at 4°C. The

supernatant fluid was discarded; the pellet was

mixed with a sterile swab, which was

subsequently used to streak prereduced BA and

CCFA plates and incubated anaerobically in the

aforementioned chamber at 37°C for 72 h (5%

hydrogen, 5% CO2, balanced nitrogen).

Confirmation of C. difficile—Plates were

examined for typical C. difficile colonies by

using the following criteria: observation of

yellow-green fluorescence UV light (350 nm)

and production of a horse-manure like odor.

Suspect colonies were subcultured to CCFA and

incubated anaerobically at 37°C for 72 h for

purity prior to further testing. After incubation,

the colonies were observed for a flat, groundglasslike surface with irregular edge

morphology, as well as the fluorescence and

odor as described above. Additionally, a Gram

stain was done to confirm that they were grampositive and posed long, thin, straight rods

under a |1,000 light microscope. Biochemical
44 / Beef 2007–08

Section III: Fecal Sample Evaluations—A. Study Methods

confirmation included testing for the production

of L-proline aminopeptidase (Pro-Disc, Remel,

Carr-Scarborough Microbiologicals, Inc.,

Decatur, GA). Definitive confirmation was made

with 16S rDNA PCR, as described by Kikuchi et

al. (2002). All positive isolates were stored in 10

mL of cooked meat medium in parafilmed

screw-capped tubes at room temperature after

48 h of anaerobic growth initiation at 37°C.

3. Antimicrobial

resistance

evaluation

The resistance profile for isolates was evaluated

using methods consistent with the National

Antimicrobial Resistance Monitoring System

(NARMS). Details of the NARMS antimicrobial

resistance testing methods can be found at: http:/

/www.fda.gov/AnimalVeterinary/SafetyHealth/

AntimicrobialResistance/

NationalAntimicrobialResistanceMonitoringSystem/

default.htm. These methods apply to the

Salmonella, Campylobacter, Enterococcus, and

E. coli isolates.

Salmonella, E. coli, Campylobacter, and

Enterococcus isolates were tested for

susceptibility to a panel of antimicrobials using

a broth microdilution system. The Salmonella

and E. coli panel consisted of 15 antimicrobial

drugs1, the Campylobacter panel 92, and

Enterococcus panel 173. Minimum inhibitory

concentration (MIC) values were used to

categorize the isolates as susceptible,

intermediate, or resistant to the antimicrobial

tested based on breakpoint values used in the

NARMS.

1

 Amikacin, amoxicillin-clavulanic acid, ampicillin, cefoxitin, ceftiofur, ceftriaxone, chloramphenicol, ciprofloxacin, gentamicin, kanamycin,

nalidixic acid, streptomycin, sulfamethoxazole, tetracycline, trimethoprim-sulfamethoxazole.

2

 Azithromycin, ciprofloxacin, clindamycin, erythromycin, florfenicol, gentamicin, nalidixic acid, telithromycin, tetracycline.

3

 Chloramphenicol, ciprofloxacin, daptomycin, erythromycin, flavomycin, gentamicin, kanamycin, lincomycin, linezolid, nitrofurantoin,

penicillin, streptomycin, synercid, tetracycline, tigecycline, tylosin, vancomycin.
USDA APHIS VS / 45

Section III: Fecal Sample Evaluations—A. Study Methods

a. Breakpoints used for susceptibility testing of Salmonella and E. coli1,2

Breakpoints (μg/mL)

Antimicrobial 

class 

Antimicrobial 

agent 

Susceptible 

(less than 

or equal) Intermediate 

Resistant 

(greater than 

or equal) 

Aminoglycosides 

Amikacin 16 32 64 

Gentamicin 4 8 16 

Kanamycin 16 32 64 

Streptomycin 32 NA 64 

β-lactam/βlactamase 

inhibitor 

combinations 

Amoxicillinclavulanic acid 8/4 16/8 32/16 

Cephems 

Cefoxitin 8 16 32 

Ceftiofur 2 4 8 

Ceftriaxone2 8 16–32 64 

Folate pathway 

inhibitors 

Sulfamethoxazole/ 

sulfisoxazole3 256 NA 512 

Trimethoprinsulfamethoxazole 2/38 NA 4/76 

Penicillin Ampicillin 8 16 32 

Phenicol Chloramphenicol 8 16 32 

Quinolones 

Ciprofloxacin 1 2 4 

Nalidixic acid 16 NA 32 

Tetracyclines Tetracycline 4 8 16 

1

Breakpoints were adopted from CLSI (Clinical and Laboratory Standards Institute), except for streptomycin, 

which has no CLSI breakpoints. 

2

CLSI revised the breakpoints for ceftriaxone in its M100-S20 document published in January 2010. The new 

resistant breakpoint is ≥4 μg/mL. The old breakpoints were used in this NAHMS report. 3

Sulfamethoxazole was tested from 1996 through 2003 and was replaced by sulfisoxazole in 2004. 

Source: USDA. National Antimicrobial Resistance Monitoring System. 2007 Executive Report. 
46 / Beef 2007–08

Section III: Fecal Sample Evaluations—A. Study Methods

b. Breakpoints used for susceptibility testing of Campylobacter1

Breakpoints (μg/mL)

Antimicrobial 

class 

Antimicrobial 

agent 

Susceptible 

(less than 

or equal) Intermediate 

Resistant 

(greater than 

or equal) 

Aminoglycosides Gentamicin 2 4 8 

Ketolides Telithromycin 4 8 16 

Lincosamides Clindamycin 2 4 8 

Macrolides 

Azithromycin 2 4 8 

Erythromycin 8 16 32 

Phenicol Florfenicol2 4 NA NA 

Quinolones 

Ciprofloxacin 1 2 4 

Nalidixic acid 16 32 64 

Tetracyclines Tetracycline 4 8 16 

1

Breakpoints were adopted from CLSI (Clinical and Laboratory Standards Institute) when available. 

2

For florfenicol, only a susceptible breakpoint (≤4 μg/mL) has been established. In this report, isolates with an 

MIC ≥8 μg/mL are categorized as resistant. 

Source: USDA. National Antimicrobial Resistance Monitoring System. 2007 Executive Report. 
USDA APHIS VS / 47

Section III: Fecal Sample Evaluations—A. Study Methods

c. Breakpoints used for susceptibility testing of Enterococcus1 

Breakpoints (μg/mL)

Antimicrobial 

class 

Antimicrobial 

agent 

Susceptible 

(less than 

or equal) Intermediate 

Resistant 

(greater than 

or equal) 

Aminoglycosides 

Gentamicin 4 8 16 

Kanamycin2 512 NA 1,024 

Streptomycin 512 NA 1,024 

Glycopeptides Vancomycin 4 8, 16 32 

Glycylcycline Tigecycline2 3 0.25 NA NA 

Lincosamides Lincomycin2 2 4 8 

Lipopeptides Daptomycin2 4 4 NA NA 

Macrolides 

Erythromycin 0.5 1, 2, 4 8 

Tylosin2 8 16 32 

Nitrofurans Nitrofurantoin 32 64 128 

Oxazolidinones Linezolid 2 4 8 

Penicillins Penicillin 8 NA 16 

Phenicol Chloramphenicol 8 16 32 

Phosphoglycolipids Flavomycin2 8 16 32 

Fluoroquinolone Ciprofloxacin 1 2 4 

Streptogramins Quinupristin/ 

Dalfopristin 1 2 4 

Tetracyclines Tetracycline 4 8 16 

1

Breakpoints were adopted from CLSI (Clinical and Laboratory Standards Institute). In 2008, Enterococcus 

plate CMV3AGPF replaced CMV2AGPF midyear. MIC ranges for Enterococcus reflect the smaller range. 2

No CLSI interpretive criteria for this bacterium/antimicrobial currently available. 

3 Only a susceptible breakpoint (≤0.25 μg/mL) has been established. Isolates with an MIC ≥0.5 μg/mL are 

reported as nonsusceptible. 

4

 Only a susceptible breakpoint (≤ μg/mL) has been established. Isolates with an MIC ≥0.8 μg/mL are reported 

as nonsusceptible. 
48 / Beef 2007–08

Section III: Fecal Sample Evaluations—A. Study Methods

For the C. difficile isolates, antimicrobial

resistance was determined using the E-test with

nine antimicrobial drugs.1 Again, the isolates

were categorized as susceptible, intermediate, or

resistant to the antimicrobial tested based on

breakpoint values shown below.

