FOOD SAFETY

Preslaughter 

Interventions Could 

Reduce E. coli in 

Cattle

Report to the Secretary of Agriculture

March 2012

GAO-12-257

United States Government Accountability Office

GAO
United States Government Accountability Office

Highlights of GAO-12-257, a report to the 

Secretary of Agriculture

March 2012

FOOD SAFETY 

Preslaughter Interventions Could Reduce E. coli in 

Cattle

Why GAO Did This Study

Since 2006, the U.S. beef industry has 

recalled over 23 million pounds of beef 

owing to contamination from 

pathogenic strains of Shiga toxinproducing Escherichia coli (STEC)

bacteria. These strains do not harm

cattle but may contaminate meat 

during slaughter. If humans eat 

contaminated meat without properly 

cooking it, STEC can cause illnesses, 

including bloody diarrhea and 

Hemolytic Uremic Syndrome, which is 

characterized by kidney failure and can

be fatal. The Departments of Health 

and Human Services (HHS) and of

Agriculture (USDA) play a role in 

reducing STEC. USDA stated that 

interventions to reduce STEC before 

slaughter offer a significant opportunity

to improve food safety.

GAO reviewed (1) interventions before 

slaughter that may help reduce STEC

in cattle; (2) USDA’s role in approving 

STEC vaccines; (3) the extent to which 

STEC strains have been determined to 

be adulterants in beef and the status of 

tests to detect them; and (4) practices, 

if any, other countries have employed 

that could reduce STEC in cattle and

may be relevant to U.S. efforts. GAO 

reviewed documents; visited cattle 

feedlots and a slaughter plant; and 

interviewed agency officials, 

researchers, and industry and 

consumer group representatives with 

expertise in STEC in cattle. 

What GAO Recommends

GAO recommends, among other 

things, that USDA provide more 

specific public guidance on the license 

approval requirements of STEC

vaccines. USDA neither agreed nor 

disagreed with this recommendation. 

What GAO Found

U.S. Department of Agriculture (USDA) and university researchers identified 

several treatments administered before cattle are slaughtered, or preslaughter 

interventions, that could reduce Shiga toxin-producing Escherichia coli (STEC) in 

cattle. Such preslaughter interventions include bacteriophages (viruses that infect 

and kill bacteria), probiotics (live bacteria that can benefit the digestive system), 

vaccines (biological preparations that alter the immune system), and sodium 

chlorate (chemical that kills the STEC O157:H7 strain). However, few

manufacturers have submitted applications for preslaughter intervention products 

to target STEC according to officials from USDA and the Food and Drug 

Administration. One exception is for vaccines to reduce STEC O157:H7. 

For preslaughter interventions, USDA exercises responsibilities for licensing and 

regulating STEC vaccines. However, USDA’s approval requirements for these 

vaccines are unclear, according to some industry representatives. Specifically, 

USDA’s general guidance does not address some of the unique challenges faced 

by manufacturers of animal health products seeking STEC vaccine approval. For 

example, the guidance does not explain that, if studies conducted in the 

laboratory are insufficient to demonstrate efficacy, the manufacturer would also 

need to demonstrate that the vaccine is effective in a field setting such as a 

feedlot. In contrast, the Canadian Centre for Veterinary Biologics provides more 

specific guidance about when it requires the use of laboratory or field studies to 

demonstrate efficacy for vaccine license applications. Without guidance that 

gives manufacturers clear and more specific information they need to submit for 

an acceptable application, the approval process for STEC vaccines could face 

potential delays. 

In addition to STEC O157:H7, which it stated in 1994 was an adulterant—a 

substance that renders food injurious to human health—in September 2011,

USDA determined that six other STEC strains were adulterants in raw ground 

beef and beef trim (meat left after steaks and roasts are cut from beef). USDA 

has tests for these six strains and plans to use them in slaughter plants starting 

in June 2012. However, it may be difficult and time-consuming to confirm positive 

test results because certain test components are either not commercially

available for all strains or do not always provide clear results. USDA is working to 

improve the tests and to find a commercial supplier for one key test component.

Also, a few companies voluntarily test for these strains. 

Some foreign governments have practices that could be relevant to U.S. efforts 

to reduce STEC in cattle such as the following: 

• The European Parliament and the Council of the European Union require

certain measures, such as verification of cleanliness by an inspector, to 

ensure that the cattle going to slaughter are clean. In contrast, USDA 

assesses the health of cattle but does not inspect for cleanliness. 

• At least 12 European Union member countries collected and reported 

data on STEC in live cattle in 2009. USDA has conducted STEC testing 

in live cattle, but has not tested since 1999.

• When a person becomes ill from E. coli in Sweden, government officials 

try to determine the specific farm that sold the contaminated cattle so 

that other carcasses from the farm can be tested for STEC. USDA does 

not trace the STEC source back to the farm.

View GAO-12-257 or key components.

For more information, contact Lisa Shames at 

(202) 512-3841 or shamesl@gao.gov.
Page i GAO-12-257 E. coli Contamination in Beef

Letter 1 

Background 3

Several Interventions Could Reduce STEC in Cattle 8

USDA Exercises Responsibility for Approving STEC Vaccines, but 

Its Approval Requirements Are Unclear 14

USDA Determined That Six Additional STEC Strains Were 

Adulterants and Has Tests to Detect Them 16

Some Countries Have Practices That Could Be Relevant to U.S. 

Efforts to Reduce STEC in Cattle 20

Conclusions 22

Recommendations for Executive Action 22

Agency Comments and Our Evaluation 22

Appendix I Objectives, Scope, and Methodology 25

Appendix II Comments from the U. S. Department of Agriculture 27

Appendix III GAO Contact and Staff Acknowledgments 29

Tables

Table 1: Agencies with Responsibilities Related to STEC 

Contamination in Beef 6

Table 2: Approval Status and Challenges for Preslaughter 

Interventions 12

Figures

Figure 1: STEC O157:H7 Bacteria 4

Figure 2: Beef Production Process 7

Figure 3: Preliminary and Isolation and Confirmation Testing 

Phases for the Six STEC Non-O157 Strains 19

Contents
Page ii GAO-12-257 E. coli Contamination in Beef

Abbreviations

APHIS Animal and Plant Health Inspection Service

ARS Agriculture Research Service

CDC Centers for Disease Control and Prevention

FDA Food and Drug Administration

FSIS Food Safety and Inspection Service

HACCP Hazard Analysis and Critical Control Point

HHS Department of Health and Human Services

NIFA National Institute of Food and Agriculture

STEC Shiga Toxin-Producing Escherichia coli

USDA U.S. Department of Agriculture

This is a work of the U.S. government and is not subject to copyright protection in the 

United States. The published product may be reproduced and distributed in its entirety 

without further permission from GAO. However, because this work may contain 

copyrighted images or other material, permission from the copyright holder may be 

necessary if you wish to reproduce this material separately.
Page 1 GAO-12-257 E. coli Contamination in Beef

United States Government Accountability Office

Washington, DC 20548

March 9, 2012

The Honorable Thomas J. Vilsack

Secretary of Agriculture

Dear Mr. Secretary:

Since 2006, the U.S. beef industry has recalled over 23 million pounds of 

beef because of contamination from pathogenic strains of Shiga toxinproducing Escherichia coli (STEC). These bacterial STEC strains can live 

in the intestines or on the hide of cattle without harming them, but they 

may contaminate meat during the slaughter process. If humans then 

consume the contaminated meat without properly cooking it, STEC 

strains can cause illnesses, including bloody diarrhea and Hemolytic 

Uremic Syndrome, which is characterized by kidney failure and can be 

fatal. The Centers for Disease Control and Prevention (CDC) does not 

have estimates specific to beef, but it estimates that STEC contamination 

of food consumed domestically causes approximately 176,000 illnesses, 

2,400 hospitalizations, and 20 deaths annually. Illnesses caused by 

STEC O157:H7, the most common STEC strain in the United States, cost 

those infected $489 million annually, in 2010 dollars, according to an 

estimate from the U.S. Department of Agriculture (USDA).

