Report on the Food Safety and Inspection Service‘s 

Microbiological and Residue Sampling Programs 

United States Department of Agriculture 

Food Safety and Inspection Service 

December 2011 

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Executive Summary .............................................................................................................................5
 

1.0 Introduction ....................................................................................................................................5
 

Background......................................................................................................................................6
 

Current Intent and Purpose of FSIS Sampling Programs ................................................................6
 

Sampling Along the Farm-to-table Continuum ...............................................................................8
 

Relationship between FSIS Sampling and USDA/FSIS Strategic Plan Goals to Utilize a DataDriven Approach and Reduce Foodborne Illness ............................................................................8
 

Organization of Sampling Program Report .....................................................................................9
 

FSIS Public Health Information System (PHIS)............................................................................ 10
 

Definition of Terms........................................................................................................................ 10
 

2.0 Domestic, Regulated Establishments .......................................................................................... 11
 

Section 2.1: Microbiological Sampling Programs ......................................................................... 11
 

2.1.1: Salmonella ........................................................................................................................... 11
 

Overview of Sampling Programs......................................................................................11
 

Salmonella Verification Program: HC01..........................................................................13
 

MT43S Sampling Program ............................................................................................... 25
 

Processed Egg Products—EM 31-37................................................................................ 26
 

Salmonella Programs Measure of Success ....................................................................... 28
 

2.1.2 Campylobacter.................................................................................................................... 32
 

Campylobacter Verification Program: HC11 ................................................................... 32
 

Campylobacter Programs Measure of Success.................................................................32
 

2.1.3: E. coli O157:H7 Raw Sampling Project ............................................................................. 34
 

Routine testing of domestic components to raw ground beef – other than trim – at 

Follow-up testing to a positive in trim or components at a domestic establishment 

Overview of Sampling Projects ........................................................................................ 34
 

Historical Basis for Sampling Raw Ground Beef ............................................................. 34
 

Historical Basis for Sampling of Products Other than Raw Ground Beef........................ 36
 

Description of the FSIS Domestic Sampling Projects for E. coli O157:H7 ..................... 38
 

Risk-based testing of raw ground beef at domestic establishments (MT43) .................... 38
 

Follow-up testing to a raw ground beef positive at a domestic establishment (MT44). ... 41
 

Routine testing of manufacturing trimmings at domestic establishments (MT50)........... 42
 

domestic establishments (MT54)......................................................................................43
 

Routine testing of bench trim at domestic establishments (MT55) .................................. 45
 

(MT53).............................................................................................................................. 46
 

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Follow-up testing at supplier establishments following a positive in raw ground beef and 

bench trim (MT52)............................................................................................................ 47
 

Limitations of Current Sampling Programs......................................................................49
 

E. coli O157:H7 Measures of Success..............................................................................49
 

2.1.4: RTE Meat and Poultry Products (Listeria monocytogenes (Lm) and Salmonella) .............. 54
 

Overview of Sampling Projects ........................................................................................ 54
 

Historical Basis of Sampling Programs ............................................................................ 55
 

Description of the FSIS RTE Domestic Sampling Projects for Lm and/or Salmonella.... 56
 

ALLRTE ........................................................................................................................... 56
 

RTE001............................................................................................................................. 58
 

RLm .................................................................................................................................. 59
 

Intensified Verification Testing (IVT)..............................................................................60
 

Limitations of Current Sampling Programs......................................................................61
 

Lm Sampling Program Measures of Success .................................................................... 63
 

Section 2.2: FSIS Microbiological Baseline Data Collection........................................................ 66
 

Section 2.3 Chemical Residues..................................................................................................... 67
 

Overview of Sampling Projects ........................................................................................ 67
 

Background Information...................................................................................................67
 

Fast Antimicrobial Screen Test (FAST) ........................................................................... 69
 

Kidney Inhibition Screen (KISTM) Test ............................................................................ 70
 

3.0 Imports.................................................................................................................................... 72
 

Section 3.1: Microbiological Sampling Programs ......................................................................... 72
 

Overview of Sampling Programs......................................................................................72
 

3.1.1: Salmonella .......................................................................................................................... 73
 

EGGIMP—Processed Egg Products.................................................................................74
 

3.1.2: E. coli O157:H7................................................................................................................... 75
 

Ground Beef (MT08) ........................................................................................................ 76
 

Non-Intact Beef (MT51)...................................................................................................76
 

3.1.3 RTE Meat and Poultry Products ........................................................................................... 78
 

IMVRTE—Imported Intact RTE Product ........................................................................ 79
 

Imports Measures of Success............................................................................................79
 

Section 3.2: Chemical Residues..................................................................................................... 81
 

Fresh and Processed..........................................................................................................81
 

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4.0 In-Commerce Activities......................................................................................................... 82
 

Overview........................................................................................................................... 82
 

MT05 and MT06—Raw Ground Beef at Retail ............................................................... 84
 

In-Commerce Measures of Success .................................................................................. 85
 

5.0 Foodborne Illness Investigation and Consumer Complaint Sampling Programs .................. 86
 

6.0 Appendices .................................................................................................................................... 89
 

Appendix A: Definition of Terms..................................................................................................90
 

Appendix B: E. coli O157:H7 Sampling Program Description and Features................................ 92
 

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Executive Summary 

Background 

The mission of the Food Safety and Inspection Service (FSIS) is to ensure that meat, poultry and 

processed egg products are safe, wholesome and properly labeled and packaged. Further, as FSIS is a 

public health agency, one of the primary goals of the Agency is to reduce and ultimately prevent 

foodborne illness in the population. 

The overall purpose of FSIS inspection and sampling is to ensure that establishments maintain control of 

their production processes and adhere to FSIS regulations, policies and performance standards, which 

the Agency believes helps protect the public from foodborne illnesses. Ensuring that products are free 

of pathogen contamination and chemical residues is a responsibility of industry, but on-going sampling 

in FSIS-regulated domestic and import establishments allows the Agency to assess the effectiveness of 

industry process controls, compliance with performance standards and efforts to control the presence of 

pathogens on products being produced for American consumers. Additionally, sampling provides a 

strong incentive for the meat, poultry and processed egg product industries to reduce the presence of 

pathogens on products they produce. It also provides the regulated industries with critical information 

to improve current processes and focus its resources as efficiently and effectively as possible. 

FSIS Sampling Programs 

Currently, FSIS maintains sampling programs in three major venues: 1) Domestic, federally inspected 

establishments, 2) In-Commerce and 3) Import. FSIS also conducts an outbreak investigation and 

consumer complaint sampling program. Further, FSIS conducts two distinct types of sampling: 1) 

Microbiological and 2) Chemical Residues. 

Purpose of Report 

In September 2011, FSIS published the FSIS Strategic Plan for 2011-2016. The Plan, as a part of FSIS‘

goal to ensure that food safety inspection aligns with existing and emerging risks, identifies the 

Agency‘s commitment to develop an annual sampling report that comprehensively identifies and 

describes the Agency‘s sampling programs. This report was developed to address that commitment and 

is being released now, subsequent to the release of the Strategic Plan, to reflect FSIS‘ commitment to 

transparency and provide information on the Agency‘s sampling programs in a timely manner. This 

report was developed with input from all FSIS program areas and includes information on how the 

Agency‘s sampling programs were carried out in fiscal year (FY) 2011. Specifically, with the 

publication of this report, FSIS is documenting its current approach to microbiological and residue 

sampling. This report includes information on the historical basis, design, statistical/policy basis and 

limitations of FSIS‘ current sampling programs. 

However, the development and maintenance of robust, responsive and meaningful sampling programs 

requires an iterative process, including review of sampling results, incorporating new technological and 

methodological advancements, new and modified FSIS policy and feedback from all stakeholders to 

promote continuous improvement. As such, this report is the first of two publications developed by 

FSIS. The second part of this effort, which is currently in development, is the FSIS annual Sampling 

Program Plan, which will identify programmatic sampling changes that will be implemented by the 

Agency in FY2012. FSIS anticipates that it will share this plan publicly by early calendar year (CY) 

2012. 

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1.0 Introduction
 

Background 

The mission of the Food Safety and Inspection Service (FSIS) is to ensure that meat, poultry and 

processed egg products are safe, wholesome and properly labeled and packaged. Further, as FSIS is a 

public health agency, one of the primary goals of the Agency is to reduce and ultimately prevent 

foodborne illness in the population. 

Product testing, whether performed by industry or FSIS, is particularly important in gauging the safety 

of regulated product. Ensuring that products meet pathogen contamination standards and chemical 

residue levels is the responsibility of industry. The routine sampling in FSIS-regulated domestic and 

import establishments allows the Agency to assess the effectiveness of industry process controls, 

compliance with performance standards and the monitoring the proportion of finished product where 

microbiological or chemical contaminants are detected on products being produced for American 

consumers. Additionally, sampling serves as a strong incentive for the meat, poultry and processed egg 

product industries to reduce the presence of pathogens on products they produce. Further, product 

sampling provides the regulated industries with critical information to improve current processes and 

focus their resources as efficiently and effectively as possible. 

The Hazard Analysis and Critical Control Points (HACCP) system is an established food safety system, 

whereby meat and poultry establishments identify and evaluate hazards that can affect the safety of their 

products, institute controls necessary to prevent those hazards from occurring or keeping them within 

acceptable limits, monitor the performance of controls and maintain records of these practices. 

Microbiological and chemical residue sampling are critical components of HACCP and, as a part of 

FSIS‘ verification responsibilities, are used to help ensure that foods regulated by the Agency are safe to 

eat, verify that prevention efforts undertaken by a domestic establishment are successfully controlling 

pathogens and chemical residues and ensuring products imported from foreign countries are safe and 

wholesome. FSIS published the  ̳ ̳Pathogen Reduction; Hazard Analysis and Critical Control Point 

(PR/HACCP) Systems‘‘ Final Rule (61 FR 38806) in July 1996. The overarching goal of FSIS‘ food 

safety strategy and the PR/HACCP regulations is to reduce, to the maximum extent possible, the risk of 

foodborne illness associated with the consumption of meat and poultry products. 

Current Intent and Purpose of FSIS Sampling Programs 

FSIS inspects regulated establishments in a comprehensive fashion. The overall purpose of FSIS 

inspection and sampling is to verify that establishments maintain control of their production processes 

and adhere to Agency regulations, policies and performance standards, which FSIS believes helps 

protect the public from foodborne illnesses. Because sampling is part of FSIS‘ verification activities, 

samples are collected at regular intervals, (e.g., once a week or month) though the frequency of 

microbiological testing is sometimes stratified based on an establishment‘s production volume. FSIS‘

microbiological testing programs were developed to be pathogen-specific. Consequently, the outcome 

of a positive sample can vary with each program. For example, some FSIS sampling programs enforce 

the Agency‘s zero tolerance policy for the presence of pathogens, such as Escherichia coli (E. coli 

O157:H7) and Listeria monocytogenes (Lm). Others, such as verification programs for Salmonella and 

Campylobacter in raw products, evaluate how well regulated establishments demonstrate process control 

for these pathogens. In the section below, the intent of each sampling program is briefly described. A 

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more complete description of the intent and purpose of each microbiological testing program, as well as 

chemical residue testing, are included in the following chapters. 

Domestic, Federally Inspected Establishments 

Microbiological 

Currently, FSIS conducts microbiological sampling for four major pathogens of human health concern: 

Salmonella, Campylobacter, E. coli O157:H71 and Lm. Briefly, for Salmonella sp., FSIS conducts a 

verification testing program per the 1996 PR/HACCP Rule to ensure that the Salmonella reduction 

performance standards are being met for the eight raw product classes, as well as a sampling program 

for processed egg products. For Campylobacter, FSIS initiated a sampling program in young chicken 

and turkeys in July 2011 based on new performance standards. For E. coli O157:H7, the objective of 

the verification testing program is to verify the effectiveness of the food safety system on a national 

level and encourage continuous industry improvement in the reduction of the pathogen in raw ground 

beef and other raw beef products. Finally, for ready-to-eat (RTE) meat and poultry products, the 

objective of the multiple regulatory testing programs is to verify the effectiveness of food safety systems 

in preventing the presence of Lm and Salmonella in RTE products and in the establishment‘s

environment. In addition to these routine sampling programs, most microbiology programs have a 

consequential (for cause) sampling component when the production process within a regulated 

establishment is determined to be out of control. 

Chemical Residue 

FSIS sampling programs for chemical residues both in domestic and import establishments are designed 

to achieve the following: (1) a structured process for identifying and evaluating compounds of concern 

by production class; (2) the capability to analyze for compounds of concern; (3) appropriate regulatory 

follow-up to reports of violative tissue chemical residues; and (4) collection, statistical analysis and 

reporting of the results of these activities. 

In-Commerce Sampling 

The in-commerce sampling program is one facet of a comprehensive set of activities conducted by FSIS 

Compliance and Investigations Division (CID) Investigators. Microbiological sampling of FSISregulated products in-commerce is intended to verify that persons and firms—whose business activities 

involve FSIS-regulated products— prepare, store, transport, sell or offer for sale or transportation these 

products in compliance with the Agency‘s statutory and regulatory requirements. 