1 Linezolid, amoxicillin-clavulanic acid, ampicillin, clindamycin,

erythromycin, levofloxacin, metronidazole, rifampicin, and

vancomycin.

d. Antimicrobials used in susceptibility testing of Clostridium difficile 

Antimicrobial Class Category 

Reason 

to test 

Range 

tested 

(μg/mL) 

Resistance 

breakpoint 

(greater than 

or equal )

[μg/mL] References 

Linezolid Oxazolidinone Both Risk factor 

for CDAD* 0.016-256 4 Zheng et al., 

2007 

Amoxicillinclavulanic acid β-lactam Bactericidal Risk factor 

for CDAD 0.016-256 16 CLSI, 2007 

Ampicillin Penicillin Bactericidal Risk factor 

for CDAD 0.016-256 2 CLSI, 2007 

Clindamycin Lincosamide Bacteriostatic Risk factor 

for CDAD 0.016-256 8 CLSI, 2007 

Erythromycin Macrolide Bacteriostatic Risk factor 

for CDAD 0.016-256 256 Drudy et al., 

2007 

Metronidazole Imidazole Bactericidal Treatment 

for CDAD 0.016-256 32 CLSI, 2007 

Levoflaxacin Fluoroquinolone Bactericidal Risk factor 

for CDAD 0.002-32 8 Martin et al., 

2008 

Rifampicin Rifamycin Bactericidal Treatment 

for CDAD 0.002-32 32 O’Conner et al., 2008 

Vancomycin Glycopeptide Bactericical Treatment 

for CDAD 0.016-256 32 Indra et al., 

2008 

*CDAD = Clostridium difficile associated disease. 
USDA APHIS VS / 49

Section III: Fecal Sample Evaluations—A. Study Methods

4. Comparison of

operations by

whether samples

were submitted

There were no differences in the number of

producers who did or did not submit fecal

samples based on herd size (p=0.77) or region

(p=0.25). A chi-square test using SAS Proc Freq

was used to test for an association between

sample submission and herd size (region).

a. Number of operations that submitted samples, by size of operation 

Number of Operations 

Herd Size (number of beef cows)

Samples submitted 1–49 50–99 100–199 200 or more Total 

Yes 49 26 42 56 173 

No 114 70 83 127 394 

b. Number of operations that submitted samples, by region 

Number of Operations 

Region 

Samples submitted West Central Southeast 

Yes 39 54 80 

No 99 142 153 
50 / Beef 2007–08

Section III: Fecal Sample Evaluations—B. Sample Testing Results

B. Sample Testing Results

Overall, fecal samples were collected and tested

on 173 operations. In the first collection

(January–April, 2008), 3,266 samples were

collected on 97 operations. In the second

collection (July–August, 2008) 2,527 samples

were collected on 76 operations.

1. Salmonella Operation level prevalence—Among the 173

operations sampled, Salmonella was cultured

from 1 or more samples on 16 operations

(9.2 percent). There was no apparent

relationship between Salmonella culture status

and operation size (P=0.39) or region (P=0.46).

There was a difference (P=0.009) in the

proportion of operations with positive samples

based on timing of the sampling, with 12 of the

16 positive operations (75.0 percent) being

collected in period 2 (July 7–August 31).

a. Number and percentage of operations positive for Salmonella, by size of 

operation* 

Number of Operations 

Herd Size (number of beef cows)

1–49 50–99 100–199 200 or more Total 

Number tested 49 26 42 56 173 

Number positive 2 2 6 6 16 

Percent positive 4.1 7.7 14.3 10.7 9.2 

*P value difference by herd size = 0.39. 

b. Number and percentage of operations positive for Salmonella, by region* 

Region 

West Central Southeast Total 

Number tested 39 54 80 173 

Number positive 5 3 8 16 

Percent positive 12.8 5.6 10.0 9.2 

*P value difference by region = 0.46. 
USDA APHIS VS / 51

Section III: Fecal Sample Evaluations—B. Sample Testing Results

None of the antibiotic-use practices on the

operations was associated with the ability to

recover Salmonella on the operation.

c. Association between antibiotic-use practices and presence of Salmonella on 

the operations 

Response Herds positive Herds negative P-value 

Antibiotic use in feed 

Any cattle or calves1 

Yes 3 55 0.19 

No 13 102 

Antibiotic use—oral or injection 

Any cattle or calves1 

Yes 14 137 1.00 

No 2 20 

Unweaned calves2 

Yes 9 99 0.59 

No 7 58 

Replacement heifers2 

Yes 6 53 0.76 

No 10 104 

Cows2 

Yes 8 76 0.90 

No 8 81 

1

Operation policy to use oral or injectable antibiotics to treat any animals 

2

Treatment of one or more animals of the specified class with either oral or injectable antibiotics in 2007.
52 / Beef 2007–08

Section III: Fecal Sample Evaluations—B. Sample Testing Results

Sample level prevalence—Of the 5,793 samples

cultured for Salmonella, 31 (0.5 percent) were

positive. The number of positive samples per

operation ranged from one to eight. There was

no apparent relationship between the percentage

of samples positive for Salmonella and

operation size (P=0.61), region (P=0.19), or

sampling period (P=0.77). Fourteen of the 31

positive samples (45.1 percent) were collected

from July 7–August 31. Among the 31 positive

samples, 34 Salmonella isolates were evaluated

further by serotyping and antibiotic resistance

testing.

Isolate characteristics—Two cow-calf

operations tested positive for four different

Salmonella serotypes, and two different

serotypes were present on three operations. On

all other positive operations, only a single

serotype was identified. S. Montevideo was the

most common serotype (17.6 percent of

isolates).

d. Number and percentage of Salmonella isolates, and number and percentage of 

positive operations, by serotype 

Isolates1 (n=34) Operations (n=16)

Serotype Number Pct. Number Pct. 

Braenderup 2 5.9 2 12.5 

Meleagridis 2 5.9 1 6.3 

Montevideo 6 17.6 2 12.5 

Newport 2 5.9 2 12.5 

I 3, 10:-:1,w 2 5.9 1 6.3 

I 6,7:k:- 3 8.8 1 6.3 

All others2 17 50.0 13 81.3 

Total 34 100.0 NA NA 

1

More than one isolate was cultured from two samples. 

2

Three untypable isolates are included here, as well as serotypes with one isolate each (Anatum, 

Javiana, Lawndale, Mbandaka, Oukam, Rubislaw, Saugas, and seven unnamed serotypes).
USDA APHIS VS / 53

Section III: Fecal Sample Evaluations—B. Sample Testing Results

Comparison to previous studies—Sample

collection methods for the Beef 2007–08 study

were similar to those used during the Beef ’97

study. The percentage of operations with

e. Number and percentage of operations, and number and percentage of cows 

sampled, positive for Salmonella 

Operations with at least 

one positive cow Positive sampled cows 

Study Number Pct. Number Pct. 

Beef ‘97 21/187 11.2 70/5,049 1.4 

Beef 2007–08 16/173 9.2 31/5,793 0.5 

positive samples and the percentage of samples

positive for Salmonella were similar between

the two studies.
54 / Beef 2007–08

Section III: Fecal Sample Evaluations—B. Sample Testing Results

All 34 isolates from the Beef 2007–08 study

were susceptible to all of the antimicrobial drugs

on the panel tested.

f. Percentage of resistant Salmonella isolates, by antimicrobial1

Percent Isolates

Antimicrobial Beef ’97 (n=78) Beef 2007–08 (n=34) 

Amikacin 0.0 0.0 

Amoxicillin-clavulanic acid 0.0 0.0 

Ampicillin 1.3 0.0 

Apramycin 0.0 NA 

Cefoxitin NA 0.0 

Ceftiofur 0.0 0.0 

Ceftriaxone 0.0 0.0 

Cephalothin 0.0 NA 

Chloramphenicol 0.0 0.0 

Ciprofloxacin 0.0 0.0 

Gentamicin 2.6 0.0 

Kanamycin 0.0 0.0 

Nalidixic acid 0.0 0.0 

Streptomycin 11.5 0.0 

Sulfamethoxazole2 11.5 0.0 

Tetracycline 2.6 0.0 

Ticarcillin 1.3 NA 

Trimethoprim-sulfamethoxazole 0.0 0.0 

Resistant to two or more 

antimicrobials 11.5 0.0 

Susceptible to all antimicrobials 

tested2 87.2 100.0 

1

Intermediate isolates were classified as susceptible. 

2

Sulfisoxazole replaced sulfamethoxazole in 2007–08. 

NA=antimicrobial not included for this study.
USDA APHIS VS / 55

Section III: Fecal Sample Evaluations—B. Sample Testing Results

Summary—Only about 10 percent of beef cowcalf operations tested Salmonella positive in the

Beef ‘97 and Beef 2007–08 studies. Overall,

antibiotic-use practices were not associated with

the ability to recover Salmonella on the

operation. Approximately 1 percent of samples

were positive for Salmonella in Beef ‘97 and

Beef 2007–08. These results suggest that

Salmonella is not very common on U.S. beef

cow-calf operations. It is possible that repeated

sampling of these same operations over time

could identify more positive operations.

Herd size and region of the United States were

not associated with the presence of Salmonella

on operations from the Beef 2007–08 study.