In addition to STEC O157:H7, over 150 other STEC strains can cause 

illness. In this report, we refer to these strains as STEC non-O157, and 

CDC has identified six common groups of such strains that cause 

approximately 113,000 illnesses in the United States each year. These 

strains are known as O26, O45, O103, O111, O121, and O145.

USDA’s Food Safety and Inspection Service (FSIS) is responsible for 

examining and inspecting the carcasses and parts of cattle at slaughter 

plants and meat processing plants that will be used for human 

consumption. The Federal Meat Inspection Act prohibits the sale of 

adulterated meat or meat products—products bearing or containing a 

poisonous or deleterious substance that may render them injurious to 

human health, among other things—and provides FSIS with the authority 

to prescribe rules and regulations concerning the sanitation at slaughter 

plants and meat-processing plants. In 1994, FSIS stated that it 

considered STEC O157:H7 an adulterant in ground beef, which according 

to a USDA report, is the most frequently implicated source of STEC 

O157:H7 outbreaks in the United States. FSIS’s inspection authority does 

not extend to the feedlot, where most cattle are fed grain for about 140 

 
Page 2 GAO-12-257 E. coli Contamination in Beef

days prior to slaughter, but the agency encourages beef producers to use 

preslaughter interventions, such as vaccinating the animal against STEC, 

to control STEC O157:H7. FSIS has stated that such interventions offer a 

significant opportunity to improve food safety because they may reduce 

the level of STEC entering the slaughter plant. The beef industry 

generally supports researching and developing these interventions and 

has funded many intervention activities for possible future use.

In this context, we reviewed USDA’s and others’ efforts to reduce STEC 

contamination in beef. Our objectives were to identify (1) preslaughter 

interventions—that is, treatments administered before cattle are 

slaughtered that can target STEC—that may help reduce STEC in cattle; 

(2) USDA’s role in approving STEC vaccines; (3) the extent to which 

STEC strains have been determined to be adulterants in beef and the 

status of tests to detect them; and (4) practices, if any, other countries 

have employed that could reduce STEC in cattle and may be relevant to 

U.S. efforts.

For all four objectives, we visited several cattle feedlots and a cattle 

slaughter plant in Colorado, which we selected because it is one of the 

largest beef producing states, and interviewed USDA officials, beef 

industry representatives, and university researchers in Colorado. In 

addition, using a nonprobability sample, we conducted a total of 71 

interviews with USDA, CDC, and Food and Drug Administration (FDA) 

officials; foreign government officials; beef industry representatives; 

manufacturers of animal health products; federal and university 

researchers; and consumer group representatives with expertise in STEC 

in cattle. Because this was a nonprobability sample, the results cannot be 

generalized to the entire United States, but can provide examples of 

research conducted on preslaughter interventions. To determine the 

preslaughter interventions that may help reduce STEC in cattle, we 

reviewed USDA and academic studies on preslaughter interventions, 

reviewed USDA documents on funding for STEC research, and met with 

USDA and university researchers and beef and pharmaceutical industry 

representatives. To determine USDA’s role in approving STEC vaccines, 

we reviewed USDA guidance and interviewed USDA officials, 

manufacturers of animal health products, and university researchers. To 

determine the extent to which STEC strains have been determined to be 

adulterants in beef and the status of tests to detect them, we reviewed 

USDA documents on STEC detection tests and interviewed FDA and 

USDA officials, beef industry representatives, and detection test 

manufacturers. To determine practices, if any, other countries have 

employed that could reduce STEC in cattle and may be relevant to U.S. 
Page 3 GAO-12-257 E. coli Contamination in Beef

efforts, we asked CDC, FDA, and USDA officials; beef industry 

representatives; university researchers; and consumer group 

representatives if they were aware of any such practices. We also 

reviewed international studies, guidance, and requirements for food 

safety in beef and interviewed international food safety officials. Appendix 

I contains an expanded explanation of our objectives, scope, and 

methodology.

We conducted this performance audit from January 2011 to March 2012 

in accordance with generally accepted government auditing standards. 

Those standards require that we plan and perform the audit to obtain 

sufficient, appropriate evidence to provide a reasonable basis for our 

findings and conclusions based on our audit objectives. We believe that 

the evidence obtained provides a reasonable basis for our findings and 

conclusions based on our audit objectives.

This section discusses STEC and agencies that play a role in reducing 

STEC contamination.

E. coli bacteria live in the intestines of healthy cattle and have a symbiotic 

relationship with the cattle, an association in which the E. coli derives the 

benefit, and cattle are not harmed. The organism has been found in 

young beef calves and older cows, as well as in dairy calves and dairy 

cows. E. coli tends to colonize at the end of a cow’s intestinal system, in 

an area known as the anorectal junction. A cow with E. coli in its intestinal 

system typically “sheds” the organism through its feces. As cattle shed 

E. coli, the bacteria can contaminate the hides and then the meat as the 

cattle are slaughtered. Several strains of E. coli have evolved to being 

highly pathogenic and capable of causing death when they infect 

humans.

STEC O157:H7, pictured in figure 1, is the strain of STEC bacteria of 

primary interest to USDA and researchers. STEC O157:H7 was first 

recognized as a disease-causing organism in 1982 and became a 

research priority in 1993, when over 700 people were affected after eating 

undercooked hamburgers at a fast-food restaurant chain. This outbreak 

was the largest reported outbreak in North America, and 55 patients, 

including 4 children who died, developed Hemolytic Uremic Syndrome. 

Symptoms of STEC O157:H7 can also include severe bloody diarrhea, 

profuse bleeding, seizures, kidney failure, coma, and death.

Background 

Shiga Toxin-Producing E. 

coli
Page 4 GAO-12-257 E. coli Contamination in Beef

Figure 1: STEC O157:H7 Bacteria

In 1994, USDA’s FSIS made public that it considered STEC O157:H7 as 

an adulterant in raw ground beef; it established a zero-tolerance policy for 

this pathogen in this food product and began a sampling program to test 

for the pathogen in federally inspected establishments and retail stores. 