Import Sampling Programs 

In order to focus FSIS resources on imported products that may pose the greatest threat to public health, 

the Agency utilizes a performance-based approach to define the scope of equivalence verification audits 

of foreign countries and to determine the frequency of Point-Of-Entry (POE) reinspections. Consistent 

with domestic programs, this approach relies on previous audit findings and inspection results, as well as 

information regarding the product types and product volumes presented for importation into the U.S. In 

1 FSIS recently published a proposed rule in the Federal Register stating the Agency‘s intention to carry out verification 

procedures, including sampling and testing manufacturing trim and other raw ground beef components, to ensure control of 

both E. coli O157:H7 and six other serogroups of Shiga toxin-producing E. coli (STEC) (O26, O45, O103, O111, O121, and 

O145). FSIS has determined that they, as well as O157:H7, are adulterants of non-intact raw beef products and product 

components within the meaning of the Federal Meat Inspection Act (FMIA). 

http://www.fsis.usda.gov/OPPDE/rdad/FRPubs/2010-0023.pdf. 

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import sampling, FSIS utilizes foreign country/establishment past performance, sampling history, 

product type and product volume produced to assist in the design of sampling plans for Salmonella, E. 

coli O157:H7, and Lm. The overall purpose of FSIS import sampling is to ensure that meat, poultry and 

processed egg products imported into the U.S. are produced under an equivalent inspection system and 

are as safe as products produced domestically. 

Sampling Along the Farm-to-Table Continuum 

FSIS‘ sampling programs in establishments, in-commerce and for imported products are key 

components of a farm-to-table approach to food safety. This approach includes all facets of the food 

production process; from animal slaughter within FSIS regulated establishments, to food processing 

within regulated establishments, to retail establishments and home environments. FSIS seeks to have an 

active presence in all these venues and includes pre-harvest activities, establishment inspection, industry 

education at retail and consumer education in the home. For example, in domestic E. coli O157:H7 

sampling, FSIS collects samples of beef, such as bench trim and components, as it is processed. FSIS 

also conducts a risk-based sample collection program in raw ground beef. If any positive samples are 

identified, FSIS conducts additional sampling to ensure that the establishment regains control of its 

processes and produces safe product. Finally, FSIS maintains an independent sampling program incommerce for raw ground beef. While these three sampling projects were designed and are maintained 

separately, by sampling in these three venues—slaughter, processing, and in-commerce—FSIS seeks to 

verify the effectiveness of industry process controls across multiple sectors and target areas for 

intervention along this continuum when more attention is needed. The same principles apply to 

sampling for other pathogens and product classes. For example, FSIS samples in establishments on food 

contact and non-food contact environmental surfaces, as well as sampling for Lm in both non-postlethality exposed and post-lethality exposed RTE products. As with E. coli O157:H7 sampling, any 

positive test results are followed-up with additional, intensified verification sampling to ensure that 

establishments identify the source of contamination and bring processes back under control. Finally, 

FSIS seeks to harmonize sampling programs for both domestic and imported meat, poultry and 

processed egg products. As such, FSIS samples for Salmonella, E. coli O157:H7 and Lm in imported 

products such as beef, processed egg products and RTE. In summary, by adopting a farm-to-table 

approach not only in FSIS‘ overall approach to food safety, but also within the Agency‘s sampling 

programs, FSIS seeks to address food safety risks along the food chain and reduce the overall number of 

foodborne illnesses associated with FSIS regulated products. 

Relationship between FSIS Sampling and USDA/FSIS Strategic Plan Goals to Utilize a DataDriven Approach and Reduce Foodborne Illness 

In September 2010, FSIS released two reports; the FSIS Strategic Data Analysis Plan for Domestic 

Inspection2 and Data-Driven Inspection for Processing and Slaughter Establishments: Public Health 

Decision Criteria.

3 These reports were developed to communicate FSIS‘ strategy for a data-driven 

approach to domestic inspection and describe the Agency‘s public health-based, data-driven decision 

criteria and a decision tree to select meat and poultry establishments for additional inspection activities. 

Further, these reports were designed to directly support FSIS‘ strategic goals by providing the data and 

analyses necessary to effectively allocate resources and measure performance. The release of this 2011 

2 Please see the following website for more information:
 

http://www.fsis.usda.gov/OPPDE/NACMPI/Sep2010/2010_Strategic_Data_Analysis_Plan.pdf. 3 Please see the following website for more information:
 

http://www.fsis.usda.gov/OPPDE/NACMPI/Sep2010/2010_Public_Health_Decsion_Criteria_Report.pdf. 

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Sampling Program report continues FSIS‘ efforts to comprehensively identify Agency activities and 

consider them in light of data-driven strategic planning efforts. 

Similarly, the U.S. food safety system involves multiple stakeholders along the farm-to-table continuum 

and includes multiple federal and state partners, regulated industries, as well as active participation from 

the American consumer. While FSIS recognizes that inspection and sampling at regulated slaughter and 

processing establishments are just two pieces of FSIS‘ food safety activities, the Agency believes that 

reducing the overall presence of harmful foodborne pathogens on products regulated by FSIS can bring 

about reductions in foodborne illnesses from Salmonella, Campylobacter, E. coli O157:H7 and Lm in 

the U.S. population. FSIS is working internally and externally with federal food safety partners to 

further refine our understanding of the relationship between Agency activities and foodborne illness. 

Organization of Sampling Program Report 

This report serves as the first of a two-part effort by FSIS to increase transparency and share information 

regarding the Agency‘s microbiological and residue sampling programs. The purpose of this report is to 

provide a historical grounding and a detailed description of FSIS‘ current sampling programs. This 

report contains information on how FSIS carries out the Agency‘s sampling programs through fiscal 

year 2011. Given the timeframe in which this report is being released, however, tables containing 

sample analysis numbers are current as of fiscal year 2010. Fiscal year 2011 sample collection and 

analysis numbers will be provided in the Agency‘s annual Sampling Program Plan, scheduled for release 

in the beginning of CY2012. 

This report comprehensively describes the current design, statistical/policy basis and current limitations 

of FSIS‘ sampling programs. For ease of understanding and to correspond with FSIS‘ current 

organizational structure, this report is organized by the major venues in which FSIS conducts sampling; 

1) Domestic, federally-inspected establishments, 2) Imports and 3) In-Commerce. FSIS also conducts 

outbreak investigation and sampling in response to illnesses and consumer complaints. Further, FSIS 

conducts two distinct types of sampling: 1) Microbiological and 2) Chemical Residues. 

In general, sampling for a specific pathogen, such as Salmonella, is referred to in this report as 

―sampling program‖, whereas individual sampling for specific pathogens, such as HC01 for Salmonella, 

are considered ―sampling projects‖. As such, this report will be organized first around the venue in 

which the sampling occurs and second, around the type of sampling program. Each major section of this 

report also contains information about the type of analysis FSIS conducts to determine whether or not, 

and to what extent, a pathogen exists on regulated product and a discussion of the volume of product 

produced by regulated industries, as it relates to FSIS sampling programs. 

Future FSIS Sampling Program Activities 

FSIS anticipates that the Agency‘s sampling activities will evolve over time for myriad reasons, 

including new and emerging public health hazards, as well as technological and methodological 

advancements and updates to FSIS policy. Consequently, the second part of this effort involves the 

development, as per the recently published FSIS Strategic Plan for 2011-2016, of a sampling program 

Plan that identifies fiscal year (FY) 2011 sample collection and analysis numbers, changes to the 

Agency‘s sampling activities to be implemented in FY2012 and provides summary measures for 

existing and emerging food safety hazards. FSIS anticipates that the plan will also be shared publicly 

and should be finalized by the beginning of calendar year (CY) 2012. 

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FSIS Public Health Information System (PHIS) 

On April 11, 2011, FSIS launched its dynamic, comprehensive data analytics system called the Public 

Health Information System (PHIS). PHIS is a web-based application that integrates and automates 

FSIS‘ paper-based business processes into one comprehensive and fully automated data-driven 

inspection system. It will help facilitate the sharing of data among inspection personnel, their managers 

and headquarters on a daily basis. PHIS is also a powerful decision-making tool that will enable FSIS to 

protect public health more efficiently, effectively and rapidly than under existing systems. 

As a result of implementing PHIS, many of FSIS' existing systems, such as the Performance Based 

Inspection System (PBIS) and, eventually, the Automated Import Information System (AIIS), will be 

phased out and replaced by PHIS. As such, the way in which sampling information is scheduled, shared 

and stored will change under PHIS. However, it is important to note that none of the fundamental 

elements of FSIS‘ sampling activities, such as the sampling frame, methodology or collection 

methodology will change and the transition to PHIS will not affect the day-to-day operations of 

pathogen verification and other FSIS sampling programs. 

Definition of Terms 

As this report focuses primarily on FSIS sampling programs, the reader may encounter several terms 

that might not be familiar. Consequently, a catalogue of technical terms utilized in this report is 

included in Appendix A. 

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2.0 Domestic, Regulated Establishments
 

Section 2.1: Microbiological Sampling Programs 

2.1.1: Salmonella 

Overview of Sampling Programs 

FSIS collects Salmonella samples in eight raw meat and poultry product classes (Salmonella Pathogen 

Reduction Performance Standards-- project code HC01 and HC11)4

, two RTE meat and poultry products 

(project codes ALLRTE and RTE001) and nine processed egg products categories (project codes EM 

and EGGDOM). Broiler and turkey samples collected under HC11 are co-analyzed for Campylobacter 

(see Section 2.1.2). In addition, Salmonella testing is conducted on some raw ground beef samples 

collected for E. coli O157:H7 testing, with the Salmonella results recorded under project code MT43S. 

In the section below, the HC01, HC11, MT43S and Egg Sampling programs are reviewed. The 

Salmonella sampling program for RTE meat and poultry products (ALLRTE and RTE001) will be 

reviewed in the Lm RTE section of this report. Information on different domestic Salmonella sampling 

projects is summarized in Table 2.1.1.1.5 

4 Sample sets for Market Hogs, Cows/Bulls, or Steers/Heifers were not scheduled in the latter half of FY 2011.
 5 As of July 1, 2011 all broiler and turkey sets are being co-analyzed for Campylobacter and scheduled as HC11, not HC01.
 

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Table 2.1.1.1 FSIS Salmonella Domestic Sampling Projects 

Product class Salmonella 

Sampling 

Projects 

Number of 

Salmonella 

Samples 

Analyzed 

FY2010 

Regulatory Purpose of 

Sampling Project 

Type of 

Sampling 

Project 

Steers/heifers6 HC01 6,550 Verify consistent process 

control Risk Based 

Cows/bulls7 HC01 1,688 Verify consistent process control Risk Based 

Raw Ground beef HC01 8,982 Verify consistent process control Risk Based 

Market hogs8 HC01 305 Verify consistent process control Risk Based 

Broilers9 HC01 

HC11 

762 Verify consistent process control Risk Based 

Ground chicken HC01 3,913 Verify consistent process control Risk Based 

Ground turkey HC01 3,811 Verify consistent process control Risk Based 

Turkeys10 HC01 

HC11 

1,303 Verify consistent process control Risk Based 

Raw Ground beef MT43S 2,957 Verify consistent process control Random 

Ready-to-eat (RTE) 

meat and poultry 

products 

ALLRTE 2990 Verify adequacy of an establishment's ability to prevent 

microbiological contamination 

Random 

Ready-to-eat (RTE) 

meat and poultry 

products 

RTE001 8700 

Verify adequacy of an 

establishment's ability to prevent 

contamination from Salmonella 

and Lm 

Risk Based 

Egg whites with or 

without added 

ingredients 

EM-31 292 Verify adequacy of a 

establishment‘s ability to prevent 

contamination from Salmonella 

Random 

Whole eggs/yolks 

with <2% added 

ingredients other 

than salt or sugar 

EM-32 389 Verify adequacy of a 

establishment‘s ability to prevent 

contamination from Salmonella 

Random 

Whole eggs/yolks 

with ≥2% added 

ingredients other 

than salt or sugar 

EM-33 141 

Verify adequacy of a 

establishment‘s ability to prevent 

contamination from Salmonella Random 

6 Supra footnote 4.
 7 Supra footnote 4.
 8 Supra footnote 4.
 9 No longer being scheduled for HC01 with the implementation of the new Salmonella and Campylobacter performance 

standards in July 2011. 

10 Supra footnote 9.
 

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Product class Salmonella 

Sampling 

Projects 

Number of 

Salmonella 

Samples 

Analyzed 

FY2010 

Regulatory Purpose of 

Sampling Project 

Type of 

Sampling 

Project 

Whole eggs/yolks 

with ≥2% salt or 

sugar added 

EM-34 287 Verify adequacy of a 

establishment‘s ability to prevent 

contamination from Salmonella 

Random 

Dried yellow egg 

products EM-35 114 Verify adequacy of a 

establishment‘s ability to prevent 

contamination from Salmonella 

Random 

Spray dried egg 

whites (with or 

without added 

ingredients) 

EM-36 104 Verify adequacy of a 

establishment‘s ability to prevent 

contamination from Salmonella 

Random 

Pan dried egg 

whites EM-37 10 Verify adequacy of a 

establishment‘s ability to prevent 

contamination from Salmonella 

Random 

Domestic liquid, 

frozen or dried egg 

products 

EGGDOM 61 Verify adequacy of a 

establishment‘s ability to prevent 

contamination from Salmonella 

Random 

Salmonella Verification Project: HC01 

Historical Basis 

In 1996, FSIS adopted the PR/HACCP final rule that instituted pathogen reduction performance 

standards in the major species and raw product classes.11 At that time, there were eight classes of raw 

products for which FSIS had conducted nationwide baseline studies. These classes were: steers/heifers, 

cows/bulls, raw ground beef, broilers, market hogs, ground turkey, ground chicken and turkeys. From 

these baseline studies, FSIS estimated the mean prevalence of Salmonella in each class and then 

developed establishment-level performance standards to encourage all establishments to produce 

product whose prevalence of contamination was less than or equal to the mean prevalence for each of 

these classes of raw product. ―Minor species,‖ such as sheep, goats, equines, ducks, geese and guineas, 

were not addressed because FSIS chose to first address the most commonly consumed foods under its 

jurisdiction. At the time, FSIS intended to address how best to gather data and develop pathogen 

reduction performance standards for these other food animals at a future date. 