Antimicrobial resistance was not observed in

any of the Salmonella isolates from the Beef

2007–08 study, and very little resistance was

seen in isolates from the Beef ‘97 study. These

results suggest that antimicrobial-resistant

Salmonella are uncommon in U.S. beef cow-calf

operations.

2. Campylobacter Operation level prevalence—Campylobacter

was identified in one or more samples from beef

cows on 77 of 173 of operations (44.5 percent).

There was a difference in the proportion of

operations with positive Campylobacter samples

by herd size (P<0.0001) and by region

(P=0.008). There was no difference in the

proportion of positive operations by sampling

period (P=0.24). For the January 14–April 15

sampling period, 47 of 97 of operations

(48.5 percent) had one or more positive

samples; for the July 7–August 31 sampling

period, 30 of 76 of operations (39.5 percent)

had one or more positive samples.

a. Number of operations that tested samples for Campylobacter, and number and 

percentage of operations with at least one sample positive for Campylobacter, 

by size of operation 

Percent Operations 

Herd Size (number of beef cows)

1–49 50–99 100–199 200 or more Total 

Number tested 49 26 42 56 173 

Number positive 8 10 23 36 77 

Percent positive 16.3 38.5 54.8 64.3 44.5 
56 / Beef 2007–08

Section III: Fecal Sample Evaluations—B. Sample Testing Results

b. Number of operations that tested samples for Campylobacter, and number and 

percentage of operations with at least one sample positive for Campylobacter, 

by region 

Percent Operations 

Region 

West Central Southeast Total 

Number tested 39 54 80 173 

Number positive 19 32 26 77 

Percent positive 48.7 59.3 32.5 44.5 
USDA APHIS VS / 57

Section III: Fecal Sample Evaluations—B. Sample Testing Results

None of the overall measures of antibiotic-use

practices on the operations was associated with

recovery of Campylobacter from fecal samples.

c. Association between antibiotic-use practices and presence of Campylobacter

on the operations 

Response Herds positive Herds negative P-value 

Antibiotic use in feed 

Any cattle or calves1

 

Yes 25 33 0.79 

No 52 63 

Antibiotic use—oral or injection 

Any cattle or calves1 

Yes 69 82 0.41 

No 8 14 

Unweaned calves2 

Yes 53 55 0.12 

No 24 41 

Replacement heifers2 

Yes 29 30 0.38 

No 48 66 

Cows2 

Yes 43 41 0.09 

No 34 55 

1

Operation policy to use oral or injectable antibiotics to treat any animals. 

2

Treatment of one or more animals of the specified class with either oral or injectable antibiotics in 2007.
58 / Beef 2007–08

Section III: Fecal Sample Evaluations—B. Sample Testing Results

Sample level prevalence—Overall, 259 of 2,917

samples (8.8 percent) were culture positive for

Campylobacter. The prevalence of positive

samples was different by herd size (P=0.0002)

and by region (P=0.024), with prevalence

increasing as herd size increased. Statistical

analysis using SAS Proc Genmod accounted for

clustering of samples within farms. The

proportion of positive samples did not vary by

collection period (P=0.097). A total of

10.6 percent of samples collected January 14–

April 15 were positive compared with 6.6

percent of samples collected July 7–August 3.

d. Number of cows tested for Campylobacter, and number and percentage of 

cows positive for Campylobacter, by size of operation 

Herd Size (number of beef cows)

1–49 50–99 100–199 200 or more Total 

Number tested 560 456 793 1,108 2,917 

Number positive 13 25 84 137 259 

Percent positive 2.3 5.5 10.6 12.4 8.8 

e. Number of cows tested for Campylobacter, and number and percentage of 

cows positive for Campylobacter, by region 

Region 

West Central Southeast Total 

Number tested 651 989 1,277 2,917 

Number positive 92 95 72 259 

Percent positive 14.1 9.6 5.6 8.9 
USDA APHIS VS / 59

Section III: Fecal Sample Evaluations—B. Sample Testing Results

Isolate characteristics—C. jejuni was recovered

from 244 samples on 75 operations, and C. coli

was recovered from 10 samples on 5 operations.

Campylobacter of an unknown type was

recovered from five samples collected from four

operations. Seven operations had more than one

species of Campylobacter isolated (counting

“not typed” as a species).

Antimicrobial resistance—Over half of the C.

jejuni isolates (56.2 percent) were susceptible to

all nine antimicrobials tested. Of the

antimicrobials in the following table,

ciprofloxacin and erythromycin are especially

important because they are often used to treat

humans infected with Campylobacter. Less than

7 percent of C. jejuni isolates were resistant to

ciprofloxacin, and less than 1 percent were

resistant to erythromycin. The highest

percentage of isolates (38.9 percent) were

resistant to tetracycline. Of the 10 C. coli

isolates tested for antimicrobial susceptibility,

6 were resistant to tetracycline, 2 were resistant

to ciprofloxacin, and 2 were resistant to

nalidixic acid.

f. Percentage of resistant C. jejuni isolates, by antimicrobial* 

Antimicrobial Percent (n=244) 

Azithromycin 0.4 

Ciprofloxacin 6.6 

Clindamycin 0.8 

Erythromycin 0.4 

Florfenicol 0.0 

Gentamicin 0.0 

Nalidixic acid 6.1 

Telithromycin 0.0 

Tetracycline 38.9 

Resistant to two or more antimicrobials 8.2 

Susceptible to all nine antimicrobials 56.2 

*Intermediate isolates were classified as susceptible. 
60 / Beef 2007–08

Section III: Fecal Sample Evaluations—B. Sample Testing Results

Summary—Campylobacter was found on less

than half of the beef cow-calf operations tested

and in less than 10 percent of the collected

samples. Antibiotic-use practices were not

associated with the ability to recover

Campylobacter on operations. About 95 percent

of the Campylobacter isolates were C. jejuni.

Campylobacter was less likely to be isolated

from smaller herds and herds in the Southeast

region. Relatively few Campylobacter isolates

were resistant to antimicrobials, and over half of

the C. jejuni isolates were susceptible to all of

the antimicrobials against which they were

tested. The highest percentage of resistance was

observed for tetracycline. Few isolates were

resistant to ciprofloxacin or erythromycin.

Resistance to two or more antimicrobials

occurred in less than 9 percent of isolates.
USDA APHIS VS / 61

Section III: Fecal Sample Evaluations—B. Sample Testing Results

3. Enterococcus Operation level prevalence—As expected,

nearly all operations (98.3 percent) had at least

one sample positive for Enterococcus. As such,

there were no differences by herd size (P=0.40)

or region (P=0.22). Nor were there differences

by sampling period (P=0.58). Furthermore,

antibiotic-use practices on the operations were

not associated with recovery of Enterococcus on

the operations.

a. Association between antibiotic-use practices and presence of Enterococcus 

Response Herds positive Herds negative P-value 

Antibiotic use in feed 

Any cattle or calves1

 

Yes 58 0 0.55 

No 112 3 

Antibiotic use—oral or injection 

Any cattle or calves1 

Yes 148 3 1.00 

No 22 0 

Unweaned calves2 

Yes 106 2 1.00 

No 64 1 

Replacement heifers2 

Yes 58 1 1.00 

No 112 2 

Cows2 

Yes 84 0 0.25 

No 86 3 

1

Operation policy to use oral or injectable antibiotics to treat any animals. 

2

Treatment of one or more animals of the specified class with either oral or injectable antibiotics in 2007.
62 / Beef 2007–08

Section III: Fecal Sample Evaluations—B. Sample Testing Results

Sample level prevalence—A total of 1,182 of

1,479 samples (79.9 percent) were culture

positive for Enterococcus. Again, there were no

differences by herd size (P=0.88) or by

sampling period (P=0.61). There were

differences in the proportion of samples positive

by region (P=0.006).

b. Number of cows tested for Enterococcus, and number and percentage of cows 

positive for Enterococcus, by region 

Region 

West Central Southeast Total 

Number tested 328 498 653 1,479 

Number positive 216 426 540 1,182 

Percent positive 65.9 85.5 82.7 79.9 
USDA APHIS VS / 63

Section III: Fecal Sample Evaluations—B. Sample Testing Results

Isolate characteristics—E. faecalis and/or E.

faecium were found on 43.9 percent of

operations. Of the 1,182 positive samples,

11.5 percent and 3.2 percent were E. faecium

and E. faecalis, respectively. The highest

percentage of isolates (39.0 percent) were

identified as E.casseliflavus. Of the operations

on which enterococci were found, 83.5 percent

had at least one E. casseliflavus isolate and

73.5 percent had at least one E. hirae isolate.