FSIS also made public that it would use available enforcement tools, such 

as requesting a recall from beef producers if the product had entered 

commerce. Any raw ground beef found to contain STEC O157:H7 must 

be disposed of or sent for further processing that involves a “lethality 

step,” such as cooking the meat before selling it.1

Under current law, thousands of FSIS regulatory inspectors maintain 

continuous inspection at slaughter facilities and examine all slaughtered 

meat carcasses. Inspectors also visit other meat-processing facilities at 

least once each operating day. In 1996, FSIS established Hazard 

 

1

According to FSIS, thorough cooking of ground beef to an internal temperature of 160° F 

throughout kills STEC O157:H7.
Page 5 GAO-12-257 E. coli Contamination in Beef

Analysis and Critical Control Point (HACCP) system requirements for all 

processing plants. The HACCP system requires that plants identify 

biological, chemical, and physical food safety hazards that are reasonably 

likely to occur and develop and implement plans to prevent and control 

those hazards.

In addition to STEC O157:H7, CDC has identified six groups of STEC 

strains—O26, O45, O103, O111, O121, and O145—that are also 

pathogenic. These STEC non-O157 strains have been found in ground 

beef and on cattle hides and feces at levels comparable to those for 

STEC O157:H7, and they have been found to cause the same human 

illnesses. In 2010, for the first time, the number of laboratory-confirmed 

STEC infections from strains other than STEC O157:H7 was greater than 

the number of STEC O157:H7 infections.

Two federal departments are primarily responsible for ensuring the safety 

of the U.S. food supply, including the prevention of STEC 

contamination—USDA and the Department of Health and Human 

Services (HHS). Each department contains agencies that contribute to 

the national effort to assess, measure, and track STEC contamination 

(see table 1).

Agencies that Play a Role 

in Reducing STEC 

Contamination 
Page 6 GAO-12-257 E. coli Contamination in Beef

Table 1: Agencies with Responsibilities Related to STEC Contamination in Beef

Department and agency Responsibilities related to STEC contamination in beef

USDA

Food Safety and Inspection Service Regulates the safety, wholesomeness, and proper labeling of domestic and imported meat 

under authority of the Federal Meat Inspection Act.

a

Animal and Plant Health Inspection 

Service (APHIS)

Inspects slaughter plants, processing 

plants, and import establishments in the United States and can keep some products from 

entering the food supply via meat inspections at the plant level. May not mandate recalls of 

contaminated meat but does provide assistance and monitors voluntary recalls by the beef 

industry. Provides guidance to the beef industry regarding best practices for reducing STEC 

contamination.

Protects U.S. livestock and poultry from domestic and foreign diseases and pests under the 

Animal Health Protection Act.b

Agricultural Research Service (ARS)

Reviews and approves applications for biological product 

licenses, such as vaccines, that could be used as part of a STEC preslaughter intervention. 

Manages the National Animal Health Monitoring System—a periodic, national survey of 

producers that focuses on management practices and animal health in feedlots. 

Conducts research on a variety of STEC-related issues, such as prevention of STEC 

colonization in cattle, interventions to reduce STEC in beef, and STEC strain detection 

methods.

National Institute of Food and 

Agriculture (NIFA)

Funds research on the prevention, detection, and colonization of STEC in cattle through 

grants to universities and other organizations.

HHS

FDA Regulates the manufacture and distribution of food, food additives, and drugs for humans and 

animals under the Federal Food, Drug and Cosmetic Act.c

CDC

Ensures the safety and 

effectiveness of animal drugs, including those intended to reduce STEC prevalence in cattle, 

such as sodium chlorate. 

Routinely gathers information from local and state health departments and laboratories and 

reports information about human STEC infections and the foods with which they are 

associated.

Source: GAO.

a

21 U.S.C. §§ 601-683.

b

7 U.S.C. §§ 8301-8322.

c

Several steps are involved in getting cattle from the farm to the consumer. 

Often, USDA and FDA provide regulatory oversight after the cattle leave 

the farm or feedlot and arrive at slaughter plants and food handling and 

manufacturing facilities. Figure 2 illustrates the beef production process 

from the farm to the consumer.

21 U.S.C. §§ 301-399d.
Page 7 GAO-12-257 E. coli Contamination in Beef

Figure 2: Beef Production Process

In 2007, GAO designated federal oversight of food safety as a high-risk 

area because of risks to the economy and to public health and safety. As 

GAO has reported, the current fragmented system has caused 

inconsistent oversight, ineffective coordination, and inefficient use of 

resources.2

 

2

See most recently in GAO, Federal Food Safety Oversight: Food Safety Working Group 

Is a Positive First Step but Governmentwide Planning Is Needed to Address 

Fragmentation, GAO-11-289 (Washington, D.C.: Mar. 18, 2011).
Page 8 GAO-12-257 E. coli Contamination in Beef

USDA and university researchers identified several potential preslaughter 

interventions—including probiotics, sodium chlorate, and vaccines—that 

could reduce STEC O157:H7 in cattle and, in some cases, may have 

potential for reducing other strains of STEC. USDA conducts and funds 

research relevant to these interventions, including research on the 

prevalence of STEC and on the interventions themselves.

Preslaughter interventions are treatments administered before cattle are 

slaughtered that can target STEC, usually the O157:H7 strain. Some 

interventions, such as sodium chlorate and vaccines, may also reduce 

other pathogenic strains, but researchers have not conducted testing for 

the effects of interventions on other strains. According to representatives 

for a beef industry group, most research on preslaughter interventions 

has focused on those administered at the feedlots, although they may 

also be administered in the holding pen of a slaughter plant. Preslaughter 

interventions are not likely to eliminate STEC O157:H7 in cattle; instead, 

the goal is to reduce the pathogen to levels that the HACCP systems at 

slaughter plants are able to control effectively, according to beef industry 

representatives and researchers. They also said that multiple 

interventions are needed to accomplish this. Some studies suggest that a 

few interventions are effective in reducing STEC O157:H7 in the digestive 

systems or on the hides of cattle, but it may be difficult to demonstrate 

that they reduce the levels of STEC O157:H7 in beef, according to 

manufacturers of animal health products and researchers.

USDA and university researchers we spoke with identified several 

potential preslaughter interventions for reducing STEC O157:H7 and, in 

some cases, these interventions may have potential for reducing other 

strains of STEC. Some of these interventions are in use for other 

purposes, but few manufacturers have submitted applications for 

preslaughter intervention products to target STEC—with the exception of 

bacteriophages (viruses that infect and kill bacteria) and vaccines—

according to officials from USDA and FDA. The following are the 

interventions that researchers identified, along with challenges for 

bringing these interventions to market:

• Antimicrobials. These are drugs used to treat infections by 

microorganisms, such as bacteria and viruses, and include synthetic 

and natural antibiotics. Antibiotics are currently used in cattle to treat 

or prevent diseases and increase growth. According to some 

researchers, it may not be feasible for industry to use antibiotics as a 

preslaughter intervention to reduce STEC because of concerns that 

Several Interventions 

Could Reduce STEC 

in Cattle

Researchers Identified 

Preslaughter Interventions 

That Could Reduce STEC

in Cattle
Page 9 GAO-12-257 E. coli Contamination in Beef

such use will lead to greater prevalence of bacteria that are resistant 

to antibiotics. If resistant bacteria were to reach humans and cause 

illness, this illness might be more difficult to treat. Researchers also 

said that, for the same reason, it is unlikely that the veterinary 

pharmaceutical industry would pursue requesting approval for 

antibiotics as a preslaughter intervention. In April 1999, we reported 

that according to scientists, resistant strains of E. coli found in 

humans acquired resistance to antibiotics while in food animals.3

• Bacteriophages. These naturally occurring viruses infect bacteria and 

are highly specific—each type typically can kill a single strain or 

species of pathogenic bacteria. USDA, in consultation with FDA, 

licensed a mixture of bacteriophages that may be applied to cattle 

hides in holding pens at slaughter plants. Other bacteriophages, 

which could be administered orally, are at the experimental stage. 