Salmonella, regardless of serogroup/serotype, was selected as the target organism for a number of 

reasons: (1) it is the most common bacterial cause of foodborne illness; (2) FSIS baseline data show that 

Salmonella colonizes a variety of mammals and birds and occurs at frequencies that permit changes to 

be detected and monitored; (3) current methodologies can recover Salmonella from a variety of meat 

The most complete record of the original design and implementation strategy for this verification testing program is contained in the 

Pathogen Reduction/Hazard Analysis and Critical Control Point System final rule (61 FR 38806, July 25, 1996; see: 

http://www.gpo.gov/fdsys/pkg/FR-1996-07-25/pdf/96-17837.pdf. In addition, on February 17, 2005, FSIS published updated pathogen 

reduction performance standards for the raw classes of product that were identified as under development but not yet ready to publish in the 

July 25, 1996, Federal Register (see: http://www.fsis.usda.gov/OPPDE/rdad/FRPubs/02-046N.pdf). FSIS‘ use of baseline studies to 

determine performance standards was also described in a May 6th, 2002 FSIS Symposium entitled ―Symposium on Pathogen Reduction: A 

Scientific Dialogue. Transcripts from this symposium can be found at: http://www.docstoc.com/docs/23091585/Pathogen-Reduction-AScientific-Dialogue---May-5-2002. 

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and poultry products; and (4) intervention strategies aimed at reducing fecal contamination and other 

sources of Salmonella on raw product should also be effective against other pathogens. 

FSIS continues to conduct baseline studies to adjust the pathogen reduction performance standards. It is 

important to note that the pathogen reduction performance standards are not lot-release standards and the 

detection of Salmonella in a specific lot of raw product does not by itself result in the condemnation of 

that lot. The pathogen reduction performance standard policy was based on the public health judgment 

that reducing the percentage of carcasses with Salmonella would reduce the risk of foodborne illness to 

the public. The policy was also based on the regulatory policy judgment that establishing a clear 

standard for Salmonella, in conjunction with the implementation of PR/HACCP, would lead to 

significant reductions in contamination rates. At the time that the pathogen reduction performance 

standards were developed, there had not been a quantitative assessment of the public health impact 

associated with implementation. 

FSIS created a verification testing project—HC01—to ensure that the Salmonella pathogen reduction 

performance standards are being met. Testing is conducted in sample sets, as described in the sampling 

methodology section below. The design of the pathogen reduction sample sets for raw classes of 

product was explicitly predicated on daily testing. When FSIS published the PR/HACCP rule, the 

Agency proposed requiring that establishments, not FSIS, conduct daily testing and to complete at least 

one sample set within a 12-month period. These design features were discussed at length at multiple 

public meetings, including a technical meeting in Philadelphia in which FSIS invited subject matter 

experts to discuss approaches to verification testing.12 Numerous comments were received on the 

proposed rule specific to these design features. In response to comments, FSIS elected to conduct the 

daily testing for Salmonella to allow the Agency to have a direct measure of accountability for 

individual establishment control in reducing harmful bacteria in raw meat and poultry. In the 

implementation of the FSIS verification testing program, the Agency maintained the consecutive day 

sampling and 12-month completion features. FSIS designed the verification testing program in a 

manner to force establishments to test process control variables during a 90-day initial validation period 

and to maintain process control that resulted in consistently wholesome and safe product, even if 

changes occur in source materials or processing conditions. Consecutive day testing, with one sample 

collected per day, was deemed to be an appropriate timeframe to cause establishments to assess potential 

variability in their pathogen control program and to provide sufficient time to adjust their control 

program to attain compliance when the production process trended out of control early in the sample set. 

Daily testing for more than 50 consecutive days of production was recognized as a means for 

establishments to cycle through numerous source material suppliers and better reflect operational control 

capability over time, rather than collecting multiple samples a day, possibly all from the same source 

material supplier, and not demonstrate sustained control of the production process. 

Under the Salmonella verification program as conducted from 1996 to 2006, the Agency verified that 

establishments were meeting a Salmonella standard or guideline by having FSIS inspection program 

personnel (IPP) collect randomly-selected product samples from randomly-selected individual 

establishments over the course of a defined number of sequential days of production to complete a 

sample set. Generally, these tests were conducted once each year for each establishment. Procedures 

for testing are described in Appendix E of the PR/HACCP Final Rule (61 FR 38917–38928). Although 

the original enforcement strategy for the Salmonella reduction performance standards was designed to 

12 Please see the following website for more information: http://www.gpo.gov/fdsys/pkg/FR-1998-10-07/pdf/98-26543.pdf 

14
 
 

 

 

 

 

 

 

 

 

 

 

cause inspection to be withdrawn from an establishment after three consecutive sample set failures, a 

court challenge (known as the Supreme Beef case) now prevents FSIS from enforcing this provision in 

raw beef grinding operations, particularly when the beef is derived from carcasses that passed the 

Agency‘s pathogen reduction performance standard. As a result, FSIS modified its enforcement strategy 

for all classes of raw products and now uses the Salmonella set result as one piece of information in 

determining the adequacy of an establishment‘s food safety system.13 

In order to address issues of resource allocation and time management, as well as provide U.S. States 

with ―equal to‖ meat or poultry inspection programs, in 1997 FSIS crafted shorter Salmonella sample 

sets than were expected to be used by the Agency for State inspection programs. FSIS recognized that 

―equal to‖ State establishments typically would be classified as HACCP establishment size ―very small‖

and that these establishments typically produce more than one class of product subject to Salmonella 

verification testing on the same day. In addition, these establishments typically processed a given class 

of product intermittently (e.g., weekly or seasonally). Because the minimum number of days for any 

sample set size was 51 days, with most sets of less than 60 days and only one set greater than 80 days, a 

sample set likely would not be completed within a 12-month period. Consequently, FSIS crafted shorter 

sample sets that were designed to achieve similar statistical confidence regarding the establishment‘s

control of Salmonella.

14 Sample collection for States was updated in FY2011 to reflect the Salmonella 

and Campylobacter performance standards. 

FSIS routinely reviews the Salmonella performance standards to identify gaps in the current policy and 

to tailor the standards to better protect the public‘s health. As a result, FSIS has made several changes 

over the years to refine the standards. One such change occurred in February 2006, when FSIS 

introduced a categorization system for Salmonella set results to address adverse trends, whereby 

establishments with consecutive sets with less than or equal to half of the current acceptable number of 

Salmonella positive test results in the sample set would be identified as being in Category 1.15 

Establishments with half or more, but not exceeding the acceptable number of Salmonella positive test 

results in a set, are placed in Category 2. Establishments exceeding the acceptable number of 

Salmonella positive test results in a set are placed in Category 3 and consequently fail the Salmonella 

pathogen reduction performance standard. FSIS also posted quarterly Salmonella sample set results on 

the Agency‘s website and provided results back to establishments immediately upon completion of each 

test, rather than waiting until the end of the sample set. 

By January 2008, FSIS was using the new sample scheduling algorithm adopted in 2006 and scheduling 

approximately 75 new verification sample sets for Salmonella in raw classes of product each month. 

FSIS allocates its sampling resources within classes of raw product based on consideration of specified 

16,17 criteria, as provided in the Salmonella HC01 description below. As a result of allocating sampling 

resources in a targeted manner, FSIS is able to fulfill many of the higher priority criteria, such as 

sampling establishments of greater concern. Now, Category 1 establishments are sampled in a period of 

time that may extend up to two years, whereas Category 2 establishments are scheduled at least once 

13 Please see the following website for more information: http://www.fsis.usda.gov/Fact_Sheets/FSIS_Sets_New_Procedures/index.asp.
 14 Please see the Salmonella (Connie Bacon) Sampling Letter for more details and sample collection requirements.
 15 Please see the following website for more information: http://www.fsis.usda.gov/OPPDE/rdad/FRPubs/04-026N.pdf.
 16 Please see the following website for more information: http://www.fsis.usda.gov/OPPDE/rdad/FRPubs/2006-0034.pdf.
 17 Please see the following website for more information:
 

http://www.fsis.usda.gov/Science/Scheduling_Criteria_Salmonella_Sets/index.asp. 

15
 
 

 

 

 

 

 

 

 

 

each year until the establishment‘s category changes. Category 3 establishments are scheduled as close 

to continuously as possible, until the establishment produces better results. 

In May 2006, FSIS implemented a program to obtain serotype data from Salmonella PR/HACCP project 

isolates and share of serotype data with establishments in a timely manner. After FSIS laboratories 

report the analysis results, isolates of Salmonella-positive HACCP samples are serotyped at the USDA 

Animal and Plant Health Inspection Service‘s (APHIS) National Veterinary Services Laboratories

(NVSL) in Ames, Iowa. In recent years, virtually all samples positive for Salmonella have been 

serotyped. Identified serotypes are communicated to establishments as soon as they are reported by 

APHIS to FSIS, usually within two weeks after a HACCP sample has been reported as positive. A 

report listing aggregate identified serotypes by year was posted in August 2007 on the FSIS website at 

http:// www.fsis.usda.gov/Science/ Serotypes_Profile_Salmonella_Isolates/ index.asp. 

Additionally, in August 2007, when FSIS and the Agricultural Research Service (ARS) signed a 

cooperative Memorandum of Agreement for subtype data sharing, FSIS implemented a program to 

obtain timely access to pulsed field gel electrophoresis (PFGE) subtype data, identifying specific strains 

of Salmonella serotypes obtained from HACCP testing. Under this agreement, PFGE subtype 

information on Salmonella isolates collected by FSIS from raw meat and poultry products is matched 

with subtype information from isolates associated with human illness in PulseNet, a database maintained 

by the Centers for Disease Control and Prevention (CDC). FSIS has routine access to subtype data for 

all isolates maintained by ARS, in a time frame short enough to be relevant to in-establishment and 

public health investigations.18 

In January 2008, FSIS chose to exclude from the Salmonella verification testing project schedule any 

slaughter establishment that processes all slaughtered carcass into RTE (e.g., cooked) product or diverts 

all of its raw products to another federally-inspected establishment for further processing into a RTE 

product. This decision is justified because FSIS conducts separate verification testing for Salmonella in 

RTE meat and poultry products via the ALLRTE and RTE001 sampling projects. If the establishment is 

undergoing sampling for Salmonella, but then elects to send all affected product to RTE, FSIS will 

continue to sample until the set is completed. At the end of the set, FSIS will verify that all products 

undergo further processing into RTE product within the establishment or in another Federal 

establishment. If and when such establishments again produce raw product for sale, they will be rescheduled for Salmonella verification sets. 

Also at that time, FSIS announced in a Federal Register Notice additional activities for low-volume 

ground beef operations, minor species and import samples, which have since been implemented by the 

Agency.19 FSIS recognized that low-volume raw ground beef producers, which produce less than 1000 

pounds of product per day, constitute a large part of the sampling frame for establishments eligible for 

verification sample set scheduling, though they account for a very small proportion of the raw ground 

beef supply. Since production of ground beef at these establishments may not occur throughout a week 

or month, sampling them for Salmonella may be extended for a year or more before a set is completed, 

as opposed to no more than a couple of months of sampling for higher volume establishments. To 

18 FSIS currently uses PFGE and Multiple Locus VNTR Analysis Method (MLVA) for subtyping pathogens. PFGE is considered the  ̳gold
 

standard‘, and MLVA may help further differentiate subtypes to assist in making connections between isolates from case patients and
 

FSIS-regulated products.
 19 Please see the following website for more information: http://www.fsis.usda.gov/OPPDE/rdad/FRPubs/2006-0034.pdf.
 

16
 
 

 

 

 

 

 

 

 

 

increase efficiency, FSIS announced that samples collected at these establishments for E. coli O157:H7 

testing would be tested for Salmonella as well. As a result, these establishments were removed from the 

Salmonella verification testing sample set scheduling frame. The FSIS laboratories now perform 

qualitative testing for the presence or absence of Salmonella using the same methodology, discard 

criteria and reporting as those in place for Salmonella ground beef HACCP samples, as described below. 

A description of this sampling project, known as MT43S, is provided below. 

Most recently, on May 14, 2010, FSIS published a Federal Register Notice (75 FR 27288) in which it 

announced the implementation on July 1, 2011 of new performance standards for Salmonella and 

Campylobacter for chilled carcasses in young chicken (broiler) and turkey slaughter establishments. 