E. faecium and E. faecalis were found on

38.8 percent and 14.1 percent of positive

operations, respectively.

c. Number and percentage of isolates, and number and percentage of positive 

operations, by Enterococcus species 

Isolates* (n=1,182) Operations (n=170)

Species Number Percent Number Percent 

E. casseliflavus 461 39.0 142 83.5 

E. hirae 303 25.6 125 73.5 

E. mundtii 169 14.3 73 42.9 

E. faecium 136 11.5 66 38.8 

Not typed 57 4.8 43 25.3 

E. faecalis 38 3.2 24 14.1 

E. gallinarum 9 0.8 6 3.5 

E. durans 6 0.5 5 2.9 

E. avium 3 0.3 3 1.8 

Total 1,182 100.0 NA NA 

*The number of isolates equals the number of positive samples since only one Enterococcus species was 

identified in each sample.
64 / Beef 2007–08

Section III: Fecal Sample Evaluations—B. Sample Testing Results

Antimicrobial resistance—Of the 1,180 isolates

tested for antimicrobial susceptibility, 11

(0.9 percent) were susceptible to all 17

antimicrobials. Two isolates were not viable at

the time of testing. All of the E. faecalis and

E. faecium isolates were resistant to at least one

antimicrobial. Vancomycin resistance is of

particular interest since it is used to treat humans

with enterococcal infections (McGowan et al.,

2006). One E. casseliflavus isolate was resistant

to vancomycin, but this was determined to be an

intrinsic resistance (naturally occurring trait)

rather than an acquired resistance. None of the

E. faecalis or E. faecium isolates was resistant

to vancomycin. Resistance to quinupristin/

dalfopristin (Synercid®) is important because

this antimicrobial is used to treat vancomycinresistant E. faecium infections (McGowan et al.,

2006). Only 0.7 percent of E. faecium and

0.9 percent of other enterococci were resistant

to Synercid. Over 90 percent of E. faecium and

other enterococci were resistant to flavomycin,

while none of the E. faecalis isolates were

resistant to flavomycin. Overall, 100.0, 54.1,

and 90.7 percent of the E. faecalis, E. faecium,

and other enterococci, respectively, were

resistant to lincomycin.
USDA APHIS VS / 65

Section III: Fecal Sample Evaluations—B. Sample Testing Results

d. Percentage of resistant Enterococcus isolates, by species and by 

antimicrobial1

Percent Isolates

Antimicrobial 

E. faecalis 

(n=38) 

E. faecium 

(n=135) 

Other Enterococci

(n=1,007) 

Chloramphenicol 0.0 0.7 0.0 

Ciprofloxacin 0.0 45.9 4.1 

Daptomycin2 0.0 0.0 5.3 

Erythromycin 0.0 0.7 0.8 

Flavomycin 0.0 92.6 90.3 

Gentamicin 0.0 0.0 0.0 

Kanamycin 0.0 1.5 0.0 

Lincomycin 100.0 54.1 90.7 

Linezolid 0.0 0.0 0.0 

Nitrofurantoin 0.0 3.0 0.1 

Penicillin 2.6 0.7 0.4 

Streptomycin 0.0 0.0 0.0 

Synercid NA3 0.7 0.9 

Tetracycline 2.6 12.6 18.2 

Tigecycline2 0.0 0.0 0.0 

Tylosin 0.0 0.0 1.1 

Vancomycin 0.0 0.0 0.14

1

Intermediate isolates were classified as susceptible. 

2

The Clinical and Laboratory Standards Institute has no approved standards for daptomycin and 

tigecycline susceptibility testing. 

3

E. faecalis exhibits an intrinsic resistance to Synercid. 4

One E. casseliflavus isolate was intrinsically resistant to vancomycin.
66 / Beef 2007–08

Section III: Fecal Sample Evaluations—B. Sample Testing Results

Summary—Enterococcus was found on

98.3 percent of the beef cow-calf operations

tested and in 79.9 percent of the samples

collected. There was no association between

recovery of Enterococcus and antibiotic-use

practices. The high prevalence of enterococci

was expected, since this organism is a normal

inhabitant of the gastrointestinal tract of animals

and humans. E. faecalis or E. faecium, the

organisms responsible for most of the human

illness caused by enterococci, were found on

less than half of operations (43.9 percent). E.

casseliflavus was the most common species

identified. Synercid and vancomycin are two of

the more important antimicrobials used in

treating human enterococcal infections. There

was very little resistance to Synercid and no

notable resistance to vancomycin. Resistance to

lincomycin and flavomycin was most commonly

observed in the isolates from this study.

4. Escherichia coli Operation level prevalence—172 of 173

operations had at least one sample positive for

E. coli.

Sample level prevalence—Overall 1,147 of

1,479 samples (77.6 percent) were positive for

E. coli. The proportion of samples positive for

E. coli was not different by herd size (P=0.09)

or region (P=0.43), but was different by

sampling time period (P=0.004).

a. Number of cows tested for E. coli, and number and percentage of cows positive 

for E. coli, by size of operation 

Herd Size (number of beef cows)

1–49 50–99 100–199 200 or more Total 

Number tested 293 230 400 556 1,479 

Number positive 242 157 298 450 1,147 

Percent positive 82.6 68.3 74.5 80.9 77.6 

b. Number of cows tested for E. coli, and number and percentage of cows 

positive for E. coli, by region 

Region 

West Central Southeast Total 

Number tested 328 498 653 1,479 

Number positive 245 373 529 1,147 

Percent positive 74.7 74.9 81.0 77.6 
USDA APHIS VS / 67

Section III: Fecal Sample Evaluations—B. Sample Testing Results

Isolate characteristics—No resistance was

detected among the E.coli isolates to amikacin,

ceftriaxone, ciprofloxacin, naladixic acid, or

trimethoprim/sulfamethoxazole. Less than 2

percent of the isolates were resistant to the

remaining antibiotics, with the exception of

sulfamethoxazole (6.7 percent), streptomycin

(6.5 percent), and tetracycline (16.0 percent).

d. Percentage of resistant E. coli

isolates, by antimicrobial 

Antimicrobial Percent (n=1,146) 

Amikacin 0.0 

Amoxicillin 0.3 

Ampicillin 1.8 

Cefoxitin 0.2 

Ceftiofur 0.2 

Ceftriaxone 0.0 

Chloramphenicol 0.4 

Ciprofloxacin 0.0 

Gentamicin 0.3 

Kanamycin 0.1 

Nalidixic acid 0.0 

Sulfamethoxazole 6.7 

Tetracycline 16.0 

Streptomycin 6.5 

Trimethoprimsulfamethoxazole 0.0 

Any 16.6 

c. Number of cows tested for E. coli, and number and percentage of cows positive 

for E. coli, by sampling period 

Sampling Period 

January 14–April 15 July 7–August 3 

Number tested 837 642 

Number positive 602 545 

Percent positive 71.9 84.9 
68 / Beef 2007–08

Section III: Fecal Sample Evaluations—B. Sample Testing Results

Overall, 83.7 percent of the E. coli isolates were

susceptible to all antibiotics in the panel tested.

An additional 6.4 percent of isolates were

resistant to only a single antibiotic. The

remaining isolates were resistant to two

antibiotics (4.6 percent) or three or more

antibiotics (5.3 percent). The maximum number

of antibiotics that any isolate was resistant to

was six.

e. Number and percentage of isolates by number of antimicrobials to which 

antimicrobial resistance was observed 

Number antimicrobials to 

which resistance was 

observed Number isolates Percent isolates 

0 959 83.7 

1 73 6.4 

2 53 4.6 

3 or more 61 5.3 

Total 1,146 100.0 

Summary—As expected for a commensal

organism, E. coli was recovered from most

of the samples cultured for E. coli

(77.6 percent). Most of these isolates were

susceptible to all antibiotics in the panel tested.

None of these isolates had a resistance type that

suggested they produced the extended spectrum

beta lactamases that have been emerging in

other areas of the world and can be associated

with severe human illness. When resistance was

present among the E. coli isolates, it was

typically for older generation antibiotics

(tetracycline, streptomycin, or

sulfamethoxazole).
USDA APHIS VS / 69

Section III: Fecal Sample Evaluations—B. Sample Testing Results

5. Clostridium

difficile

Operation level prevalence—Overall 76 of 173

operations (43.9 percent) had at least one

sample positive for C. difficile. There was no

difference in the percentage of operations with

positive samples by herd size (P=0.50). The

percentage of operations with a sample positive

for C. difficile differed by region (P=0.01).

a. Number of operations that tested samples for Clostridium difficile, and number 

and percentage of operations with at least one sample positive for C. difficile, 

by size of operation 

Herd Size (number of beef cows)

1–49 50–99 100–199 200 or more Total 

Number tested 49 26 42 56 173 

Number positive 26 11 17 22 76 

Percent positive 53.1 42.3 40.5 39.3 43.9 

b. Number of operations that tested samples for C. difficile, and number and 

percentage of operations with at least one sample positive for C. difficile, by 

region 

Region 

West Central Southeast Total 

Number tested 39 54 80 173 

Number positive 11 21 44 76 

Percent positive 28.2 38.9 55.0 43.9 
70 / Beef 2007–08

Section III: Fecal Sample Evaluations—B. Sample Testing Results

c. Association between antibiotic-use practices and presence of C. difficile on the 

operations 

Response Herds positive Herds negative P-value 

Antibiotic use in feed 

Any cattle or calves1

 

Yes 23 35 0.42 

No 53 62 

Antibiotic use—oral or injection 

Any cattle or calves1 

Yes 66 85 0.88 

No 10 12 

Unweaned calves2 

Yes 47 61 0.89 

No 29 36 

Replacement heifers2 

Yes 28 31 0.50 

No 48 66 

Cows2 

Yes 40 44 0.34 

No 36 53 

1

Operation policy to use oral or injectable antibiotics to treat any animals. 