According to researchers, it is possible for STEC O157:H7 to become 

resistant to some bacteriophages.

Resistant strains of E. coli may be transferred to humans through food 

or through contact with animals or animal waste.

• Colicins. These antimicrobial proteins are produced by certain STEC 

strains and can kill other strains. According to researchers, studies to 

date on the use of colicins to reduce STEC in cattle are few, and 

colicins are difficult to produce and expensive to use in studies.

• Natural product extracts. These are compounds that are generally 

extracted from spices, aromatic herbs, fruits, and flowers, but can also 

be obtained from other natural products, such as marine plants. In 

particular, essential oils—a type of natural product extract—

demonstrate antimicrobial activity that may reduce STEC O157:H7, 

according to researchers. Studies on the effect of essential oils on 

STEC O157:H7 in cattle are limited to the laboratory, but USDA and 

university researchers are developing field trials of citrus by-products, 

such as orange peel, which contain essential oils. Some compounds, 

or the products from which they are extracted, such as orange peel 

and brown seaweed extract, are currently used in cattle feed in some 

 

3

GAO, Food Safety: The Agricultural Use of Antibiotics and Its Implications for Human

Health, GAO/RCED-99-74 (Washington, D.C.: Apr. 28, 1999). For more information about 

the use of antibiotics in animals, see GAO, Antibiotic Resistance: Agencies Have Made 

Limited Progress Addressing Antibiotic Use in Animals, GAO-11-801 (Washington, D.C.: 

Sept. 7, 2011).
Page 10 GAO-12-257 E. coli Contamination in Beef

feedlots. Research is unclear on how much of the compounds or the 

products from which they are extracted, such as citrus and thyme oils, 

will pass through the cattle’s stomach, and it may be challenging to 

obtain a large quantity of these compounds to feed to cattle on a 

commercial basis, according to researchers.

• Prebiotics. These nondigestible organic compounds can promote the 

growth and activity of beneficial bacteria in the digestive system of 

cattle, which in turn can reduce the prevalence of bacterial pathogens. 

According to USDA researchers, little work has been conducted on 

the effects of these compounds on STEC O157:H7 in cattle. 

Furthermore, the compounds may be expensive to use in cattle and 

may not pass through the cattle’s stomach.

• Probiotics. These are live bacteria that can benefit the digestive 

system of cattle. According to USDA researchers, probiotics can 

prevent harmful colonization by bacteria by producing antibacterial 

compounds or by promoting healthy immune function. Researchers 

have conducted field trials to test whether varying amounts of certain 

probiotic strains reduce STEC O157:H7. Probiotics are widely used to 

increase weight gain. According to a few researchers, in order for 

probiotics to reduce STEC O157:H7, cattle may need to be fed large 

quantities, which may be costly to producers.

• Sodium chlorate. This chemical kills STEC O157:H7 when it 

transforms to toxic chlorite inside the bacterial cell. This 

transformation occurs in both the stomach and the intestinal tract of 

cattle. According to representatives for a veterinary pharmaceutical 

manufacturer, the manufacturer is discussing with FDA applying for 

approval of sodium chlorate as an animal drug. According to a few 

researchers, it is likely that sodium chlorate would also reduce STEC 

non-O157.

• Vaccines. These are biological preparations that alter the immune 

system to better fight specific pathogens. At least two manufacturers 

of animal health products have developed vaccines to target STEC 

O157:H7 in cattle and are seeking approval from APHIS to market 

them. One of these manufacturers received a conditional license for a 

vaccine in 2009 and, according to representatives from these 

manufacturers, applications for full licenses for two vaccines are 
Page 11 GAO-12-257 E. coli Contamination in Beef

pending.4

Table 2 provides a summary of preslaughter interventions, their approval 

status, the agency responsible for their approval, and challenges for the 

use of intervention.

According to a few researchers and representatives for a 

veterinary pharmaceutical manufacturer, administering higher doses 

of a vaccine would increase its efficacy but may be costly. For 

example, handling the cattle to specifically administer a STEC vaccine 

may increase labor costs. USDA officials also said that cattle 

producers may not directly benefit from administering these vaccines. 

Additionally, according to one university researcher and one animal 

health product manufacturing official, vaccines have the potential to 

reduce STEC non-O157, but a vaccine study of STEC non-O157 has 

not been conducted on animals. APHIS officials told us that they have 

not received information that could support this theory.

 

4

Conditional licenses are effective for a finite period, usually 1 year and may be renewed 

at the discretion of APHIS. The data required for conditional licensure are reduced from 

that needed for full licensure in that there needs only to be a “reasonable expectation” of 

efficacy as defined by APHIS. Conditional licenses are not required prior to receiving a full 

license but can be used to bring a product to market. For example, the conditional license 

for the STEC O157:H7 vaccine allows cattle producers to use the vaccine under the 

supervision of a veterinarian.
Page 12 GAO-12-257 E. coli Contamination in Beef

Table 2: Approval Status and Challenges for Preslaughter Interventions 

Preslaughter intervention 

Approved for use to 

reduce STEC O157:H7 

in cattle

Agency 

responsible 

for approval Challenges for use of intervention 

Antimicrobials No FDA STEC O157:H7 may become resistant.

Bacteriophages Yes USDA 

FDA

a STEC O157:H7 may become resistant. 

Colicins No FDA Expensive and difficult to produce. 

Natural product extracts No FDA May not pass the cattle’s stomach and may be 

difficult to obtain in large quantities. 

Prebiotics No FDA May be costly and may not pass the cattle’s 

stomach. 

Probiotics No FDA Cattle may need to be fed large amounts to 

reduce STEC.

Sodium chlorate No FDA Nonec

Vaccines

 

Yes USDA b Cost associated with specifically administering a

STEC vaccine. 

Source: GAO analysis of interviews with USDA officials, FDA officials, and university researchers. 

a

USDA, in consultation with FDA, licensed a bacteriophage hide wash to be applied at the 

slaughterhouse prior to slaughter. Bacteriophages could also be administered orally, but FDA has not 

licensed any such product.

b

USDA granted conditional approval to one vaccine manufacturer.

c

USDA, the beef industry, and several researchers also identified 

preslaughter management practices that may affect STEC prevalence in 

cattle but that are not targeted to STEC. For example, basic sanitation 

practices—such as providing clean feed and water and keeping feedlots 

drained—have been identified by the beef industry and USDA as 

important steps in reducing the risk of STEC contamination in beef 

products. These practices are believed to be beneficial for the cattle’s 

health and welfare, although they have not been shown to be effective in 

reducing the pathogen, according to the beef industry and a USDA study. 