The new performance standards were developed in response to a charge from President Obama‘s Food 

Safety Working Group (FSWG) and based on recent FSIS Nationwide Microbiological Baseline Data 

Collection Programs. The standards are applied to sample sets collected and analyzed by FSIS to 

evaluate establishment performance with respect to requirements of the PR/HACCP Rule. These 

performance standards are the basis for assessing an establishment‘s process control for Salmonella and 

Campylobacter and for determining whether an establishment passes or fails a Salmonella or 

Campylobacter verification set. All sample sets scheduled for young chicken and turkey establishments 

are analyzed for both Salmonella and Campylobacter and follow-up sample sets responding to sample 

set failures for either organism are analyzed for both organisms. 

In addition to process control, FSIS identifies the serotype, PFGE and antimicrobial susceptibility 

pattern of Salmonella isolates from each positive verification sample. FSIS uses the subtyping results to 

identify historical trends within the sampling data to determine whether an isolate has a historical 

association with human illness, and to identify clusters of patterns. Since FSIS has not established a 

regulatory performance standard for Salmonella subtypes, this information is not used to determine the 

status of a Salmonella verification set, including whether the establishment has passed or failed the set. 

Effective with samples sets starting in or after July 2011, Salmonella performance Categories 1 and 2, 

based on the new performance standards, are applied exclusively for FSIS internal analysis and not for 

web-posting purposes. FSIS posts quarterly aggregate reports showing the Category 1/2/3 distribution 

for each relevant product class subject to FSIS Salmonella testing, but does identify individual 

establishments. 

Intent of Program 

FSIS considers Salmonella verification testing to be a direct indicator of the effectiveness of process 

control. The raw pathogen performance standards program also serves a variety of other functions, 

including assessing establishment compliance with the performance standard, comparing industry-wide 

and peer-to-peer trends regarding percent positives over time, identifying serogroups of public health 

concern and their origins, as well as capturing pathogen isolates for PulseNet comparison and analyzing 

chilled product at specific points in the production process. 

Type of Analysis 

For each pathogen, FSIS performs different types of analysis on the sample collected. There are two 

possible types of analysis that the FSIS laboratories can conduct. First, FSIS laboratories can determine 

if the pathogen is present or absent in the sample. This is considered to be qualitative analysis. Second, 

FSIS laboratories can determine not only whether the pathogen is present, but also what the level of 

contamination is or the number of microorganisms present in the sample. This is considered to be 

17
 
 

 

 

 

 

 

 

 

 

 

 

 

 

quantitative analysis. FSIS uses several types of quantitative analyses, including direct plating 

enumeration methods and the Most Probable Number (MPN) enumeration procedure, which is used to 

estimate the population density of viable microorganisms in a test sample. 

For Salmonella, analysis of samples for the HC01 sampling project are qualitative, in that samples are 

tested for the presence or absence of Salmonella, rather than a count of the number of organisms in the 

sample. For the MT43S testing project for Salmonella in raw ground beef, FSIS also uses the MPN 

enumeration procedure to estimate the level of contamination in samples that first test positive on a 

qualitative screening test. 

Volume Data 

Yearly production volumes for raw intact beef, chicken, turkey and pork are acquired from slaughter 

volume data in the Electronic Animal Disposition Reporting System (eADRS) database. Volumes for 

ground beef production are obtained by FSIS inspectors during sampling. The inspector classifies the 

establishment‘s volume into one of four volume groups and notes monthly days of production, from 

which an average annual volume can be estimated. Yearly production volumes for ground chicken and 

turkey are obtained from the PBIS, which contains each establishment‘s most recent production volume 

for various product types over the past 30 days. Each product class has a minimum slaughter volume, 

under which an establishment is excluded from sampling eligibility. For example, young chicken and 

turkey sampling eligibility requires a minimum of 20,000 birds slaughtered per year. For livestock, a 

minimum of 500 animals slaughtered per year is required. 

Sampling Methodology 

FSIS schedules eight product classes (young chickens, young turkeys, cows/bulls, steers/heifers, market 

hogs, ground chicken, ground turkey and ground beef) for Salmonella sampling on monthly basis—see 

Table 2.1.1.2.20 An establishment's compliance with the applicable pathogen reduction performance 

standard is evaluated by taking the indicated number of samples—generally at the rate of one or more 

per day— and testing each sample for Salmonella to determine whether the number of positive results is 

above the maximum acceptable for that product class. Daily testing is considered the minimal sampling 

necessary to detect process deviations within a realistic time frame. FSIS currently collects multiple 

samples from each establishment in the form of sets. FSIS verifies that establishments are meeting the 

Salmonella standards by having IPP collect product samples from individual establishments over the 

course of a defined number of sequential days of production to complete a sample set, as described 

previously. Once a sample set begins, sampling is conducted daily until the set is completed. 

Depending on the frequency of production, product type and availability of resources, the time for FSIS 

to complete a sample set ranges from two months to over a year. Salmonella sets are scheduled using a 

―risk-based‖ approach, where establishments with a higher rate of Salmonella are scheduled more 

frequently than establishments with lower Salmonella rates. In establishments that produce more than 

one product subject to Salmonella verification testing, only one product is tested at a time. Annual 

reports summarizing results for calendar years are available on the FSIS web site.21 Raw products with 

established performance standards are carcasses of cows/bulls, steers/heifers, market hogs, broilers and 

turkeys.22 Processed products with performance standards are raw ground beef, ground chicken and 

20 Supra note 6
 21 Please see the following website for more information: http://www.fsis.usda.gov/Science/Microbiology/index.asp.
 22 Supra note 6.
 

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ground turkey. The performance standards are currently based on the prevalence of Salmonella as 

determined from FSIS‘ nationwide microbiological baseline studies. 

Table 2.1.1.2: Salmonella Performance Standard Set Definitions by Product Class 

Product class Performance 

standard 

Number 

of 

samples 

tested 

Sampling Method Testing 

Method 

Maximum 

number of 

positives to 

achieve 

standard 

Steers/heifers 1.0% 82 

Flank, brisket, rump 

surface sampling- 100 

cm 2 for each using one 

cellulose sponge 

hydrated with BPW23 

MLG 4.xenrich sponge 

and BPW 

diluent 

1 

Cows/bulls 2.7% 58 

Flank, brisket, and rump 

surface sampling- 100 

cm 2 for each using one 

cellulose sponge 

hydrated with BPW 

MLG 4.xenrich sponge 

and BPW 

diluent 

2 

Ground beef 7.5% 53 One sample per event 

MLG 4.x-25 

gram test 

portion 

5 

Market hogs 8.7% 55 

Ham, belly, and jowl 

surface sampling- 100 

cm 2 for each using one 

cellulose sponge 

hydrated with BPW 

MLG 4.xenrich sponge 

and BPW 

diluent 

6 

Broilers 7.5% 51 400 ml BPW rinsate MLG 4.x- 30 

ml test portion 5 

Ground 

chicken 44.6% 53 One sample per event 

MLG 4.x-25 

gram test 

portion 

26 

Ground turkey 49.9% 53 One sample per event 

MLG 4.x-25 

gram test 

portion 

29 

Turkeys 1.7% 56 

Back and thigh surface 

sampling- 50 cm2 for 

each using one cellulose 

sponge hydrated with 

BPW 

MLG 4.xenrich sponge 

and BPW 

diluent 

4 

Constructing the Sampling Frame 

The Salmonella HC01/HC11 project includes eight different product classes for sampling: cow/bull, 

steer/heifer, market hog, broilers, turkeys, ground beef, ground chicken and ground turkey.24 Eligibility 

requirements for the intact raw products differ from the intact ground products. This multiple step 

process is described below. 

23 BPW is Buffered Peptone Water 24 Supra note 6. 

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I. Establishments Producing Eligible Product 

The first step in this process is to create a list of all establishments that produce sufficient volumes of 

eligible products. 

1) Intact Raw Products 

Using the eADRS, the total number of each class of eligible intact product that has been 

slaughtered at FSIS regulated establishments in the last 12 months is collected. Establishments 

that meet the minimum production volume requirements are kept in the sampling frame. The 

minimum requirement is as follows for each product class: 

A. Cow/Bull: minimum of 500 heads/year slaughtered 

B. Steer/Heifer: minimum of 500 heads/year slaughtered 

C. Market Hog: minimum of 500 heads/year slaughtered 

D. Broilers: minimum of 20,000 heads/year slaughtered 

E. Turkeys: minimum of 20,000 heads/year slaughtered 

2) Raw Ground Beef 

Establishments that had samples successfully collected and analyzed under the MT43 sampling 

project (E. coli O157:H7 in raw ground beef) in the last 12 months are eligible for Salmonella 

Verification Sampling. Inspectors report the daily raw ground beef production volume every 

time a MT43 sample is collected, so that the mode (most frequent) response over the last 12 

months can be used to determine whether an establishment meets minimum production volume 

requirements.25 

A. Raw Ground Beef: minimum of 1000 pounds/day produced26 

3) Raw Ground Poultry (Chicken and Turkey) 

Salmonella Verification Sampling Program eligibility for raw ground poultry is currently limited 

to establishments included in the ground chicken and ground turkey baseline studies conducted 

in the 1990‘s.27 This is because currently FSIS neither collects detailed production volume data 

for ground poultry, nor does the sampling program include establishments that produce ―raw 

comminuted poultry‖ products.28 

II. Active Establishments 

The second step is to include only establishments that are currently listed as active in their establishment 

profiles. Establishments that are shut down or withdrawn from inspection are removed from eligibility, 

as well as establishments that are currently inactive for any reason, such as seasonal producers and 

temporary closure. 

III. Exclusions 

Next, establishments that meet certain exclusionary criteria are removed from the sampling frame. 

These criteria include the following: 

25 With the implementation of PHIS, production volume data will be available in establishment profiles, which may affect how FSIS
 

determines establishments that meet production volume requirements for raw ground product (i.e. MT43 response no longer necessary). 

26 Establishments producing less than 1,000 pounds per day are tested for Salmonella under the MT43S (low volume) sampling program.
 27 Please see the following website for more information: http://www.fsis.usda.gov/Science/Baseline_Data/index.asp.
 28 FSIS Notice to expand Salmonella Verification testing to include other raw comminuted poultry products is currently in development.
 

This will help in increasing the number of establishments eligible for ground poultry sampling.
 

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1) At Establishment Level 

A.	 Establishments that are currently in an ongoing set for any product are removed from the 

sampling frame.29 

B.	 Establishments that completed and passed a set within 30 days of the date the sets are 

scheduled to start collection are removed from the sampling frame. This is also known as 

the Category 1 exemption, where establishments are excluded from sampling for up to 

two years. 

2) At Establishment Product Level 

A.	 Occasional producers of products are identified by responses to prior sampling requests. 

Establishments for which IPP returned a Salmonella verification sampling request form 

with a code 72 response (product not produced in last 30 days) within 60 days of the date 

the sets are being scheduled to start collection are removed from the sampling frame for 

that product. 

B.	 Establishments that perform only exempt slaughter (custom or religious slaughter) are 

identified by responses to prior sampling requests.30 Establishments for which IPP 

returned a Salmonella verification sampling request form with a code 60 response 

(product no longer produced) within 12 months of the date the sets are being scheduled to 

start collection are removed from the sampling frame for that product. 

Exclusion Criteria 

FSIS maintains a number of additional exclusion criteria in its HC01 sampling methodology not 

mentioned in the exclusion section list provided above. FSIS maintains exclusion criteria for lowvolume establishments. For raw ground beef, establishments that produce less than 1,000 pounds per 

day are excluded from Salmonella verification sampling, although these establishments are sampled 

using the MT43S program. Please see MT43S sampling section for more information on this program. 

Establishments which slaughter less than 20,000 birds and less than 500 animal head per year are also 

excluded from Salmonella set-based sampling. Finally, FSIS maintains product class exclusions. All 

production classes other than young chickens, young turkeys, ground chicken, ground turkey, 

cows/bulls, steer/heifers and market hog are not eligible for Salmonella verification sampling. For 

example, sheep and lambs fall under this exclusion. 

FSIS Scheduling Criteria and Algorithm for the Salmonella HC01/HC11 for Raw Meat and 

Poultry31 

Objective: 

FSIS schedules up to 75 new sample sets each month for raw meat and poultry.32 The establishments 

and products selected for sample sets are chosen according to a risk-based algorithm that involves 

sorting the list of eligible establishments and their respective products by certain criteria and selecting 

33	 34 the top 75 from this list. These priority groups are sorted in descending order of importance.

29 If an establishment products multiple products, these products are scheduled independently; however, it will not be scheduled for more
 

than one set at a time.
 30 Establishments that perform both exempt and non-exempt slaughter are eligible for Verification Sampling for the non-exempt products.
 31 Includes Campylobacter testing for broiler and turkey carcass sets begun after July 1, 2011.
 32 See Federal Register Notice of July 25, 1996 regarding the HACCP Systems Final Rule;
 

http://www.fsis.usda.gov/OPPDE/rdad/FRPubs/93-016F.pdf 

33 See ―SOP to Identify Establishments Eligible for Inclusion in Salmonella and Campylobacter Verification Sampling Program‖ on FSIS 

website at http://www.fsis.usda.gov/Science/Microbiology/index.asp 

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Criteria: 

I. Establishment Category or Establishment Status35 

Establishments are initially sorted by category or status: 

1) Category 3 Establishments (includes establishments with one completed set that was 

failing) 

2) New Establishments and existing establishments with newly eligible product36 

3) Establishments with one completed set that was passing37 

4) Category 2 Establishments 

5) Category 2T Establishments 

6) Category 1 Establishments (≥660 days since last set)

7) Category 1 Establishments (365 to 659 days since last set)38 

II. Product 

Within each status category, establishments are then sorted based on product priority: 

1) Broilers39 

2) Young Turkeys40 

3) Market Hogs41 

4) Ground Chicken42 

5) Ground Turkey43 

6) Ground Beef44 

7) Cows/Bulls45 

8) Steers/Heifers46 

III. Most Recent Set Result
 

Within each product class, priority is assigned based on the result of the most recent Salmonella set.
 