2

Treatment of one or more animals of the specified class with either oral or injectable antibiotics in 2007.
USDA APHIS VS / 71

Section III: Fecal Sample Evaluations—B. Sample Testing Results

Sample-level prevalence—Overall, 186 of 2,922

of samples (6.4 percent) were positive for

C. difficile. There was no difference in the

percentage of positive cows by herd size

(P=0.11), but there was a difference by region

(P=0.01).

d. Number of cows tested for C. difficile, and number and percentage of cows 

positive for C. difficile, by size of operation 

Herd Size (number of beef cows)

1–49 50–99 100–199 200 or more Total 

Number tested 561 457 794 1,110 2,922 

Number positive 44 32 65 45 186 

Percent positive 7.8 7.0 8.2 4.1 6.4 

e. Number of cows tested for C. difficile, and number and percentage of cows 

positive for C. difficile, by region 

Region 

West Central Southeast Total 

Number tested 652 990 1,280 2,922 

Number positive 17 43 126 186 

Percent positive 2.6 4.3 9.8 6.4 
72 / Beef 2007–08

Section III: Fecal Sample Evaluations—B. Sample Testing Results

Isolate characteristics—No C. difficile isolates

were resistant to vancomycin. Very few isolates

were resistant to amoxicillin-clavulanic acid or

metronidazole (0.5 percent each). More than

90 percent of isolates were resistant to

clindamycin and levofloxacin.

f. Number and percentage of resistant C. difficile isolates, by antimicrobial 

Antimicrobial Number isolates n=188) Percent isolates 

Linezolid 2 1.1 

Amoxicillin-clavulanic acid 1 0.5 

Ampicillin 29 15.6 

Clindamycin 169 90.9 

Erythromycin 6 3.2 

Metronidazole 1 0.5 

Levofloxacin 181 97.3 

Rifampicin 27 14.5 

Vancomycin 0 0 

The highest percentage of isolates were resistant

to two antibiotics, usually clindamycin and

levofloxacin (62.4 percent).

g. Number and percentage of isolates by number of antimicrobials to which 

antimicrobial resistance was observed 

Number of antimicrobials to 

which resistance was 

observed Number isolates Percent isolates 

1 16 8.6 

2 116 62.4 

3 48 25.8 

4 6 3.2 

Total 186 100.0 
USDA APHIS VS / 73

Section III: Fecal Sample Evaluations—B. Sample Testing Results

Summary—C. difficile was found on less than

half of the beef cow-calf operations tested and

in less than 10 percent of the collected samples.

Antibiotic-use practices were not associated

with the ability to recover C. difficile on

operations. Presence of C. difficile on operations

was not associated with herd size but was

associated with region, with the organism more

likely to be identified from herds in the

Southeast region. All C. difficile isolates were

resistant to at least one antimicrobial. However,

none of the C. difficile isolates was resistant to

vancomycin, and 0.5 percent of isolates were

resistant to metronidazole and amoxicillinclavulanic acid. When treatment is used for

human cases of C. difficile-associated disease,

vancomycin and metronidazole are the

antimicrobials most commonly used.

Future work to be accomplished for C.

difficile—In 2004, an epidemic strain of C.

difficile was identified that appears to be more

virulent than other strains, as it has the ability to

produce greater quantities of toxins A and B. In

addition, it is more resistant to the antibiotic

group known as fluoroquinolones. More

advanced testing methods than were used in this

report are needed to identify this epidemic

strain. The techniques listed below will be used

to further characterize C. difficile isolates from

this study, and results from this testing will be

reported at a later time.

1. Pulsed field gel electrophoresis (PFGE)

2. Toxinotyping

3. repPCR typing

4. Toxin gene assays

5. Toxin detection
74 / Beef 2007–08

Section III: Fecal Sample Evaluations—B. Sample Testing Results

Summary of operation culture status for organisms of interest based on operations characteristics 

Organism 

Salmonella Campylobacter Enterococcus C. difficile 

Operation 

characteristic Level Pos Neg 

Pvalue Pos Neg P-value Pos Neg Pvalue Pos Neg Pvalue 

Herd size (cows) 

 1-49 2 47 0.39 8 41 <0.0001 47 2 0.40 26 23 0.50 

 50-99 2 24 10 16 26 0 11 15 

 100-199 6 36 23 19 41 1 17 25 

 200 or more 6 50 36 20 56 0 22 34 

 16 157 77 96 170 3 76 97 

Region 

 West 5 34 0.46 19 20 0.008 37 2 0.22 11 28 0.01 

 Central 3 51 32 22 54 0 21 33 

 Southeast 8 72 26 54 79 1 44 36 

Antimicrobial use in feed 

 Yes 3 55 0.19 25 33 0.79 58 0 0.55 23 35 0.42 

No 13 102 52 63 112 3 53 62 

 16 157 77 96 170 3 76 97 

Antimicrobial use—oral or injection 

Any cattle 

or calves Yes 14 137 1.0 69 82 0.41 148 3 1.0 66 85 0.88 

 No 2 20 8 14 22 0 10 12 

 16 157 77 96 170 3 76 97 

Unweaned 

calves Yes 9 99 0.59 53 55 0.12 106 2 1.0 47 61 0.89 

 No 7 58 24 41 64 1 29 36 

 16 157 77 96 170 3 76 97 

Replacement 

heifers Yes 6 53 0.76 29 30 0.38 58 1 1.0 28 31 0.50 

No 10 104 48 66 112 2 48 66 

 16 157 77 96 170 3 76 97 

Cows Yes 8 76 0.90 43 41 0.09 84 0 0.25 40 44 0.34 

 No 8 81 34 55 86 3 36 53 

 16 157 77 96 170 3 76 97 
USDA APHIS VS / 75

Section IV: Methodology

Section IV: Methodology

A. Needs Assessment

The National Animal Health Monitoring System

(NAHMS) develops study objectives by

exploring existing literature and contacting

stakeholders about their informational needs and

priorities during a needs assessment phase.

Stakeholders for NAHMS studies include

industry members, allied industry

representatives, other government agencies,

animal health officials, and many others. The

objective of the needs assessment for the

NAHMS Beef 2007–08 study was to collect

information about the most important health and

productivity issues of cow-calf production. A

driving force for the needs assessment was the

desire of NAHMS to receive as much input as

possible from a variety of producers, as well as

from industry experts and representatives,

veterinarians, extension specialists, universities,

and beef organizations. Information was

collected via interviews with key industry

figures and through a Needs Assessment Survey.

The Needs Assessment Survey was designed to

identify the most critical information gaps

regarding animal health, and health and

production management from producers,

veterinarians, extension personnel, university

researchers, and allied industry groups. The

survey, created in SurveyMonkey, was available

online from September 9, 2006, through

February 15, 2007. The survey was promoted

via electronic newsletters, magazines, and Web

sites. Organizations/magazines promoting the

study included “Beef Magazine,” “Drovers,”

“Feedstuffs,” “Bovine Veterinarian,” and “The

National Cattleman.”

Email messages identifying the online site and

asking for input were also sent to State

extension personnel as well as State and Federal

animal health officials. A total of 94 people

completed the survey. Universities/extensions

accounted for 41.5 percent of respondents, and

veterinarians/consultants accounted for

31.9 percent.

Objectives for the Beef 2007–08 study, using

input from interviews, literature searches, and

the online survey, were drafted and circulated to

stakeholder groups. Following this review, six

final study objectives were identified:

1. Describe trends in beef cow-calf health and

management practices.

2. Evaluate management factors related to

beef quality assurance.

3. Describe record-keeping practices on cowcalf operations.

4. Determine producer awareness of bovine

viral diarrhea (BVD) and management

practices used for BVD control.