Researchers from one university noted interest in testing the effects of 

this and other preslaughter practices on STEC in cattle.

Researchers we spoke with did not identify challenges when we asked them to discuss the 

challenges or roadblocks for each intervention. This does not mean that the intervention is without 

challenges, because there may be challenges that researchers are not aware of.

Another preslaughter management practice researchers identified is diet 

modification, which includes modifying feed type, from feed grain to 

grasses, or the reverse; the frequency of feeding; and the quality of the 

grasses. Researchers have examined diet modification’s effect on the 

prevalence of STEC O157:H7 but have not reached a consensus about it. 
Page 13 GAO-12-257 E. coli Contamination in Beef

For example, some researchers have found that a diet with distillers 

grains—a co-product of the production of ethanol from corn—increases 

STEC O157:H7 prevalence in cattle, but others have found that it has no 

effect. Furthermore, according to several USDA and university 

researchers, diet modification may not be practical for reducing STEC 

O157:H7 in cattle, partly because of the potentially high cost.

USDA has funded and conducted research on STEC prevalence in cattle, 

as well as research specific to preslaughter interventions. In fiscal years 

2009 and 2010, USDA’s NIFA, through its Agriculture and Food Research 

Initiative, approved approximately $35 million in research grants related to 

understanding and reducing STEC prevalence in cattle. NIFA provided a 

total of about $28 million in five grants for research on how preslaughter 

interventions may reduce STEC in cattle, a total of about $5 million in 

three grants for research on how STEC behaves in the digestive system 

of cattle, and about $2.5 million for one grant for research on both 

preslaughter interventions and the behavior of STEC in the digestive 

system of cattle.

In addition, USDA’s ARS has worked closely with other USDA agencies, 

university researchers, and pharmaceutical manufacturers to research the 

prevalence of STEC in cattle’s digestive systems and potential 

preslaughter interventions, according to ARS officials. For example, these 

officials said that ARS has conducted research on “super-shedders,” 

which are cattle that appear to shed more STEC than other cattle in the 

same herd. Regarding preslaughter interventions, ARS researchers have 

investigated the effect of sodium chlorate on STEC in the digestive 

system and, according to agency officials, ARS has collaborated with 

companies to develop preslaughter interventions such as prebiotics, 

bacteriophages, and sodium chlorate.

USDA Has Funded and 

Conducted Relevant 

Research
Page 14 GAO-12-257 E. coli Contamination in Beef

USDA’s APHIS exercises responsibility for licensing and regulating 

animal biologic products that diagnose, prevent, manage, cure, or 

otherwise treat diseases of animals, including vaccines that can be used 

as a preslaughter intervention. Industry representatives have identified at 

least two manufacturers of animal health products that have each 

submitted an application to APHIS for approval of a STEC vaccine to treat 

the O157:H7 strain in cattle, and USDA announced the approval of a 

conditional license for one of these manufacturers.

According to representatives from two manufacturers of animal health 

products that sought a license for STEC O157:H7 vaccines, it was 

unclear whether FDA or USDA was responsible for reviewing and 

approving their applications when they wanted to apply in 2001 and 2003. 

It took more than a year before APHIS accepted their applications for 

review, in part because of lack of clarity over whether FDA or APHIS 

should be responsible for approving such vaccines, according to these 

representatives. Specifically, APHIS is responsible for regulating vaccines 

that diagnose, prevent, manage, cure, or otherwise treat diseases of 

animals, but APHIS officials told us that because STEC O157:H7 does 

not harm cattle, the agency had found prior to 2005 that regulatory 

jurisdiction for STEC O157:H7 vaccines resided with FDA as a food 

safety issue. According to these officials, the manufacturers of animal 

health products told them that the licensing process would be clearer 

under APHIS because it had more experience regulating conventional 

veterinary vaccines than FDA.

In 2005, APHIS stated its policy on animal vaccines in a directive 

explaining that it was responsible for regulating biological products such 

as the STEC O157:H7 vaccine.5

 

5

Animal and Plant Health Inspection Service, USDA, Center for Veterinary Biologics 

Notice No. 05-07 (Mar. 4, 2005).

Specifically, the directive stated that 

APHIS had the authority to approve products that claim to reduce 

colonization or shedding of organisms that may not cause significant 

clinical disease in animals but have the potential to cause the animal to 

be a disease carrier. According to an FDA official, if a manufacturer 

contacts FDA’s Office of New Animal Drug Evaluation seeking a license 

for a STEC O157:H7 vaccine product, this office assists APHIS by 

immediately directing the manufacturer to APHIS. The APHIS directive 

expired as guidance in 2006, but because APHIS has not issued any 

USDA Exercises 

Responsibility for 

Approving STEC 

Vaccines, but Its 

Approval 

Requirements Are 

Unclear 
Page 15 GAO-12-257 E. coli Contamination in Beef

subsequent statements on this policy, an APHIS official said that the 

policy in the directive remains in effect. This 2005 directive clarified 

APHIS’s approval authority and role concerning vaccine approvals, but 

APHIS’s approval requirements for STEC vaccines are not clear, 

according to industry representatives.

APHIS officials said that they direct potential applicants for STEC vaccine 

licensing to both the agency’s general guidance on demonstrating the 

safety and efficacy of biological products and to its 2005 directive.6

 

6

APHIS’s general guidance includes Veterinary Services Memorandum No. 800.202 and 

No. 800.204.

According to an APHIS official, the STEC vaccine is one of the most 

difficult vaccines for which to show definitive, consistent, and reproducible 

efficacy results. However, APHIS’s general guidance does not address 

this and other unique challenges faced by manufacturers of animal health 

products seeking STEC vaccine approval. For example, APHIS officials 

said that a STEC vaccine manufacturer may need to demonstrate that its 

vaccine is effective in a field setting—such as a feedlot in which cattle can 

be naturally exposed to pathogens—if studies conducted in the laboratory 

in which cattle are intentionally exposed to pathogens are insufficient to 

demonstrate efficacy. With other vaccines, a laboratory study is often 

sufficient because it can demonstrate consistent efficacy. However, 

information on when laboratory and field studies are required to 

demonstrate efficacy is not documented in the general guidance or 2005 

directive. In contrast, the Canadian Centre for Veterinary Biologics 

provides more specific guidance about when it requires the use of 

laboratory or field studies to demonstrate efficacy for vaccine license 

applications. In addition, neither the 2005 directive nor APHIS’s general 

guidance provides clear, specific instruction to manufacturers on the 

application process for STEC vaccines. For example, the 2005 directive 

states that the vaccine products will be required to show “clinically 

relevant efficacy as defined by APHIS” but does not explain what such 

efficacy means. According to an APHIS official, “clinically relevant 

efficacy” is the expectation that the vaccine’s efficacy is measurable, 

reproducible, consistent, and shows a long-term effect in reducing the 

disease in the animal, but this clarification is not specified in written 

guidance. Guidance that does not give manufacturers the information 

they need to submit an acceptable application could delay the approval 
Page 16 GAO-12-257 E. coli Contamination in Beef

process even with the clarification on APHIS’s role concerning vaccine 

approvals.