1) Failed; Exceeded Performance Standard 

2) Passed; > 50% Performance Standard 

3) Passed; ≤ 50% Performance Standard 

34 This algorithm is subject to periodic intra-program review and adjustment; during natural disasters (e.g., hurricane), Category 2 

establishments not currently scheduled may be scheduled.
 35 See FSIS method to categorize Salmonella establishments published in Federal Register Notice of January 28, 2008 (73 FR 4767-4774; 

http://www.fsis.usda.gov/OPPDE/rdad/FRPubs/2006-0034.htm).
 36 Includes eligible turkey slaughter establishments (carcasses) as of May 2006, and any new establishment operating for at least 90 days
 

(to accommodate 9 CFR 304.3).
 37 These establishments, technically category 2 or 2T, are placed ahead of other category 2 and category 2T establishments.
 38 Category 1 establishments are not routinely scheduled for sampling until at least 12 months after their last set.
 39 Broiler and young turkey establishments are considered new establishments until 2 sets have been completed under the 

new Salmonella/Campylobacter performance standards, and will be targeted for expedited sampling. If an establishment fails 

EITHER Salmonella OR Campylobacter it will be treated as a failed set (for the purposes of scheduling only) and be
 

scheduled for an immediate follow-up set the next month.
 40 Supra note 39.
 41 Supra note 6.
 42 If establishment is combination carcass/grinding operation, these products are scheduled independently (these 

establishments will have a category for each product); carcass and ground product sets will not be scheduled concurrently.
 43 Supra note 42. 44 Supra note 42.
 45 Supra note 6.
 46 Supra note 6.
 

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IV. Human Health Serotypes Linked to Product Class 

Within each group of recent set results, the next priority is given to the number of human health serotype 

isolates identified in samples from an establishment‘s last set.47 

V. Days Since Last Completed Set 

Final priority is given to the number of days since each establishment‘s last completed set.

Additional Requirements: 

As monthly availability permits, additional establishments may also be scheduled for Salmonella sample 

sets by request from FSIS. 

As of July 1, 2011, the new Salmonella performance standards for broilers and young turkeys became 

effective. For the purposes of scheduling only, Salmonella categorization of establishments for these 

two market classes will be determined as if the standards had been in place at the time an 

establishment‘s most recent two Salmonella verification sets were performed, including sets performed 

prior to July 1, 2011.48 Also, broiler and turkey Salmonella sets scheduled after July 1, 2011 are being 

co-analyzed for Campylobacter. All broiler and turkey establishments will maintain their Salmonella 

category status, but will be marked as having ―newly eligible product‖ or ―one completed set‖ until two 

sets are completed under the new testing program.49 

Establishment categories for these poultry establishments are based on the Salmonella set results. 

However, if a establishment fails a set for either Salmonella or Campylobacter, it will be treated as a 

failed set (for the purposes of scheduling only) and be scheduled for immediate follow-up set the next 

month. 

In the initial phase of implementation with regard to FSIS laboratory sampling capacity, a maximum of 

16 broiler and turkey sets can be scheduled each month. Currently, the goal is to schedule the top 12 

broiler establishments and the top four turkey establishments from the sorted list of eligible 

establishments. These target numbers are subject to quarterly review and adjustment by FSIS. The 

remainder of the 75 sample sets will come from other products. A discussion of FSIS‘ new sampling 

project for Campylobacter is included in Section 2.1.2. 

Statistical or Policy Basis for Current Sampling Plan 

The procedure for determining a compliance criterion to evaluate an individual establishment‘s

performance with respect to the standard is based on an approximate 80% probability of passing the 

criterion, when the establishment‘s prevalence is equal to the performance standard percentage. Stated 

differently, the type 1 error rate of asserting (incorrectly) that the establishment‘s prevalence is greater

than the performance standard is about 0.2 (20% probability of failing) when the establishment is 

performing at the performance standard. For a given performance standard equal to a proportion; p; the 

compliance criterion should be no more than m positive results in n analyzed samples comprising a 

sample set. Thus, m is selected such that P(m) – the probability of a random, binomially distributed 

variable with number parameter, n, and proportion parameter, p is less than or equal to m – is closest to 

47 Number calculated using top 20 Human Health Serotypes for most recent calendar year as reported by the CDC. 48 See FSIS Notice 31-11 (dated 6/30/11) for information on how actual individual and aggregate set results and establishment
 

categorizations will be reported.
 49 Once 90% of broiler and turkey establishments have 2 completed sets under the new standard, FSIS will begin putting them into
 

categories for Campylobacter as well as Salmonella.
 

23
 
 

 

 

 

 

 

 

 

0.8 compared to any other value of P(m′) for m′ not equal to m. The other constraint is that n is a 

minimum of 50 samples. 

Output from Sampling Results 

End of Set Letters 

At the completion of each Salmonella set, FSIS sends an ―end-of-set (EOS) letter‖ to the sampled 

establishment explaining the establishment‘s status based on the overall set results. Each letter lists 

specific set factors: the number of Salmonella serotypes associated with human illness (high, average or 

low for the product class tested) and the timeframe for when the next sample set will begin at that 

establishment. With the new FSIS performance standards, the EOS Letter will report the 

establishment‘s Salmonella Category status based on the standard in effect when each reported set was 

started. FSIS is working with the CDC and the ARS to establish mechanisms to routinely share and 

compare subtyping information. As a result, when reporting sampling results, FSIS will include 

information on subtypes found in the sampling that are associated with human illness when that 

information becomes available. In the interim, the EOS letter will now include information regarding 

not only positive or negative test results, but also detailed serotype information for all positive 

Salmonella results. In addition, for young chicken and young turkey sets, the EOS letter will include 

Campylobacter results. 

Volume-Weighted Percent Positive 

From these sampling results, the volume weighted percent positive is calculated. This method gives 

weight to the establishment-level percent positive estimates using the volume of each product type that 

is produced at the sampled establishments, which is necessary to estimate the amount of contaminated 

product. Thus, samples testing positive for Salmonella from establishments that generate higher 

volumes of product have greater influence on the final statistic because the public health risk increases 

in proportion to the production volume. 

Limitations of Current Sampling 

1.	 Risk-based Sampling 

The current scheduling algorithm is risk-based, which is critical in positively affecting public health, 

but disproportionately focuses sample collection. This means that there is a large difference between 

well-performing establishments (Category 1) and poor, or potentially poor, ones (Category 3), in that 

the former might not be scheduled for sampling for a year or more, whereas the latter could be 

scheduled quite often. For this reason, not all establishments in the collection frame have a non-zero 

probability of selection each month. 

2.	 Product Priority 

Establishments producing certain products are scheduled ahead of others. This prevents those 

establishments/products with lower priority from being sampled regularly because only a given 

number of sample sets can be scheduled each month. This results in data that are not representative 

of certain product classes. Furthermore, some product classes that have been completely excluded 

during certain months would not have a probability of selection for sampling for that period. 

3.	 Announced Sampling 

Once a sample set begins, an establishment is aware that it will be sampled every day the product is 

being produced over the next few months (or longer for smaller establishments that produce less 

frequently), until the set is completed. This knowledge might create a bias because establishments 

may, intentionally or not, be more conscientious in adhering to proper sanitary procedures during 

24
 
 

 

 

 

 

 

 

 

 

 

 

 

 

this time. This could result in an abnormally low number of positive Salmonella results than would 

occur otherwise. 

4.	 Sample Sets 

Salmonella samples are scheduled in sets, which results in a high degree of clustering. That is, 

establishments are sampled intensively, but then not at all for a period of time. Moreover, this is 

problematic from a process control perspective because historical data from well-performing 

(Category 1) establishments does not exist. Thus, it is unknown whether these establishments are 

consistently maintaining low levels of Salmonella, or if their good performance was a temporary 

result of announced sampling. 

5.	 Production Volume 

The major difference between the sampling data for intact and ground products is that volume 

information is not available at the establishment level for ground chicken or ground turkey and only 

a rough estimate can be determined for ground beef. 

6.	 Exclusion Criteria 

As discussed above, FSIS maintains a number of different exclusion periods. For example, 

establishments that reach Category 1 status are not scheduled for another Salmonella set for up to 

two years. Category 2 status establishments are not scheduled for up to 100 days. These exclusion 

periods mean that establishments do not have a consistent probability of selection across all time 

periods. FSIS also maintains exclusion criteria for low-volume establishments, though these criteria 

also apply to FSIS baseline studies. Excluding these establishments prevents the sampling project 

from representing all production under FSIS jurisdiction, but allocates resources for logistical 

reasons. 

7.	 Regulatory Restrictions 

FSIS has published the Salmonella Performance Standards in the Federal Register. Therefore, changes 

to the current project require policy changes. 

8.	 Seasonal Fluctuations 

Many types of pathogenic microorganisms exhibit seasonal patterns, but FSIS verification sampling 

programs currently make no allowances for season fluctuations. 

MT43S Sampling Project 

Historical Basis 

In 2008, FSIS established the MT43S sampling project so that sample collection at very low volume 

establishments (producing less than 1,000 pounds of product per day) would not be overly burdensome 

to the establishments. These establishments were already receiving regular raw ground beef sample 

requests under the E. coli O157:H7 sampling program. FSIS therefore decided to perform an additional 

Salmonella analysis under MT43S on the same sample. In this way, FSIS can effectively test for two 

sampling projects, without overly burdening IPP and the establishment with additional sample 

collection. 

Type of Analysis 

Samples that confirm positive are quantitatively analyzed. For example, the Salmonella organisms 

present are enumerated using the MPN procedure.50 

50 MPNs are only done if there is enough product left over for that analysis. Also, E. coli O157 MPN analysis needs trump those of 

Salmonella if there is limited product available and the sample confirms for both E. coli O157:H7 and Salmonella. 

25
 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Volume Data 

Ground beef production volumes under the MT43S sampling program are obtained by FSIS inspectors 

51, 52 during the sampling process. The IPP classifies the establishment‘s volume into one of four volume 

groups, from which average annual ground beef volumes are estimated. The volume classes are as 

follows; 

1) > 250,000 pounds per day, 

2) 50,001 – 250,000 pounds per day, 

3) 1,000 – 50,000 pounds per day, and 

4) < 1,000 pounds per day. 

Sampling Methodology 

FSIS does not schedule establishments sampled under MT43S in the regular Salmonella verification 

testing project (9 CFR 310.25(b)). Rather, these establishments are selected under the MT43 E. coli 

O157:H7 sampling project.53 The MT43 monthly sample is randomly selected with replacement and 

weighted by production volume and historical test results from the frame of eligible establishments. In 

addition, the MT43 project limits very low volume establishments to no more than one sample per 

month (sampling ceiling) and each establishment must be selected at least three times per year (sampling 

floor). The very low volume establishments selected every month under MT43 are also selected in the 

same month for MT43S. These establishments produce less than 1,000 pounds of raw ground beef on 

an average production day. The Salmonella results are recorded as part of the MT43 project. 

Limitations of Current Sampling 

The MT43 sampling algorithm has both ceilings and floors, which impedes the ability of the weights to 

perform optimally. Additionally, prior notification is required, so establishments can prepare to hold 

product, as recommended by FSIS, pending Agency test results. 

Processed Egg Products—EM 31-37 

Historical Basis 

FSIS carries out its food safety responsibilities with respect to processed egg products under the 

provisions of the Egg Products Inspection Act (EPIA) (21 U.S.C. 1031-1056). Section 1036(a) of the 

Act requires egg products inspected at any official egg products establishment and found not to be 

adulterated and must be pasteurized before they leave the official establishment. Section 1043 delegates 

to the USDA Secretary of Agriculture the authority to promulgate such rules and regulations deemed 

necessary to carry out the purposes or provisions of the EPIA. This authority was delegated to the 

USDA‘s Under Secretary of Agriculture for Food Safety in October 1994. Under the provisions of 9 

CFR 590.580, ―Laboratory tests and analyses‖, FSIS operates a directed microbiological sampling 

program to verify official establishment control of Salmonella; the pathogen of concern when the EPIA 

was originally enacted in 1970. In addition, the processed egg products industry has to conduct lot 

acceptability testing. Establishment or private contract laboratories who analyze egg product official 

54 55 surveillance samples are approved and audited under the PEPRLab program administered by FSIS.