5. Describe current biosecurity practices.

6. Determine the prevalence and antimicrobial

resistance patterns of potential food safety

pathogens.
76 / Beef 2007–08

Section IV: Methodology

B. Sampling and Estimation

1. State selection The preliminary selection of States to be

included in the study was done in October 2006

using the National Agricultural Statistics Service

(NASS) Cattle Report. A goal for NAHMS

national studies is to include States that account

for at least 70 percent of the animals and

producer population in the United States. The

initial review identified 24 States representing

87.8 percent of the Nation’s beef-cow inventory

and 79.6 percent of operations with beef cows

(cow-calf herds). The States were: Alabama,

Arkansas, California, Colorado, Florida,

Georgia, Idaho, Iowa, Kansas, Kentucky,

Louisiana, Mississippi, Missouri, Montana,

Nebraska, New Mexico, North Dakota,

Oklahoma, Oregon, South Dakota, Tennessee,

Texas, Virginia, and Wyoming.

A memo identifying the States was provided in

November 2006 to the USDA–APHIS–VS

CEAH Director and, in turn, the VS Regional

Directors. Each Regional Director sought input

from the respective States about being included

or excluded from the study.

2. Operation

selection

The list sampling frame was provided by NASS.

Within each State a stratified random sample

was selected. The size indicator was the number

of beef cows for each operation. NASS selected

a sample of beef producers in each State for

making the January 1 cattle estimates. The list

sample from the January 2007 survey was used

as the screening sample. Those producers in the

24 States reporting 1 or more beef cows on

January 1, 2007, were included in the sample for

contact in October 2007.

3. Population

selection

a. Phase I: General Beef Management

Report; and Phase II: VS Initial and Second

Visits

Inferences cover the population of beef

producers with at least 1 beef cow in the 24

participating States. As of January 1, 2008, these

States accounted for 79.6 percent (28.6 million)

of beef cows and 79.6 percent (603,000) of

operations with beef cows in the United States.

(See Appendix III for respective data on

individual States.) All respondent data were

statistically weighted to reflect the population

from which they were selected. The inverse of

the probability of selection for each operation

was the initial selection weight. This selection

weight was adjusted for nonresponse within

each State and size group to allow for inferences

back to the original population from which the

sample was selected.
USDA APHIS VS / 77

Section IV: Methodology

C. Data and Sample Collection

1. Data collectors

and data collection

periods

a. Phase I: General Beef Management Report

From October 22 through November 30, 2007,

NASS enumerators administered the General

Beef Management Report. The interview took

slightly over 1 hour.

b. Phase II: VS Initial Visit Questionnaire

From January 14 through March 31, 2008, State

and Federal animal health personnel

administered the Beef 2007–08 VS Initial Visit

Questionnaire.

c. Phase II: VS Second Visit Questionnaire

From July 1 through August 15, 2008, State and

Federal animal health personnel administered

the Beef 2007–08 VS Second Visit

Questionnaire.

2. Biological

sample collection,

culturing, and

testing for

antimicrobial

resistance

A convenience sample of 175 operations was

identified for collection of fecal samples from

beef cows to evaluate enteric bacteria. The total

number of operations was determined by

laboratory capacity. Sample collection occurred

over two sampling periods: January 14 through

April 15, 2008, and July 7 through August 31,

2008. The number of operations in each State

was determined according to the size of the beef

cow population in the State. Operations were

selected for sampling to be approximately

representative of the distribution of herd sizes

participating in the study. Up to 40 fecal

samples of approximately 30 grams were

collected per herd, depending on number of beef

cows present. Samples were collected from

fresh fecal pats from beef cows. Samples were

shipped overnight on ice packs to a single

laboratory for further processing.

Each sample was cultured for Salmonella. Every

other sample was cultured for Campylobacter.

Every fourth sample was cultured for

Escherichia coli. Representative isolates from

each culturing effort were evaluated for

susceptibility to panels of antimicrobial drugs

using a semi-automated microdilution testing

system.

Isolates were further characterized by serotyping

(Salmonella) or speciation (Enterococcus,

Campylobacter).
78 / Beef 2007–08

Section IV: Methodology

D. Data Analysis

1. Phase I:

Validation—

General Beef

Management

Report

Initial data entry and validation for the General

Beef Management Report were performed in

individual NASS State offices. Data were

entered into a SAS® data set. NAHMS national

staff performed additional data validation on the

entire data set after data from all States were

combined.

2. Phase II:

Validation—Initial

and Second Visit

Questionnaires

After completing both VS questionnaires, data

collectors sent them to their respective State

NAHMS Coordinators who reviewed the

questionnaire responses for accuracy. Data entry

and validation were completed by CEAH staff

using SAS.

E. Sample Evaluation

The purpose of this section is to provide various

performance measurement parameters.

Historically, the term “response rate” was used

as a catchall parameter, but there are many ways

to define and calculate response rates.

Therefore, the following table presents an

evaluation based on a number of measurement

parameters, which are defined with an “x” in

categories that contribute to the measurement.
USDA APHIS VS / 79

Section IV: Methodology

1. Phase I:

General Beef

Management

Report

A total of 4,001 operations were selected for the

survey. Of these operations, 3,648

(91.2 percent) were contacted. There were 2,872

operations that provided usable inventory

information (71.8 percent of the total selected

and 78.7 percent of those contacted.) In

addition, there were 2,159 operations

(54.0 percent of total selected) that provided

“complete” information for the questionnaire.

Of operations that provided complete

information, 1,033 (47.8 percent) consented to

be contacted for consideration/discussion about

further participation in Phase II (VS collection)

of the study.

Responses for Phase I: General Beef Management Report 

Measurement Parameter

Response category 

Number 

operations 

Percent 

operations Contacts Usable1 Complete2

Survey complete and 

VMO consent 1,033 25.8 x x x 

Survey complete, 

refused VMO consent 1,126 28.1 x x x 

No beef cows on 

October 1 and July 1, 

2007 

469 11.7 x x 

Out of business 244 6.1 x x 

Out of scope (prison 

and research farms, 

etc.) 

7 0.2 

Refusal of GBMR 776 19.4 x 

Office hold (NASS 

elected not to 

contact) 

46 1.2 

Inaccessible 300 7.5 

Total 4,001 100.0 3,648 2,872 2,159 

Percent of total 

operations 91.2 71.8 54.0 

Percent of total 

operations weighted3 92.9 77.8 52.1 

1 Useable operation—respondent provided answers to inventory questions for the operation (either zero or 

positive number on hand). 

2

Survey complete operation—respondent provided answers to all or nearly all questions. 

3

Weighted response—the rate was calculated using the initial selection weights. 
80 / Beef 2007–08

Section IV: Methodology

2. Phase II: VS

Initial Visit

There were 1,033 operations that consented

during Phase I to be contacted by a veterinary

medical officer (VMO) for Phase II. Of these

1,033, 567 (54.9 percent) agreed to continue in

Phase II of the study and completed the VMO

Initial Visit Questionnaire; 365 (35.3 percent)

refused to participate. Approximately 8 percent

of the 1,033 operations were not contacted, and

2.0 percent were ineligible because they had no

beef cows at the time they were contacted by the

VMO during Phase II.

Responses for Phase II: VS Initial Visit 

Measurement Parameter 

Response category 

Number 

operations 

Percent 

operations Contacts Usable1 Complete2

Survey complete 567 54.9 x x x 

Survey refused 365 35.3 x 

Not contacted 80 7.8 

Ineligible3 21 2.0 x x 

Total 1,033 100.0 953 588 567 

Percent of total 

operations 92.2 56.9 54.9 

Percent of total 

operations weighted4 91.1 49.1 45.9 

1

Useable operation—respondent provided answers to inventory questions for the operation (either zero or 

positive number on hand). 

2

Survey complete operation—respondent provided answers to all or nearly all questions. 

3

Ineligible—no beef cows at time of interview, which occurred from January 14 through March 31, 2008. 

4

Weighted response—the rate was calculated using the turnover weights. 
USDA APHIS VS / 81

Section IV: Methodology

3. Phase II: VS

Second Visit

There were 567 operations that completed the

VS initial visit. Of these 567, 470 (82.9 percent)

agreed to continue in Phase II of the study and

completed the VMO Second Visit

Questionnaire; 60 (10.6 percent) refused to

participate. A total of 5.1 percent of the 567

operations were not contacted, and

1.2 percent were ineligible because they had no

beef cows at the time they were contacted by the

VMO during Phase II for the second visit.

Responses for Phase II: VS Second Visit 

Measurement Parameter 

Response category 

Number 

operations 

Percent 

operations Contacts Usable1 Complete2

Survey complete 470 82.9 x x x 

Survey refused 60 10.6 x 

Not contacted 29 5.1 

Ineligible3 8 1.4 x x 

Total 567 100.0 538 478 470 

Percent of total 

operations 94.9 84.3 82.9 

Percent of total 

operations weighted4

 93.9 77.7 75.8 

1

Useable operation—respondent provided answers to inventory questions for the operation (either zero or 

positive number on hand). 

2

Survey complete operation—respondent provided answers to all or nearly all questions. 

3

Ineligible—no beef cows at time of interview, which occurred from July 1 through August 15, 2008. 