More specific guidance on the vaccine approval requirements may be 

especially important to manufacturers of animal health products working 

on STEC because of the challenges they face in demonstrating the 

efficacy of targeted preslaughter interventions. This difficulty is due to 

several biological factors specific to STEC, according to USDA officials, 

industry representatives, and university researchers. First, the prevalence 

of STEC is highly variable. For example, researchers said that STEC can 

be absent from cattle—or present only at low levels—during a field trial at 

a feedlot. That is, both treated and untreated cattle can have little or no 

detectable STEC, and thus it can be difficult for researchers to 

demonstrate that treated cattle have significantly lower levels of the 

pathogen. Second, many factors—such as weather, the time of year, and 

the cleanliness of the cattle’s hide—may affect the level of pathogenic 

STEC in cattle, making it difficult to isolate the effects of an intervention. 

Third, unlike other pathogens, STEC causes no visible symptoms in 

animals, so detection requires testing for the presence of the pathogen 

rather than just observation of the cattle.

APHIS officials said that APHIS does not have specific guidance on 

STEC vaccines because it typically does not release such guidance for a 

particular biological product until it has reviewed and approved three 

applications, which gives the agency sufficient information to provide 

specific guidance. They said that the agency’s general vaccine guidance 

offers it flexibility during the application review process by not being too 

prescriptive on requirements. During the course of our study, APHIS 

addressed some of the concerns we raised by releasing a one-page 

summary on licensing of preslaughter vaccines for a public meeting on 

food safety, but it still does not have documented guidance on the 

application process, including requirements specifically for these 

vaccines.

USDA determined that six additional STEC non-O157 strains were 

adulterants in beef in September 2011, has developed a method to test 

for them in beef, and plans to use this method starting in June 2012. 

Commercial tests are also available, and a few companies are voluntarily 

testing for these strains.

USDA Determined 

That Six Additional 

STEC Strains Were 

Adulterants and Has 

Tests to Detect Them 
Page 17 GAO-12-257 E. coli Contamination in Beef

In September 2011, USDA’s FSIS announced that it determined that six 

pathogenic strains of STEC—O26, O45, O103, O111, O121, and O145—

were adulterants in raw ground beef and beef trim (the meat left over after 

steaks and roasts are carved from a side of beef), in addition to STEC 

O157:H7. According to CDC, at least 150 STEC non-O157 strains have 

been associated with illness, but the majority of those illnesses have been 

traced to these six STEC non-O157 strains. There are several 

consequences to these strains being adulterants, including the following:

• Sale of beef contaminated with these strains is prohibited.

• Beef slaughter and processing plants must have a HACCP plan in 

place to identify and control the strains and to verify that the methods 

used to control the strains are working properly. Verification could 

include testing, but testing is not mandatory.

• FSIS has more reason to routinely test a subset of products for these 

strains and to request a recall for products deemed to be adulterated.

According to a September 20, 2011, notice in the Federal Register,

7

Preliminary testing involves two main steps. First, beef samples are 

tested for two genes—known as stx and eae—that are known to make 

E. coli pathogenic. Second, the samples are tested for other genes that 

are specific to each of the six STEC non-O157 strains. Positive results in 

both steps are considered a “potential positive,” which means the 

pathogen may be present. According to an ARS official, if used as 

planned, preliminary tests for the six strains are reliable. However, it is 

possible that these genes are present in a beef sample but come from 

FSIS 

intended to begin testing for these six strains in samples of raw ground 

beef and beef trim at slaughter and processing plants in March 2012, 

after it has reviewed comments from the public. Subsequent to this 

notice, FSIS moved its test date to June 4, 2012. In conducting these 

tests, FSIS plans to use a method developed by USDA’s ARS that was 

first published in October 2010 and revised in November 2011. This 

method has two key phases: (1) preliminary testing, which may take up to 

2 days, and (2) isolation and confirmation, which may take an additional 2 

to 4 days. These two phases are also used for STEC O157:H7 testing.

 

7

76 Fed. Reg. 58,157 (Sept. 20, 2011).

USDA Determined That 

Six Additional Strains 

Were Adulterants and Has 

Tests to Detect Them, but 

It Can Be Difficult to 

Confirm Positive Results
Page 18 GAO-12-257 E. coli Contamination in Beef

different strains of bacteria. It is, therefore, necessary to isolate the 

suspect strain and confirm that it is the source of the two genes that make 

E. coli pathogenic.

Several steps are involved in the isolation and confirmation phase; two of 

these steps may be difficult and time-consuming, according to ARS 

officials. The first involves separating the suspected strain of pathogenic 

E. coli from other bacteria using immunomagnetic separation beads that 

contain antibodies (components of the human immune system) that 

adhere to a specific strain of E. coli. According to an ARS official, it would 

be very difficult to isolate the target strain without the use of these beads. 

However, the official also said that the beads are not commercially 

available for two of the six strains—O45 and O121. ARS currently buys 

beads from a commercial supplier for the other four strains but has to 

make them for O45 and O121, which is a time-consuming and costly 

process, according to an ARS official. FSIS is currently searching for 

companies willing to produce beads for the two strains and make them 

commercially available and, according to an FSIS official, expects to have 

test manufacturers in place by June 2012.

The second step involves growing the target strain by placing the 

immunomagnetic beads onto a solid growth medium containing a mix of 

nutrients that is specific to this strain and suppresses the growth of other 

bacteria. According to an ARS official, scientists allow the bacteria 

sticking to the beads to grow and multiply on the medium, using methods 

that ensure the bacteria form colonies that are all from the same strain. 

This makes it easier to identify the target strain and confirm that it has the 

two disease-causing genes—stx and eae. However, according to the 

ARS official, some of the six STEC non-O157 strains may not always 

grow well on the medium that FSIS is currently using. If the strains do not 

grow well, it will be difficult to confirm potentially positive results and, 

consequently, beef samples that contain one of the six pathogenic strains 

could incorrectly test negative. According to the ARS official, a revised 

November 2011 testing method includes an improved growth medium for 

the six strains. This official added that ARS has conducted various tests 

to find the optimal growth medium for the six strains, and the medium 

FSIS is using is the best currently available. Research is ongoing by ARS 

and in the broader scientific community to develop a better growth 

medium, according to this ARS official, and ARS will evaluate other 

mediums as they become commercially available. See figure 3 for a 

summary of the testing process.
Page 19 GAO-12-257 E. coli Contamination in Beef

Figure 3: Preliminary and Isolation and Confirmation Testing Phases for the Six STEC Non-O157 Strains

Note: This figure shows the two main phases for E. coli detection testing. For a comprehensive 

description of all of the detection testing steps, see USDA’s Microbiology Laboratory Guidebook MLG 

5B.01. 