51 Volume groups were developed by a multi-disciplinary team of scientists and technical staff within the FSIS prior to 2003.
 52 With the implementation of PHIS, volume information will be obtained from the establishment profile data. For this reason, questions 

referring to product volume were taken off of all forms collected through PHIS.
 53 Further information on the MT43 sampling project can be found in this document under Section 2.1.4 E. coli O157:H7.
 54 Pasteurized Egg Product Recognized Laboratory Program (PEPRLab) at
 

http://www.fsis.usda.gov/Science/PEPRLab_Program/index.asp. 55 Program is administered by the Laboratory Quality Assurance Division (LQAD), Office of Public Health Science, FSIS 

26
 
 

 

 

 

 

 

 

 

 

 

Processed egg product establishments are not currently operating under HACCP and only limited 

information about establishments is collected in PBIS. Further, compliance/non-compliance data is 

documented manually. In addition, processed egg product establishments are not included in the current, 

phased approach to PHIS implementation for meat and poultry establishments. However, FSIS processed 

egg product inspection is expected to be incorporated in the future into PHIS and implementation of 

HACCP will be considered after full implementation of PHIS for meat and poultry establishments is 

complete. 

Volume Data 

Production volume data for processed egg products is collected from establishments producing these 

products and submitted to FSIS on a monthly basis. Volume data on each of the seven processed egg 

products categories are not currently collected. Instead, summary data on the volume of whole eggs 

broken or received for further processing is provided by establishments. These data are further 

subdivided into categories of whole egg, yolks and whites. Egg processing establishments also provide 

volume information on the total number of ingredients added to processed egg products, the volume of 

liquid, frozen and dried egg products distributed in commerce and the volume of product sent to other 

establishments for further processing. Using this information, the total volume of processed egg 

products produced by each establishment can be determined. This can be further broken down into the 

volume of liquid, frozen and dried processed egg products produced. Using this data, establishments are 

placed into four volume groups, based on their annual production.56 

Current Design of Sampling Project 

There are four liquid and three dried processed egg product process categories in the domestic processed 

egg products sampling program—see Table 2.1.1.3. Each month, one processed egg products sample 

per process is collected from each establishment that produces processed eggs products. 

Table 2.1.1.3: FSIS Processed Egg Products Classes 

EM-31 egg whites with or without added ingredients 

EM-32 whole eggs/yolks with <2% added ingredients other than salt or sugar 

EM-33 whole eggs/yolks with ≥2% added ingredients other than salt or sugar

EM-34 whole eggs/yolks with ≥2% salt or sugar added

EM-35 dried yellow egg products 

EM-36 spray dried egg whites (with or without added ingredients) 

EM-37 pan dried egg whites 

EGGDOM Pasteurized domestic liquid, frozen or dried egg products 

Frame Definition 

The number of processed egg products establishments has stayed fairly consistent over the past 15 years, 

generally ranging from 75 to 85 active establishments. When changes are identified in the types of 

processed egg products that an official establishment is producing, an establishment withdraws or a new 

establishment comes on board, FSIS District Office and FSIS field personnel notify FSIS Headquarters 

staff of the changes so that the database that generates the FSIS sampling forms for egg products can be 

updated. Once processed egg products establishments are included in PHIS, this will be done 

automatically. 

56 Group 1 (≤ 5,000,000 lbs.), Group 2 (5,000,001 - 45,000,000 lbs.), Group 3 (45,000,000 - 75,000,000 lbs.), Group 4 (> 75,000,000 lbs.) 

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Sampling Methodology 

Each month, FSIS conducts a census by sending one processed egg product sample request per process 

from each establishment that produces eggs products. Thus, an egg products processing establishment 

could be selected for collection up to seven times per month, depending on the number of production 

processes occurring during the month. 

Collection Methodology 

FSIS inspection personnel are directed to follow the instructions set forth in FSIS Directive 10,210.1, 

Unified Sampling Form, dated December 18, 2003. The directive lists each sampling project by number 

(EM31, EM32, EM33, EM34, EM35, EM36 and EM37). The directive also provides instruction to the 

FSIS inspector on how to collect the sample, complete the form and ship the sample. Finally, the 

directive provides instruction to IPP on notifying establishment management. FSIS has also developed 

guidance for IPP on how the establishments should be sampled under FSIS Directive 10,230.4, 

Microbial Sampling of Ready-to-Eat (RTE) Products for the FSIS Verification Testing Program for the 

Salmonella sampling project. 

Mean Response Rate 

FSIS collected 60% of all processed egg products forms that were assigned and 58% of forms scheduled 

by FSIS were analyzed. 

Statistical or Policy Basis 

Neither the sample size nor the sampling frequency for processed egg products is statistically based on a 

national prevalence estimate, as calculated from a baseline study. Further, there is currently no policy 

basis for the current sampling program. Rather, the processed egg products sampling program was 

historically designed to make certain that enough samples were collected and analyzed to ensure a broad 

understanding of contamination rates among the different types of processed egg products. Future 

efforts to introduce a HACCP-based processed egg products program will likely mark the development 

of a statistical analysis of the processed egg product data and therefore the development of a 

statistically-based sampling program. 

Limitations of Current Sampling 

Processed egg products sampling frames are not part of PBIS and no instructions have been provided to 

FSIS field personnel on how to update establishment profile data to incorporate processed egg products. 

Additionally, no baseline studies have been conducted to inform the sampling methodology. Therefore, 

statistics produced from the testing data are likely to be biased and have high levels of error. In 

September 2011, FSIS did begin the shakedown period for the Agency‘s Nationwide Raw Liquid Egg 

Microbiological Baseline Survey (RLEBS), though this baseline study will focus on pre-pasteurized egg 

products.57 

Salmonella Programs Measure of Success 

Each Salmonella sampling project has slightly different goals. However, the overall purpose of the 

Salmonella verification testing program to ensure that the pathogen reduction performance standards are 

being met, which ensures that the industry is maintaining process control. 

57 http://www.fsis.usda.gov/OPPDE/rdad/FSISNotices/52-11.pdf 

28
 
 

 

 

 

 

 

 

 

 

 

 

 

Consequently, FSIS believes it is appropriate to measure the success of the different sampling projects in 

broad terms. Further, as FSIS recently implemented new performance standards for Salmonella,

58 

adjustments to these measures may be appropriate moving forward. 

As such, to measure the success of the Salmonella sampling projects, FSIS evaluates its efforts in terms 

of five key metrics: 

1.	 Volume-weighted percent positives for Salmonella in eight raw product classes; 

2.	 Estimated number of Salmonella foodborne illnesses associated with FSIS-regulated products; 

3.	 Establishment categorization based on new Salmonella performance standards; 

4.	 FSIS End of Set Letters; and 

5.	 Reductions in case rates (as reported by the CDC) for the top 10 serotypes of human health 

concern. 

Volume-Weighted Percent Positives 

FSIS conducts pathogen verification testing for many of the Agency‘s sampling projects. FSIS uses this

sampling to calculate a percent positive for many of the Salmonella sampling projects. FSIS believes 

that percent positives are a good measure of the effectiveness and success of the sampling project 

maintained by the Agency, with declines in percent positives potentially indicating greater control of 

Salmonella in raw product. Table 2.1.1.4 provides the production category volume-weighted percent 

positive rate for Salmonella in all raw products and on broiler chickens alone. 

Table 2.1.1.4: Quarterly Salmonella Volume-Weighted Percent Positive Rates for All Raw 

Products and Broiler Carcasses Alone 

Year/Quarter 

Volume Weighted 

Percent Positive Rate 

(All Raw Products) 

Volume Weighted 

Percent Positive 

Rate (Broilers) 

FY 2009 2.74% 5.31% 

FY10Q3 2.88% 5.29% 

FY10Q4 2.62% 5.14% 

FY11Q1 2.70% 5.22% 

FY11Q2 2.58% 5.05% 

FY11Q3 2.32% 5.11% 

Foodborne Illness Estimates: 

As FSIS‘ ultimate goal is to prevent foodborne illnesses from regulated products, it is important to 

measure reductions in foodborne illness as a result of FSIS inspections, sampling, policies and other 

activities. FSIS calculates a performance measure, known as the All-Illness Measure, which represents 

all foodborne Salmonella, Lm and E. coli O157:H7 illnesses from FSIS-regulated meat, poultry and 

processed egg product. FSIS updated the All Illness Measure in Q3, FY2011 to reflect the release of 

59	 60 new illness burden estimates from the CDC and the Healthy People 2020 goals , as well as to coincide 

with the release of the FSIS Strategic Plan for 2011-2016. Objectives for the All-Illness measure were 

58 Please see the following website for more information: http://www.fsis.usda.gov/OPPDE/rdad/FRPubs/2009-0029.pdf
 59 Scallan E, Hoekstra RM, Angulo FJ, Tauxe RV, Widdowson M-A, Roy SL, et al. Foodborne illness acquired in the United States—
 

major pathogens. Emerg Infect Dis [serial on the Internet]. 2011 Jan [November 2011]. http://www.cdc.gov/EID/content/17/1/7.htm
 60 Please see the following website for more information:
 

http://www.healthypeople.gov/2020/topicsobjectives2020/objectiveslist.aspx?topicId=14. 

29
 
 

 

 

 

set using a combination of data from published CDC FoodNet case rates and outbreak data and are 

aligned with Healthy People 2020 goals. For Salmonella, FSIS uses a rolling 12 month window of case 

rate data from the CDC, in addition to an attribution estimate, to estimate the total number of Salmonella 

illnesses from FSIS regulated products. Using this methodology, the illness measure is the estimate of 

the total annual illnesses for the fiscal year, rather than independent measures of illness for each quarter. 

Performance Measure 

Using the newly updated All Illness Measure data sources and methodology, FSIS set a target of 

399,852 Salmonella illnesses associated with FSIS regulated products for Q3, FY 2011; FSIS missed 

that target with 472,859 estimated illnesses. However, there was an approximate 4,000 illness decline 

from the second quarter to the third quarter of FY2011. Figure 2.1.1.1 illustrates the quarterly targets 

for Salmonella illnesses and the estimated illnesses for the most recent four quarters. 

Figure 2.1.1.1: Estimated Salmonella illnesses associated with FSIS regulated products 

Establishment Categorization 

As described in this section, FSIS employs a ―category‖ system to measure the performance of 

establishments producing raw products. This ―Category 1‖ measure is publicly reported in the USDA

Strategic Plan for FY2010-FY2015 and the annual USDA Performance and Accountability Report 

(PAR), and tracked internally at FSIS in the Quarterly Performance Report. As described above, 

starting in July 2011, the new Salmonella performance standard accepted five positive samples in a 51­

sample set for young chickens and four positive samples in a 56-sample set for turkeys. Salmonella 

performance Categories 1 and 2 for young chicken and turkey establishments, based on the new 

performance standards, will be applied exclusively for Agency internal analysis and quarterly aggregate 

reporting. FSIS will track industry progress in achieving Category 1 status and achieving the new 

standard, with greater numbers of establishments maintaining Category 1 status conveying a public 

health benefit in reduced Salmonella illnesses in the population. Finally, FSIS will web-post the names 

of young chicken and turkey establishments that fail the new Salmonella standards (―Category 3‖) for 

30
 
 

 

 

 

 

 

 

 

 

 

 

 

their last set. This web posting will begin as sample sets scheduled for July 2011 are completed. This 

new standard is also a key metric in the recently published FSIS Strategic Plan for 2011-2016. 

End of Set Letters 

FSIS developed a set of performance measures that allow the Agency to evaluate its progress in meeting 

a variety of human health and other goals. These measures focus on both short-term, process-oriented 

goals and long-term, outcome-based FSIS goals, including reducing the burden of foodborne illness 

from FSIS regulated products. One of measures developed by FSIS was the ―percent of slaughter 

establishments with an End of Set (EOS) Letter indicating a Salmonella serotype of human health 

concern was detected‖—see Table 2.1.1.5. The CDC produces a list each year of the top 20 Salmonella 

serotypes (PFGE patterns) of human health concern through its PulseNet program. FSIS also uses 

information from the ARS VetNet program. FSIS seeks to achieve a one percent decrease annually in 

the percent of establishments with an EOS letter with a serotype of human health concern. 

Table 2.1.1.5: FSIS Performance Measure for EOS Letters 

Objectives Goal 

Measures 

Baseline 

FY 2009 FY 2010 FY 2011 FY 2012 FY 2013 FY 2014 FY 2015 

Percent of slaughter establishments 

with an End of Set Letter indicating 

a Salmonella serotype of human 

health concern was detected. 

37.5% 

37.1% 36.8% 36.4% 36.0% 35.7% 35.3% 

31.1% 

Top Ten Salmonella Serotypes 

In the CDC‘s annual FoodNet report, the Agency identifies the ten most common Salmonella serotypes 

as reported by states and localities participating in the FoodNet program.61 FSIS also collects individual 

Salmonella subtype (serotype and PFGE pattern) results from positive samples as part of the FSIS 

Salmonella sampling program. FSIS has established the technical mechanisms to automatically 

populate Salmonella EOS Letters with this enhanced serotype information, in addition to what is 

currently included in EOS letters to establishments from the appropriate data tables in the FSIS data 

warehouse. FSIS and CDC are currently working to finalize both the data sharing agreement and the 

data itself. Once available, FSIS will provide establishments with this information. Additionally, once 

the data pathways are finalized, FSIS will provide the information to establishments and verify that they 

appropriately consider it when evaluating their food safety systems through the performance of a Food 

Safety Assessment (FSA). An FSIS Notice announcing the inclusion of this information in FSIS 

Salmonella EOS Letters has been developed and will be issued once the data pathways between FSIS 

and CDC have been finalized. Changes in the types of serotypes identified over time can be tracked via 

the annual FoodNet report. 

61 Please see the following website for more information: http://cdc.gov/foodnet/factsandfigures/2009/Table6_top10ss_09.pdf. 