4

Weighted response—the rate was calculated using the turnover weights. 
82 / Beef 2007-08

Appendix I: Sample Profile—Responding Operations

Appendix I: Sam Appendix I: Sample Profile—

Responding Oper esponding Operations

a. Number of responding operations, by herd size 

Herd size (total beef 

cow inventory) 

Phase I: General 

Beef 

Management 

Report 

Phase II: VS 

Initial Visit 

Enteric Bacteria 

Sampling 

1 to 49 819 163 49 

50 to 99 386 96 26 

100 to 199 381 125 42 

200 or more 573 183 56 

Total 2,159 567 173 

b. Number of responding operations, by region 

Region

Phase I: General 

Beef 

Management 

Report 

Phase II: VS 

Initial Visit 

Enteric Bacteria 

Sampling 

West 370 138 39 

Central 612 196 54 

South Central* 483 

233 80 

East* 694 

Total 2,159 567 173 

* Regions were combined for VS portion of study. 
USDA APHIS VS / 83

Appendix II: Organism Overviews

Appendix II: Or Appendix II: Organism

Overviews

1. Salmonella Salmonella is a gram-negative, rod-shaped

bacterium that can cause diarrheal illness in

humans and animals. Humans often acquire

Salmonella by eating foods contaminated with

animal feces. Foodborne salmonellosis in the

United States most commonly results from

Salmonella serovars enteritidis, Typhimurium,

and Newport (CDC, 2009c).

Salmonellae cause an estimated 1 million cases

of foodborne illness in the United States each

year and are estimated to result in 378 deaths

annually (Scallan, 2011b). Symptoms of

salmonellosis in humans generally occur within

8 to 72 hours following infection and include

diarrhea, abdominal cramps, and fever. Chills,

headache, nausea, and vomiting may also occur.

Antibiotics may not eliminate the infection and

may lead to resistant strains or more severe

infections; therefore, antibiotic treatment is

rarely warranted and most individuals recover

without incident in 4 to 7 days. The disease can

be life threatening, however, in infants under

2 months of age, the elderly, immune-suppressed

individuals, and people with signs of

extraintestinal infection. Treatment with

ciprofloxacin is highly effective in adults.

Antimicrobial resistance is variable and, when

detected, TMP-SMX and chloramphenicol

become appropriate alternatives (Chin, 2000).

Beef, poultry, milk, eggs as well as other foods

such as produce can be contaminated with

Salmonella. Contamination of meat more

commonly results from contamination of

carcasses with intestinal contents during

slaughter (Todar, 2000). While Salmonella is

occasionally found in raw milk, the

pasteurization process effectively kills the

organism. Cross-contamination of vegetables

can also result in disease transmission via

contact with juices from raw meat or poultry or

contamination on the farm prior to harvesting.

Safe food-handling practices are paramount, as

properly cooking meat and poultry kills the

bacteria. Likewise, food containing raw eggs

and unpasteurized milk should be avoided to

reduce the risk of salmonellosis. Sporadic cases

of salmonellosis also occur following exposure

to the feces of an infected pet or handling of

reptiles that commonly harbor salmonellae

(CDC, 2009c).
84 / Beef 2007-08

Appendix II: Organism Overviews

2. Campylobacter Campylobacter spp. are estimated to cause

approximately 850,000 cases of gastroenteritis

each year in the United States, 80 percent of

which are food related, resulting in 76 deaths

annually (Scallan, 2011b).

The infective dose, or bacterial load sufficient to

cause disease in susceptible individuals, is less

than 500 organisms. Infection can cause

diarrhea, cramping, abdominal pain, and fever

within 2 to 5 days after exposure. The diarrhea

may be bloody and associated with nausea and

vomiting as well. The infection is generally self

limiting and will resolve in 7 to 10 days without

antibiotics, although treatment with

erythromycin will decrease the amount of time

the organism is shed (Chin, 2000). Rarely,

affected individuals will develop arthritis or

Guillain-Barré syndrome as a sequela to

infection in which the immune system attacks

the body’s own nerves (CDC, 2009a).

Campylobacter is a gram-negative, slender,

curved, and motile rod. The bacterium is

microaerophilic, meaning it requires an

environment with reduced levels of oxygen.

Organisms of the genus Campylobacter are

commonly found in the intestinal tract of

companion and food animals. Disease in humans

most often occurs following exposure to raw or

undercooked poultry meat (Corry and Atabay,

2001). C. jejuni is most often responsible for

disease in humans, but rarely causes disease in

birds due to their elevated body temperatures.

Campylobacter rarely causes gastrointestinal

disease in cattle but is commonly harbored in

the intestinal tract of up to 9 percent of cattle,

C. jejuni more so than C. coli (Wesley et al.,

2000). Fecal contamination of carcasses at

slaughter yields potential for foodborne

transmission, although the organism is rarely

isolated from such sources (Hakkinen et al.,

2007). Campylobacter is rarely associated with

outbreaks; sporadic, single cases are much more

common. Outbreaks have occurred in the past,

however, and are usually related to

contaminated dairy products (Schildt et al.,

2005). Unpasteurized milk and contaminated

water also can result in outbreaks of

campylobacteriosis.
USDA APHIS VS / 85

Appendix II: Organism Overviews

3. Clostridium

difficile

Clostridium difficile is a bacterial organism

capable of producing a toxin-causing diarrheal

disease in humans and food animals.

Traditionally, the disease in humans has been

acquired in hospital settings (Kuijper et al.,

2006), more commonly in individuals with

prolonged hospitalization, greater than 65 years

of age, and antibiotic exposure (McDonald et

al., 2006). However, changes have been

observed in the epidemiology of the pathogen,

and what were previously classified as low-risk

individuals are succumbing to disease (Chernakl

et al., 2005). Furthermore, C. difficile has been

recognized as an emerging animal pathogen

(Songer and Anderson, 2006).

Molecular testing has been used to classify

strains of C. difficile and has demonstrated that

the prevalence of strains with the binary toxin

gene could indicate that animal and human

reservoirs have begun to overlap in recent years

(Rupnik, 2007). Also, nearly 30 percent of retail

ground-meat products are reported to be

positive for the organism (Rodriguez-Palacio et

al., 2007). Of note, C. difficile spores in

contaminated meats are not completely

destroyed via cooking, suggesting that all meat

products, including ready-to-eat foods, may act

as a potential source of foodborne transmission

of C difficile to humans.

C. difficile is a spore-forming, gram-positive,

anaerobic bacillus that produces a number of

different exotoxins resulting in gastrointestinal

infections in humans and animals. In recent

years, reports indicate that C. difficile-associated

disease has increased in terms of rates and

severity of disease (Jhung et al., 2008), which

has also led to a heightened public health

concern over the disease. C. difficile infection in

humans results in watery diarrhea consisting of

three or more bowel movements per day for 2 or

more days, fever, loss of appetite, nausea, and

abdominal pain. The disease generally responds

to 10-day treatments with metronidazole or

vancomycin (Johnson and Gerding, 1998).

4. Commensal

Escherichia coli

Commensal Escherichia coli are normal

inhabitants of the gastrointestinal tract of

livestock and humans and do not typically cause

disease. Shiga toxin-producing E. coli, of which

O157:H7 is included, rarely causes clinical

disease in cattle but can cause food-related

outbreaks of gastrointestinal disease in humans

(CDC, 2009b). Antimicrobial resistance remains

a concern in commensal E. coli of cattle and

other food animals due to the potential transfer

of resistance elements to zoonotic pathogens

inhabiting the gut (Sharma et al, 2008).

Commensal E. coli is also important as it is

often used as an indicator organism to assess the

extent and type of resistance in the

gastrointestinal tract, since it plays a dynamic

role in the ecology of multidrug-resistant

bacteria and has shown to be a reservoir of

resistance (Carson et al, 2001).
86 / Beef 2007–08

Appendix III: Number of Beef Cows by Region

Number of Beef Cows on January 1, 2008* 

Region State 

Beef cow 

inventory 

Jan. 1, 2008 

(Thousand Head) 

Beef cow 

operations 

2007 

West California 655 11,200 

Colorado 730 9,900 

 Idaho 460 7,100 

Montana 1,523 11,000 

 New Mexico 460 5,900 

Oregon 605 11,500 

 Wyoming 733 4,800 

Total 5,166 61,400 

Central Iowa 1,015 25,000 

Kansas 1,511 26,000 

 Missouri 2,080 54,000 

Nebraska 1,883 20,000 

 North Dakota 922 10,500 

South Dakota 1,644 14,500 

 Total 9,055 150,000 

Southeast Alabama 677 23,000 

Arkansas 943 26,000 

Florida 936 15,500 

Georgia 553 17,500 

Kentucky 1,159 38,000 

Louisiana 513 12,100 

Mississippi 519 18,500 

Oklahoma 2,053 48,000 

Tennessee 1,079 42,000 

Texas 5,240 130,000 

Virginia 692 21,000 

Total 14,364 391,600 

Total (24 States) 28,585 603,000 

Percentage of U.S. 87.8 79.6 

Total U.S. (50 States) 32,553 757,900 

*Source: NASS Cattle report, February 1, 2008, and NASS Farms, Land in Farms, and Livestock Operations 

2007 Summary report, February 2008. An operation is any place having one or more head of beef cows, 

excluding cows used to nurse calves, on hand at any time during the year. 