Preliminary tests to detect the six strains are commercially available, and 

at least one test manufacturer sells these tests for all six strains. ARS 

collaborated with this manufacturer to develop the tests and is now 

collaborating with other manufacturers, many of which became interested 

in developing tests after USDA’s announcement that it had determined to 

consider the six strains as adulterants, according to an ARS official. A 

representative from one test manufacturer told us he was confident that 

his company could produce enough tests to meet the demand of the U.S. 

beef industry. Similarly, a representative from a second manufacturer told 

us that it is preparing to meet the demand.

Starting on June 4, 2012, FSIS will expect slaughter and processing 

plants to have a plan in place to identify and control the six STEC nonO157 strains. Such a plan may include information on how the plant will 

use testing to verify that food safety systems are working properly. FSIS 

officials estimate that about 20 percent of U.S. slaughter plants are 

currently testing for STEC non-O157 strains, although FSIS did not know 

for which specific strains these plants are testing. Representatives from 

two beef processing plants—one of which is also a retailer—told us that 

they are testing for all six strains. The plant that is also a retailer will also 

require its beef suppliers to test for these strains before it accepts the 

beef. The retailer will also test for STEC O104, an additional STEC nonO157 strain, as soon as a test is commercially available for beef. The 

Commercial Tests Are 

Available and Some 

Companies Are Testing
Page 20 GAO-12-257 E. coli Contamination in Beef

representative from this retailer did not report challenges with using the 

commercially available preliminary test for the six strains. However, 

commercial preliminary tests for the six strains are new, and according to 

representatives from a test manufacturer, the manufacturer recently 

started conducting field trials on the tests.

Both beef processing plants said they also carry out confirmation tests for 

potential positive results through a third-party laboratory. An official from 

one of these plants told us that he has not observed any difficulty in 

growing the six strains after separation using the commercially available 

growth mediums, but he noted confirmation of potentially positive results 

for the six pathogenic strains can be a time-consuming process. 

According to a test manufacturer representative, confirmation of 

potentially positive results will likely be difficult for the beef industry, for 

the same reasons it is proving difficult for FSIS.

If a plant detects one of the six strains in ground beef or beef trim, its 

response is generally dictated by FSIS requirements. Possible responses 

to a positive test include disposing of the beef or cooking it to kill bacteria.

Several researchers, U.S. agency officials, and a foreign government 

official said that the United States is the leader in researching and 

employing preslaughter interventions. USDA officials, however, 

commented that they would consider preslaughter practices other 

countries have conducted if they are relevant to U.S. efforts to reduce 

STEC in cattle. The following are some practices other countries have 

employed that may help reduce STEC in cattle and that are not currently 

used in the United States:

Cattle cleanliness inspections. Several foreign governments conduct 

cleanliness inspections that may reduce STEC in beef. For example, 

European Parliament and the Council of the European Union regulations, 

referenced by European Commission officials, require that (1) farmers 

take adequate measures to ensure the cleanliness of cattle going to 

slaughter, (2) operators of slaughter plants ensure cattle are clean before 

accepting them, and (3) meat inspectors verify that the cattle about to be 

slaughtered are clean. In the United Kingdom, meat inspectors use a fivecategory rating system for cattle cleanliness that ranges from “clean and 

dry” to “filthy and wet,” according to a 2002 guidance document from the 

Food Standards Agency. Only cattle rated in the two highest categories 

for cleanliness may proceed to slaughter. In Australia, according to its 

standard for the hygienic production and transportation of meat and meat 

Some Countries Have 

Practices That Could 

Be Relevant to U.S. 

Efforts to Reduce 

STEC in Cattle
Page 21 GAO-12-257 E. coli Contamination in Beef

products for human consumption, an inspector must determine that cattle 

are clean prior to slaughter. If they are not, they can be passed for 

slaughter subject to conditions that ensure that they do not contaminate 

other animals, carcasses, and carcass parts. According to New Zealand 

government officials, their inspectors check for hide cleanliness to help 

prevent meat contamination. In contrast, in the United States, FSIS 

assesses the health of cattle prior to slaughter but does not inspect for 

cleanliness.

Testing for STEC. At least 12 European Union member countries 

collected and reported data on STEC in live cattle in 2009, according to a 

2011 European Food Safety Authority and European Centre for Disease 

Prevention and Control report.8

Testing cattle from specific farms in Sweden. When a person becomes ill 

from E. coli in Sweden, Swedish government officials try to determine its 

source by interviewing this person, according to an official from Sweden’s 

National Food Administration. If this person is suspected of having been 

in contact with cattle from a specific farm, cattle from this farm will be 

sampled. If there is an E. coli strain match with that of the ill person, this 

official said that Sweden’s Board of Agriculture would then recommend 

that the cattle from this farm be slaughtered at a slower rate so that the 

carcasses can be tested for STEC and heat-treated if found positive. 

Although this is a recommendation, this official stated that its 

Such data are important to identify the 

main sources of infections. In countries such as Sweden and Denmark, 

this testing is conducted regularly. For example, in Sweden, government 

officials collect about 2,000 fecal samples every 3 years, according to an 

official from Sweden’s National Veterinary Institute. These samples are 

collected at geographically distributed slaughterhouses throughout 

Sweden. Sweden tests for STEC O157:H7 and started to test 1,000 fecal 

samples for STEC O26 in its 2011 study. In Denmark, the National Food 

Institute collects fecal samples from approximately 200 bulls per year to 

test for STEC O157:H7, according to an institute official. In the United 

States, APHIS has conducted feedlot studies that involved testing for 

STEC in live cattle, but this testing was voluntary and last conducted in 

1999.

 

8

European Food Safety Authority, European Centre for Disease Prevention and Control; 

The European Union Summary Report on Trends and Sources of Zoonoses, Zoonotic 

Agents and Food-borne Outbreaks in 2009; EFSA Journal 2011 (Parma, Italy: Mar. 22, 

2011).
Page 22 GAO-12-257 E. coli Contamination in Beef

slaughterhouses follow the board’s recommendations. According to this 

official, since 1996, Sweden has had 52 cases of human illnesses from 

STEC—46 from the O157:H7 strain, 2 from O26, 2 from O121, 1 from O8, 

and 1 from O103. In the United States, STEC O157:H7 in beef can be 

traced back to the beef supplier, but USDA officials said that they do not 

trace the source of the pathogen back to the farm and thus cannot make

recommendations for special testing from specific farms.

Preslaughter interventions for cattle have the potential to help reduce 

STEC-related illnesses, although they are unlikely to be able to eliminate 

all pathogenic strains in cattle. USDA, the beef industry, and university 

researchers have been working to develop these interventions. Few 

manufacturers have submitted applications for preslaughter intervention 

products to target STEC, but at least two have submitted applications for 

STEC vaccines. However, the approval requirements are unclear. In 

2005, USDA’s APHIS clarified its responsibility for vaccines, but it still has 

not provided specific guidance on the information it needs to approve a 

vaccine for STEC. Without guidance that gives manufacturers clear and 

more specific information they need to submit an acceptable application, 

the approval requirements for STEC vaccines could face delays and 

thereby increase the risk to public health. In addition, some countries 

have employed practices not currently used in the United States that 

potentially can inform U.S. efforts for reducing STEC in cattle.