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2.1.2 Campylobacter 

Campylobacter Verification Project: HC11 

Historical Basis 

As discussed in Section 2.1.1, on May 14, 2010, FSIS published a Federal Register Notice (75 

FR 27288) in which it announced the implementation on July 1, 2011 of new performance 

standards for Salmonella and Campylobacter for chilled carcasses in young chicken (broiler) and 

turkey slaughter establishments. The new performance standards were developed in response to 

a charge from the FSWG and based on results from the FSIS Nationwide Microbiological 

Baseline Data Collection Program. The standards are being applied to sample sets collected and 

analyzed by FSIS to evaluate establishment performance with respect to requirements of the 

PR/HACCP Rule. All sample sets scheduled for young chicken and turkey establishments will 

be analyzed for both Campylobacter and Salmonella, and follow-up sample sets responding to 

sample set failure for either organism will be analyzed for both organisms. 

Intent of Project 

FSIS considers Campylobacter verification testing to be a direct indicator of the effectiveness of 

process control. The raw pathogen reduction performance standards program for Campylobacter 

also serve, once fully established and once sampling has been conducted for an extended period 

of time, a variety of other functions, including assessing establishment compliance with the 

performance standard and comparing industry-wide and peer-to-peer trends regarding percent 

positive over time. 

Type of Analysis 

Although the Campylobacter performance standards are based on the positive/negative results 

from the quantitative test portion, the Campylobacter laboratory method includes both a 

qualitative and quantitative method that will further inform FSIS of the presence of this pathogen 

in regulated product. 

Volume Data 

Yearly production volumes for chicken and turkey are acquired from slaughter volume data in 

the eADRS database. 

Constructing the Sampling Frame 

Campylobacter verification sampling is applicable only to broiler and young turkey carcass sets 

scheduled to begin after July 1, 2011. Establishment categories for these poultry establishments 

are based on the Salmonella set results. However, if a establishment fails a set for either 

Salmonella or Campylobacter it will be treated as a failed set (for the purposes of scheduling 

only) and be scheduled for immediate follow-up set the next month. Additional details about the 

sampling criteria, exclusion criteria and sampling algorithm and frame are provided above in the 

Salmonella Section 2.1.1. 

Campylobacter Programs Measure of Success 

The overall purpose of the Campylobacter verification testing program is to ensure that the 

pathogen reduction performance standards are being met, which ensures that the industry is 

maintaining process control. Consequently, FSIS believes it is appropriate to measure the 

success of the different sampling project in broad terms. As FSIS recently implemented the new 

32
 
 

 

performance standards for Campylobacter, 

62 the measures of success listed below are under 

currently being developed and therefore adjustments to these measures may be made moving 

forward. 

To measure the success of the Campylobacter sampling project, FSIS is considering evaluating 

its efforts in terms of three key metrics: 

1.	 Volume-weighted percent positives for Campylobacter 

2.	 Reductions in case rates (as reported by the CDC FoodNet) for Campylobacter 

3.	 Estimated number of Campylobacter foodborne illnesses associated with FSIS-regulated 

products 

62 Please see the following website for more information: http://www.fsis.usda.gov/OPPDE/rdad/FRPubs/2009-0029.pdf. 

33
 
 

 

 

 

 

 

 

 

 

 

2.1.3: E. coli O157:H7 Raw Sampling Projects 

Overview of Sampling Projects 

FSIS maintains many E. coli O157:H7 sampling projects for domestic establishments. The 

different E. coli O157:H7 sampling projects are summarized in Table 2.1.3.1. 

Table 2.1.3.1 FSIS E. coli O157:H7 Sampling Projects 

Product Type 

E. coli 

Sampling 

Projects 

Number of 

E. coli 

Analyzed 

samples 

CY201063 

Regulatory 

Purpose of 

Sampling 

Program 

Type of Sampling 

Program 

Raw ground beef MT43 11,291 Verify zerotolerance Weighted Random 

Follow-up testing to a raw 

ground beef positive MT44 309 Verify corrective measures Targeted Consecutive 

Beef Manufacturing trim MT50 1,274 Verify HACCP 

compliance Random 

Raw ground beef 

components other than 

trim 

MT54 169 Verify HACCP 

compliance Random 

Bench trim MT55 547 Verify HACCP 

compliance Random 

Follow-up testing at 

supplier establishments 

following MT43, MT44, 

or MT55 positive 

MT52 636 Verify corrective 

measures Targeted Consecutive 

Follow-up testing to a 

MT50, MT54, MT55, or 

MT52 positive 

MT53 125 Verify corrective 

measures Targeted Consecutive 

Domestic Sampling Programs (Federally inspected establishments) 

Historical Basis for Sampling Raw Ground Beef 

The following section provides a general overview of the historical progression of FSIS 

sampling for E. coli O157:H7. In addition to the material provided below, a timeline of FSIS 

activities related to E. coli O157:H7 can be found on the FSIS website. 64 

In 1994, FSIS announced that raw ground beef products contaminated with E. coli O157:H7 

would be considered adulterated, unless the ground beef was processed further to destroy the 

pathogen. A sampling project for E. coli O157:H7 in raw ground beef was initiated in October 

1994. The objectives of the verification testing project were to verify the effectiveness of control 

measures at individual grinding establishments and to stimulate industry action to reduce the 

presence of the pathogen in ground beef. FSIS initiated the verification testing program on raw 

ground beef, rather than on source materials (e.g., carcasses or beef manufacturing trimmings 

used to make ground beef) for a number of reasons, including that ground product was well63 Please see the following website for more information:
 

http://www.fsis.usda.gov/Science/Ecoli_Raw_Beef_Testing_Data_YTD/index.asp.
 64 Please see the following website for more information: http://www.fsis.usda.gov/PDF/Ecoli_O157_Timeline.pdf.
 

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blended, was in the form closest to the consumer and was the product most frequently associated 

with foodborne illness. 

The verification testing program was not statistically designed at initiation; some samples were 

randomly selected and others were targeted. The frame also contained retail stores and federally 

inspected establishments that produced raw ground beef. Random samples were scheduled at 

retail and federally inspected establishments. Targeted samples were scheduled at 

establishments identified as performing below average using Review and Assessment data,65 

PBIS performance data for sanitation, receiving, or processing deficiencies or consent orders. 

Additional targeted follow-up samples were collected when a confirmed positive was detected. 

These samples were collected from the establishment that tested positive for E. coli O157:H7 

and from all other establishments associated with the same corporate structure. Targeted 

samples were also collected from State-inspected establishments and imported ground beef 

products. 

In February 1998, FSIS issued updated instructions for raw ground beef sampling to verify the 

effectiveness of controls at individual grinding establishments.66 It was and is FSIS policy that 

the establishment is responsible for having a high degree of confidence that E. coli O157:H7 

does not contaminate the production lot. Each month, FSIS randomly selected establishments, 

while FSIS Compliance Investigators (CI) targeted retail stores for sample collection. 

At that time, FSIS based its sampling plan on information from the CDC FoodNet sentinel sites‘

historical data of outbreaks (e.g., geographical locations in the U. S. where public health 

laboratories actively collect human illness data).67 If an establishment or a retail outlet initiated 

its own routine sampling program, had certification from suppliers that the product was tested, 

or, in the case of an inspected establishment, used in-establishment validated pathogen reduction 

interventions on beef carcasses, FSIS did not collect samples. When a sample tested positive for 

E. coli O157:H7, subsequent samples from new lots were collected daily until negative results 

were obtained in 15 consecutive samples. Additionally, if ground beef at an FSIS inspected 

establishment or retail outlet was associated with an outbreak of foodborne illness linked to E. 

coli O157:H7, FSIS sampled daily until 15 consecutive samples tested negative. All raw, 

comminuted beef products produced on the shift represented by the positive sample were subject 

to voluntary recall. 

In 1999, FSIS further clarified in a Federal Register Notice an expanded adulteration policy, 

where raw beef source materials used to manufacture ground beef, as well as beef that had been 

handled in a way that could transfer the external surface contamination to the interior of the 

65 From 1995-1996, FSIS had a program office called Review and Assessment. The office would visit establishments and 

develop review reports that could lead to suspensions in establishments where in-establishment inspection personnel had never 

written a PDR (a predecessor of the NR). A major focus area was establishment review triggered by high levels of fecal 

contamination. 

66 FSIS Directive 10,010.1 "Microbiological Testing Program for Escherichia coli 0157:H7 in Raw Ground Beef," February 1, 

1998. 

67 The CDC FoodNet sites were used for retail sample guidance as, prior to HACCP implementation, retail stores were thought to 

be closest potential source of contamination for consumers. Retail samples were requested from the Compliance Offices located 

in or near FoodNet sites. The FoodNet site priority did not apply to Federally Inspected Establishments. Directive 10,010.1 

(February 1, 1998) included the policy for inspected establishments, but the exemptions were canceled in 2002. 

35
 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

product, would also be considered adulterated.68 In Apri1 2003, FSIS announced with FSIS 

Notice 11-03 that it would begin testing all products that met the standard of identity in 9 C.F.R. 

319.15 (a-c), which could include coarse, ground beef. Thus, if an establishment producing 

coarse ground beef shipped that product to another establishment that re-ground the coarse 

ground product into finely ground beef, FSIS would now sample the product at both 

establishments. 

In March 2004, FSIS implemented a major revision to FSIS Directive 10,010.1, Microbiological 

Testing Program for Escherichia coli 0157:H7 in Raw Ground Beef. All establishments 

producing raw ground beef products, raw ground beef components or raw beef patty components 

were eligible for FSIS sampling for E. coli O157:H7. In addition, the directive provided the 

following instructions to FSIS field personnel: 

1.	 Traceback procedures were to be performed to collect source supplier information after 

an FSIS positive test result.69 This information was entered into a database, and suppliers 

identified repeatedly in the database were subject to a comprehensive FSA of the 

supplier; 

2.	 Verification of process control for lots testing presumptive positive or positive for E. coli 

O157:H7 was required; and 

3.	 Follow-up actions to an FSIS positive test result were to be implemented both at the 

original positive establishment and at all supplier establishments. 

In 2008, an FSIS analysis found that production volume is a better determinant of risk for E. coli 

O157:H7 than HACCP size. This analysis determined that E. coli O157:H7 in cattle and the 

incidence of foodborne illness from E. coli O157:H7 positive products displayed positive 

seasonal effects during warmer months. As a result, in January 2008, FSIS implemented riskbased sampling of raw ground beef, weighted by production volume and historical test results.70 

Under this new verification testing program, larger volume operations are tested more frequently 

than in the past. FSIS also implemented a change in the laboratory testing method at this time 

that included a single 325 gram test portion, enriched at a 4:1 ratio of enrichment broth in 

product as an alternative sample preparation procedure. 

FSIS analytical capacity has allowed for increased sampling over time. FSIS analyzed 

approximately 3,000 to 7,000 samples per year from 2001 – 2003. Starting in 2005, FSIS 

laboratories started analyzing around 11,000 samples per year. 

Historical Basis for Sampling of Products Other than Raw Ground Beef 

In a January 1999 policy statement, FSIS noted that when the E. coli O157:H7 sampling 

methodology became sufficiently refined to enhance the likelihood of finding the pathogen on 

source materials used to make ground beef, the Agency expected to begin supplementing the 

verification testing project for ground beef with FSIS testing of source materials. 

68 See: http://www.federalregister.gov/articles/1999/01/19/99-1123/beef-products-contaminated-with-escherichiacoli-o157h7.
 69 With FSIS Notice 58-10, this information is collected at the time the sample is collected.
 70 Withee J., Schlosser, W. (February 2008). Risk-based sampling for Escherichia coli in O157:H7 in ground beef
 

and beef trim. USDA/FSIS/OPHS/Risk Assessment Division: 

http://www.fsis.usda.gov/PDF/Ecoli_Sampling_RA_Report_Feb08.pdf, accessed on November 18.
 

36
 
 

 

 

 

 

 

 

 

 

 

 

 

 

In April 2003, FSIS Directive 10,010.1 stated that head and cheek meat used for production of 

ground beef not treated with antimicrobial interventions could present an elevated risk for 

presence of E. coli O157:H7 and should be addressed in an establishment‘s HACCP plan. FSIS 

also stated that the Agency would soon begin testing manufacturing trimmings and carcasses to 

supplement the ground beef testing project, although implementation was delayed as FSIS had 

not developed a laboratory procedure at that time to effectively test manufacturing trimmings. 

In August 2003, FSIS requested that the National Advisory Committee on Microbiological 

Criteria for Foods (NACMCF) provide feedback on the Agency‘s baseline study design for raw 

ground beef components to ensure that appropriate priority was given to the different categories 

of product. NACMCF reordered the priority ranking of the categories provided by USDA/FSIS 

based on volume, the perceived contribution to the risk of illness, expert opinion on the use of 

the components in ground beef and processing variables, such as chilling rates during 

production. NACMCF recommended that FSIS reprioritize the rank order for engaging in 

baseline studies as follows: 

1. Domestic trim and subprimals, 

2. Advanced Meat Recovery (AMR), 

3. Low-Temperature-Rendered Products (LTRP ), 

4. Imported frozen and fresh beef, and 

5. Weasand, cheek, and head meat. 

Domestic trim and subprimals were considered the number one priority since these components 

comprise the largest volume of raw materials used in ground beef and are known to contain E. 

coli O157:H7.71 

In March 2007, FSIS began routine verification sampling of beef manufacturing trimmings 

intended for use in raw ground beef, hamburger or beef patty products at the slaughter 

establishments that produced those trimmings. Trim sampling was initiated with FSIS Notice 

18-07 in March 2007 at a rate of 50 scheduled samples per week (MT50 project). This decision 

was partly informed by grinding establishments‘ claim that meat was already contaminated upon 

receipt by the establishment. FSIS conducted a baseline study in 2007 that showed a higher level 

of E. coli O157:H7 in tested beef manufacturing trimmings than in tested raw ground beef. 