Appendix III: N Appendix III: Number of umber of

Beef Co Beef Cows, by Region
USDA APHIS VS / 87

Appendix IV: American Veterinary Medical Association Judicious Use Principles

Appendix IV Appendix IV: American

Veterinary Medical y Medical

Association Judicious Use Association Judicious Use

Principles inciples

American Veterinary Medical Association

Position Statement1

”When the decision is reached to use

antimicrobials for therapy, veterinarians should

strive to optimize therapeutic efficacy and

minimize resistance to antimicrobials to protect

public and animal health.”

AVMA Judicious Use Principles

• Preventive strategies, such as appropriate

husbandry and hygiene, routine health

monitoring, and immunization, should be

emphasized.

• Other therapeutic options should be

considered prior to antimicrobial therapy.

• Judicious use of antimicrobials, when

under the direction of a veterinarian,

should meet all requirements of a

veterinarian-client-patient relationship.

• Prescription, Veterinary Feed Directive,

and extralabel use of antimicrobials must

meet all the requirements of a

veterinarian-client-patient relationship.

Extralabel antimicrobial therapy must be

prescribed only in accordance with the Animal

Medicinal Drug Use Clarification Act

amendments to the Food, Drug, and Cosmetic

Act and its regulations.

Veterinarians should work with those

responsible for the care of animals to use

antimicrobials judiciously regardless of the

distribution system through which the

antimicrobial was obtained.

Regimens for therapeutic antimicrobial use

should be optimized using current

pharmacological information and principles.

Antimicrobials considered important in treating

refractory infections in human or veterinary

medicine should be used in animals only after

careful review and reasonable justification.

Consider using other antimicrobials for initial

therapy.2

Use narrow spectrum antimicrobials whenever

appropriate.

Utilize culture and susceptibility results to aid in

the selection of antimicrobials when clinically

relevant.

Therapeutic antimicrobial use should be

confined to appropriate clinical indications.

Inappropriate uses such as for uncomplicated

viral infections should be avoided.

Therapeutic exposure to antimicrobials should

be minimized by treating only for as long as

needed for the desired clinical response.

Limit therapeutic antimicrobial treatment to ill

or at risk animals, treating the fewest animals

indicated.

Minimize environmental contamination with

antimicrobials whenever possible.

Accurate records of treatment and outcome

should be used to evaluate therapeutic regimens. 1 AVMA, 2008.

2

In this context, this principle takes into account development of

resistance or cross-resistance to important antimicrobials.
88 / Beef 2007–08

Appendix V: AABP Revised Prudent Drug Usage Guidelines

Appendix V: AABP Revised

Prudent Drug Usage

Guidelines

The production of safe and wholesome animal

products for human consumption is a primary

goal of members of the AABP. In reaching that

goal, the AABP is committed to the practice of

preventive immune system management through

the use of vaccines, parasiticides, stress

reduction and proper nutritional management.

The AABP recognizes that proper and timely

management practices can reduce the incidence

of disease and therefore reduce the need for

antimicrobials.

Nevertheless, antimicrobials remain a necessary

tool to manage infectious diseases in beef and

dairy herds. Prudent use of antimicrobials is

necessary to reduce animal pain and suffering,

to protect the economic livelihood of beef and

dairy producers, to ensure the continued

production of foods of animal origin, and to

minimize the shedding of zoonotic bacteria into

the environment and potentially the food chain.

Following are general guidelines for the prudent

use of antimicrobials in beef and dairy cattle.

1. The veterinarian’s primary responsibility to

the client is to help design management,

immunization, housing and nutritional

programs that will reduce the incidence of

disease and the need for antimicrobials.

2. Antimicrobials should be used only within

the confines of a valid veterinarian-clientpatient relationship; this includes both

dispensing and the issuance of

prescriptions. Extra-label usage should be

within the provisions contained within the

AMDUCA regulations.

3. The veterinarian should have strong clinical

evidence of the identity of the pathogen

causing the disease, based upon clinical

signs, history, necropsy examination,

laboratory data and past experience. He/she

should periodically monitor herd pathogen

susceptibility and therapeutic response to

detect changes in microbial susceptibility

and to re-evaluate antimicrobial selections.

4. Product choices and regimens should be

based on available laboratory and package

insert information, additional data in the

literature and consideration of the

pharmacokinetics, spectrum and

pharmacodynamics of the drug.

Antimicrobials should be used with a

specific clinical outcome(s) in mind, such

as fever reduction or return of mastitic milk

to normal.

5. Antimicrobials should be used at a dosage

and duration appropriate for the condition

treated. The goals of therapy should be to

alleviate clinical signs and minimize

recurrence of clinical disease.

6. Treatment of chronic cases should be

avoided if the likelihood of antimicrobial

resistance outweighs the chances of

pathogen elimination. Chronic cases should

be removed or isolated from the remainder

of the herd to minimize disease spread

within the herd.

7. When appropriate, local therapy (e.g.

intramammary, intrauterine, topical) is

preferred over systemic therapy.
USDA APHIS VS / 89

Appendix V: AABP Revised Prudent Drug Usage Guidelines

8. Combination antimicrobial therapy should

be discouraged unless there is information

to show an increase in efficacy or

suppression of resistance development for

the target organism.

9. Prophylactic or metaphylactic use of

antimicrobials should be based on a group,

source or production unit evaluation rather

than standard practice.

10. Compounding of antimicrobial

formulations should be avoided unless

science based pharmacokinetic and

pharmacodynamic data to support the use of

such products are available.

11. Quantities of antimicrobials prescribed or

dispensed should be appropriate in order to

avoid stockpiling of antimicrobials on the

farm.

12. Veterinarians should participate in

continuing education programs regarding

emergence and/or development of

antimicrobial resistance and prudent drug

usage. Whenever possible, veterinarians are

encouraged to utilize this information to

provide written guidelines that describe

conditions and instructions for

antimicrobial use at each farm or unit.

13. Veterinarians should play a major role in

training farm personnel who use

antimicrobials on diagnosis of common

diseases, indications for antimicrobial use,

dosage, withdrawal times, route of

administration, injection site precautions,

storage, handling and record keeping.

Guidelines 1-13 adapted from American

Veterinary Medical Association, American

Association of Bovine Practitioners, and

Academy of Veterinary Consultants Appropriate

Veterinary Antibiotic Use Guidelines.
90 / Beef 2007–08

Appendix VI: References

Appendix VI: R Appendix VI: References

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HR, Low DE, Weese JS. Use of a selective

enrichment broth to recover Clostridium difficile

from stool swabs stored under different

conditions. J Clin Microbiol 2005; 43:5341–

5343.

AVMA. Judicious Therapeutic Use of

Antimicrobials. 2008. Available at:

http://www.avma.org/issues/policy/jtua.asp

Kikuchi E, Miyamato Y, Narushima S, Iton K.

Design of species-specific primers to identify 13

species of Clostridium harbored in human

intestinal tracts. Microbiol Immunol 2002;

46:353–358.

Linton AH. Antibiotic resistance: the present

situation reviewed. Vet Rec 1977; 100(17):354–

360.

Mascaretti OA. Bacteria versus Antibacterial

Agents. ASM Press, Washington, DC. 2003.

National Research Council. The Use of Drugs in

Food Animals, Benefits and Risks. National

Academy Press, Washington, DC. 1999.

Prescott JF, Baggot JD, Walker RD.

Antimicrobial Therapy in Veterinary Medicine.

Iowa State Univ Press, Ames, IA. 2000.

Scallan E, Griffin PM, Angulo FJ, Tauxe RV,

Hoekstra RM. Foodborne illness acquired in the

United States—unspecified agents. Emerg Infect

Dis 2011a; 17(1):16–22.

Scallan E, Hoekstra RM, Angulo FJ, Tauxe RV,

Widdowson MA, Roy SL, Jones JL. Foodborne

illness acquired in the United States—major

pathogens. Emerg Infect Dis 2011b; 17(1):7–15.

Scharff RL. Health-related costs from

foodborne illness in the United States. 2010.

Available at http://ww.producesafetyproject.org/

admin/assets/files/Health-Related-FoodborneIllness-Costs-Report.pdf-1.pdf. Accessed

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Stern NJ, Line JE. Comparison of three methods

for recovery of Campylobacter spp. from broiler

carcasses. J Food Prot 1992; 55(9):663–666.