GAO recommends that the Secretary of Agriculture take the following two 

actions:

• Direct the Administrator of APHIS to provide more specific public 

guidance on the license approval requirements for STEC vaccines in 

order to help improve clarity and reduce potential delays in the 

application process for these vaccines. 

• Explore practices employed by other countries that are not currently 

used in the United States for reducing STEC in cattle and consider 

whether the identified practices can inform U.S. efforts.

We provided a copy of our draft report to the Departments of Agriculture 

and of Health and Human Services. In its written response, USDA 

generally agreed with the information in the draft report. USDA neither 

agreed nor disagreed with our recommendation that it provide more 

Conclusions 

Recommendations for 

Executive Action

Agency Comments 

and Our Evaluation
Page 23 GAO-12-257 E. coli Contamination in Beef

specific public guidance on the license approval requirements for STEC 

vaccines. USDA’s APHIS acknowledged that additional public guidance 

may be beneficial to applicants and stated that it is committed to providing 

as much specific public guidance as possible. However, APHIS stated 

that more specific requirements may discourage product development 

efforts, and APHIS does not release specific guidance about a new 

product until it has reviewed and approved at least three applications. 

Further, according to industry representatives, APHIS’s approval 

requirements for STEC vaccines are not clear. Our recommendation is 

intended to help improve clarity and reduce potential delays in the 

application process for STEC vaccines. As stated in our report, we found 

that guidance that does not give manufacturers the information they need 

to submit an acceptable application could delay the approval process. We 

also provided examples of areas in which more specific guidance, such 

as clarifying the term “clinically relevant efficacy,” could reduce confusion. 

APHIS addressed some of the concerns we raised by releasing a onepage summary on licensing of preslaughter vaccines for a public meeting, 

but this is not documented as guidance. We encourage APHIS to provide 

more specific guidance that can reduce confusion without discouraging 

product development of STEC vaccines. USDA agreed with our 

recommendation to explore practices that are currently not used in the 

United States for reducing STEC in cattle and consider whether the 

identified practices can inform U.S. efforts. USDA’s letter is presented in 

appendix II. The Department of Health and Human Services did not 

comment on the draft report but provided technical comments. As 

appropriate, we incorporated these technical comments and those 

provided by USDA.

This report is intended for use by USDA management. We are sending 

copies of this report to the appropriate congressional committees and 

members, the Secretary of Health and Human Services, and other 

interested parties. In addition, this report is available at no charge on the 

GAO website at http://www.gao.gov. 
Page 24 GAO-12-257 E. coli Contamination in Beef

We acknowledge and appreciate the cooperation and assistance 

provided by USDA management and staff during our audit. If you have 

questions about this report, please contact me at (202) 512-3841 or 

shamesl@gao.gov. Contact points for our Offices of Congressional 

Relations and Public Affairs may be found on the last page of this report. 

GAO staff who made key contributions to this report are listed in 

appendix III.

Sincerely yours,

Lisa Shames

Director, Natural Resources and Environment
Page 25 GAO-12-257 E. coli Contamination in Beef

Our objectives were to determine (1) preslaughter interventions that may 

help reduce Shiga toxin-producing Escherichia coli (STEC) in cattle; (2) 

the U.S. Department of Agriculture’s (USDA) role in approving STEC 

vaccines; (3) the extent to which STEC strains have been determined to 

be adulterants in beef and the status of tests to detect them; and (4) 

practices, if any, other countries have employed that could reduce STEC 

in cattle and may be relevant to U.S. efforts.

For all four objectives, we visited several cattle feedlots and a cattle 

slaughter plant in Colorado, which we selected because it is one of the

largest beef-producing states. While in Colorado, we also interviewed 

USDA officials, beef industry representatives, and university researchers. 

In addition, in a nonprobability sample, we conducted a total of 71 

interviews with USDA, Centers for Disease Control and Prevention 

(CDC), and Food and Drug Administration (FDA) officials; foreign 

government officials; beef industry representatives; manufacturers of 

animal health products; federal and university researchers; and consumer 

group representatives with expertise in STEC in cattle. Our questions 

included descriptions of preslaughter interventions, roles of federal 

government in preslaughter interventions, and practices other countries 

have employed to reduce STEC in cattle that may be relevant to U.S. 

efforts. Because this was a nonprobability sample, the results cannot be 

generalized to the entire United States, but they can provide examples of 

research conducted on preslaughter interventions.

To determine the preslaughter interventions that may help reduce STEC 

in cattle, we reviewed USDA and academic studies on preslaughter 

interventions, reviewed USDA documents on funding for STEC research, 

and met with USDA and university researchers and beef and 

pharmaceutical industry representatives. We identified these studies 

through interviews with USDA and university researchers.

To determine USDA’s role in approving STEC vaccines, we reviewed 

USDA guidance, and interviewed USDA officials, manufacturers of animal 

health products, and university researchers.

To determine the extent to which STEC strains have been determined to 

be adulterants in beef and the status of tests to detect them, we reviewed 

USDA documents on STEC detection tests and interviewed FDA and 

USDA officials, beef industry representatives, and detection test 

manufacturers.

Appendix I: Objectives, Scope, and 

Methodology 
Page 26 GAO-12-257 E. coli Contamination in Beef

To determine practices, if any, other countries have employed that could 

reduce STEC in cattle and may be relevant to U.S. efforts, we interviewed 

CDC, FDA, and USDA officials; beef industry representatives; university 

researchers; and consumer group representatives to determine if they 

were aware of any such practices. We also reviewed international 

studies, guidance, and requirements for food safety in beef and 

interviewed international food safety officials. We did not independently 

verify statements of foreign law.

We conducted this performance audit from January 2011 to March 2012 

in accordance with generally accepted government auditing standards. 

Those standards require that we plan and perform the audit to obtain 

sufficient, appropriate evidence to provide a reasonable basis for our 

findings and conclusions based on our audit objectives. We believe that 

the evidence obtained provides a reasonable basis for our findings and 

conclusions based on our audit objectives.
Appendix II: Comments from the U. S. 

Department of Agriculture

Page 27 GAO-12-257 E. coli Contamination in Beef

Appendix II: Comments from the U. S. 

Department of Agriculture
Appendix II: Comments from the U. S. 

Department of Agriculture

Page 28 GAO-12-257 E. coli Contamination in Beef
Appendix III: GAO Contact and Staff 

Acknowledgments

Page 29 GAO-12-257 E. coli Contamination in Beef

Lisa Shames, (202) 512-3841, or shamesl@gao.gov

In addition to the individual named above, Thomas Cook, Assistant 

Director; Kevin Bray; Mark Braza; Christina E. Bruff; Allen T. Chan; 

Barbara El Osta; Brenda Muñoz; Katherine M. Raheb; Sushil Sharma; 

Benjamin Shouse; Carol Herrnstadt Shulman; and Kiki Theodoropolous 

made key contributions to this report.

Appendix III: GAO Contact and Staff 

Acknowledgments 

GAO Contact

Staff 

Acknowledgments 

(361260)
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