Incorporating the results of the baseline study, FSIS performed a statistical analysis to determine 

the minimal number of samples needed to be analyzed in a year to be able to detect a 50% 

change in positive rates, as compared to the prevalence estimate calculated from the baseline 

study (under standard statistical assumptions). The evaluation concluded that an increase to 

approximately 3,500 analyses per year was necessary and, at the time, FSIS was sending out 

2,600 sample request forms per year. However, due to budgetary constraints, this proposed 

change was never implemented in the MT50 project. 

Starting in late 2007, FSIS made several changes to the sampling program to expand the scope of 

products tested for E. coli O157:H7. FSIS began collecting samples of raw ground beef 

components other than trim in December 2007 (MT54 project). FSIS also began testing trim and 

other raw ground beef components to enforce the policy that E. coli O157:H7 adulterates intact 

71 http://www.fsis.usda.gov/OPHS/NACMCF/2003/gb_base.pdf 

37
 
 

 

 

 

 

 

 

 

 

 

 

 

 

product intended for use in raw non-intact product. Consequently, FSIS began verifying that 

both grinders and slaughter supplier establishments had effective controls for E. coli O157:H7 to 

incentivize suppliers and grinders to maintain effective controls for the pathogen. The frame 

definition for manufacturing trimmings (MT50 project) was used for this new sampling project 

and the sample size was calculated based on the capacity of the FSIS laboratories, which allotted 

780 analyses per year. No oversampling to account for response rate was incorporated into the 

sample size. 

Based upon research resulting from the 2007 FSIS E. coli Checklist,72 the Agency decided to 

begin testing bench trim intended for use in raw ground beef, hamburger or beef patty products 

(MT55 project). Bench trim is a component of raw ground beef that is not produced at slaughter 

establishments. Rather, it is produced in the process of cutting down purchased carcasses, primal 

or subprimals into steaks or roasts. The trim produced in this process is then sold to a grinding 

establishment as a component of raw ground beef. Bench trim sampling began in 2009 and FSIS 

allocated 1,800 analyzed samples annually for this new project. No oversampling to account for 

response rate was incorporated into the sample size. 

Type of Analysis 

In general, samples for E. coli O157:H7 are qualitatively and quantitatively assessed for the 

presence of the organism. FSIS collects information on samples that confirm positive using the 

MPN procedure on sample reserves and this information is captured by the FSIS laboratories, 

though not routinely reported in public venues. 

Description of the FSIS Domestic Sampling Projects for E. coli O157:H7 

A description of each of the domestic sampling projects for E. coli O157:H7 follows below. 

Please see Appendix B for additional information on the E. coli O157:H7 sampling projects. 

Risk-based testing of raw ground beef at domestic establishments (MT43) 

Purpose 

The purpose of the MT43 risk-based sampling project is to provide verification of HACCP 

policy and to assess, and minimize, the risk to the public‘s health from contaminated raw ground 

beef. FSIS initially implemented risk-based sampling of raw ground beef, weighted by 

production volume and historical test results, in January 2008.73 The MT43 project replaced the 

MT03 project, which was simple random sampling of raw ground beef. The current 

methodology was implemented in late 2009. 

Sampling Frame Definition 

The frame includes establishments that meet one of the following requirements: 1) Federally 

inspected establishments that have the 9 CFR flag identified in their PBIS profile (per FSIS 

Notice 105-08, previously FSIS Notice 86-07) or report producing raw ground beef finished 

products in their PHIS profile and 2) Federally inspected establishments that have had an MT43 

72 Alvares, C., Lim, C., & Green, K. (August 2008). Results of checklist and reassessment of control for Escherichia coli in
 

O157:H7 in beef operations. USDA/FSIS: http://www.fsis.usda.gov/PDF/Ecoli_Reassement_&_Checklist.pdf, accessed on
 

November 18, 2010.
 73 Withee J., Schlosser, W. (February 2008). Risk-based sampling for Escherichia coli in O157:H7 in ground beef and beef trim. 

http://www.fsis.usda.gov/PDF/Ecoli_Sampling_RA_Report_Feb08.pdf.
 

38
 
 

 

 

 

 

 

 

 

 

 

 

 

 

sample collected in the last 12 months. An exclusion list is maintained to exclude establishments 

for special circumstances when documentation is provided by FSIS field personnel. 

Average Frame Size 

Generally, the frame is around 1,300 establishments. This value fluctuates monthly as new 

establishments become eligible and others become ineligible. Ineligibility may result from 

seasonal processing, closure, withdrawal of inspection, change in business practices and other 

reasons. 

Sample Size 

FSIS selects 1,300 establishments from the frame every month. The decision was not 

statistically based, but based upon lab capacity constraints at the time the MT03 project was 

initiated. 

Sampling methodology 

MT43 is weighted random sampling with replacement under the constraints of sampling ceiling 

by volume strata and annual sampling floors. See below for discussion of weights, ceilings and 

floors. A sampling algorithm is used, which selects the sample from the frame. The 

methodology was based upon the results of an FSIS analysis that identified production volume 

and historical test results as a significant risk factor for public health exposure. 

Sampling weights 

Sample selection is weighted by scaling factors to produce a probability of selection for each 

establishment, pi. The scaling factor formula for n establishments has a number of inputs. 

1.	 Historical testing data - those establishments that have had a positive test result within the 

last six months are five times more likely to have a positive in the near future, so the weight 

for these establishments has a factor of five applied. This is referred to as the hazard score, 

hsi. The hazard score is five for establishments that have had a recent positive and one for 

establishments without a positive test result. 

2.	 Production volume data - those establishments that have higher estimated annual production 

volume are weighted more heavily. The volume weights are calculated from the four daily 

production volume groups, as described below, and are reported on every MT43 form or in 

the PBIS (and, moving forward, PHIS) establishment profile.74 An establishment‘s volume 

group is assigned by taking the mode of all the reported groups from every form collected in 

the last 12 months. See Table 2.1.3.2 for details on assigning estimated annual volume by 

volume group. A volume score, vsi, is then calculated that transforms the data relative to the 

smallest production volume. 

74 Volume groups were developed by a multi-disciplinary team of scientists and technical staff within the FSIS prior to 2003. 

There are currently more volume groupings for MT43 sampling within PHIS, but they map exactly to the Agency‘s existing PBIS 

categories. 

39
 
 

 

 

 

Table 2.1.3.2: Estimated Annual Volume by Volume Group for E. coli O157:H7 Sampling 

Projects 

Assigning Estimated Annual Volume by Volume Group 

Volume 

Group (i) 

Estimated daily volume 

in lbs/day 

Midpoint of volume 

in lbs/day (Vi) 

Volume Score 

( 

1 > 250,000* 375,000 32 

2 50,001 – 250,000 150,000 13.375 

3 1,000 – 50,000 25,500 3.069 

4 < 1,000 500 1 

* 500,000 lbs/day is assumed to be the maximum. 

3.	 Scaling factor constants - FSIS decided that the volume factor of the weight being allowed to 

function freely did not meet needs of the Agency. That is, very large volume producers were 

selected at too burdensome a rate and very small volume producers were selected at a rate too 

low to support HACCP verification. FSIS tested various scaling factors until the Agency 

was satisfied with the general rate of selection by production volume group. The scaling 

factors, = 32 and , cause the volume scores to range from 1 to 32 rather than from 

1 to 750. 

Sampling ceilings 

FSIS established sampling ceilings to ensure that the Agency does not over-burden very small 

establishments. The sampling ceilings were raised for large volume establishments in 2009 

because sampling at a higher frequency in establishments that produce more volume of product 

results in a higher level of confidence in an estimate that is weighted by production volume.75 

Please see Table 2.1.3.3 for sampling ceilings. 

Table 2.1.3.3: Sampling Ceilings for E. coli O157:H7 Sampling Projects 

Sampling Ceilings 

Volume Group Maximum Samples Allowed per Month 

1 4 per month for large volume producers 

2 3 per month for medium volume producers 

3 2 per month for small volume producers 

4 1 per month for very small volume producers 

Sampling floors 

FSIS established sampling floors to ensure that each establishment in the frame is sampled every 

year. The current sampling floor is three analyzed samples in 12 months. 

Collection methodology 

Field inspectors are to collect one pound of raw ground beef per FSIS Directive 10,010.1, 

Revision 3 Ch. II, III.76 

75 FSIS temporarily implemented sampling ceiling and sample size increases in August and September 2011 through 

FSIS Notice 36-11. 

76 http://www.fsis.usda.gov/OPPDE/rdad/FSISDirectives/10010.1Rev3.pdf 

40
 
 

 

 

 

 

 

Mean response rate 

Since 2006, the mean annual response rate of collected samples, as compared to printed forms, is 

72%. Sample requests have a 30 day window, which means that it is likely that some establishments 

will be scheduled, but may not have product available within that 30 day window due to a 

combination of intermittent production and changing FSIS inspector patrol assignments. 

Mean analyzed samples 

Since 2006, FSIS laboratories have analyzed a mean of 11,482 samples per year. 

Follow-up testing to a raw ground beef positive at a domestic establishment (MT44). 

Purpose 

An MT44 sample follows an MT43 positive. The purpose of the MT44 sampling project is to 

follow-up in establishments that recently had an MT43 positive, providing more frequent, 

targeted sampling at these establishments as a means of verifying that HACCP systems are back 

in control. MT44 replaced the MT04 project at the same time that MT43 replaced MT03. 

Sampling Frame definition 

This methodology does not define a frame because it is not a statistical sampling project. Rather, 

establishments that receive MT44 sample request forms are those that have recently had an 

MT43 positive sample. 

Average frame size 

This does not apply because MT44 is targeted sampling based upon MT43 results. 

Sample size 

For each MT43 positive at an establishment, 16 follow-up sample request forms are 

automatically scheduled at that establishment. In the case where the establishment produces less 

than a thousand pounds per day, then only eight follow-up sample request forms are collected at 

that establishment. The decision to collect 16 follow-up samples was made in 2008, when an 

FSIS analysis showed that establishments that test positive were five times more likely to receive 

another positive in the next 160 days than those that do not. At that time, the national average 

for grinders was approximately 0.17% positive in sampled lots. Under binomial distribution, 16 

negative samples from 16 lots gives a 95% confidence that the establishment is less than 100 

times above the national average. While FSIS performed these calculations, they were not 

seriously considered out of practicality as 1,750 follow-up samples over four months would need 

to be scheduled to verify that the establishment was at or below 0.17% positive. 

Sampling methodology 

Samples for the MT44 project are automatically scheduled for the establishment following an 

MT43 positive. 

Collection methodology 

Inspectors are to collect one pound of raw ground beef per FSIS Directive 10,010.1, Revision 3, 

Ch. II, III. 

41
 
 

 

 

 

 

 

 

 

Mean response rate 

Between 2006 and 2009, the mean annual response rate of collected samples, as compared to 

printed forms, was 56%. However, there was marked improvement in samples received for 

analysis starting in 2009, with a mean response rate of 83%. Also, 16 forms are sent to all 

establishments, but inspectors are instructed to collect only eight samples in very small volume 

establishments. The non-response rate may therefore be artificially inflated. Additionally, some 

establishments choose to stop producing raw ground beef after an MT43 positive, eliminating the 

possibility of follow-up sampling. 

Mean analyzed samples 

The annual mean of analyzed samples is 254 per year, but this value ranges from 24 samples 

analyzed in 2006 to 484 samples analyzed in 2009. This variation can partly be attributed to 

changes in the number of follow-up samples scheduled in response to a single positive. 

Additionally, the annual tally is based on the number of positive MT43 samples analyzed during 

the year. 

Routine testing of manufacturing trimmings at domestic establishments (MT50) 

Purpose 

The intended purpose of the MT50 sampling project is to verify HACCP. The program was 

initiated to randomly sample establishments that produce beef manufacturing trimmings. The 

intention was to enhance the program at some future date to make it more risk-based and support 

measuring prevalence. In January 2011, FSIS published a report entitled the National Prevalence 

Estimate of Pathogens in Domestic Beef Manufacturing Trimmings (Trim). This report was 

based on data collected from a 2007 baseline study on trim. The report indicates that, from 

2005-2007, the estimated national prevalence of E. coli O157:H7 in beef trim was 0.39%, with a 

95% confidence interval between 0.05% and 0.73%. 77 Currently, the beef manufacturing 

trimmings verification sampling program is conducted as originally designed. Enhancements to 

the program are still being considered. 

Sampling Frame definition 

The frame includes all active, federally inspected beef and veal slaughter establishments that 

produce trim for use in raw ground beef and identified sister establishments. If an MT50 

sampling form is returned to the laboratories with code 60 (product not produced) selected, then 

the establishment is excluded from the frame for 12 months. An exclusion list is maintained to 

exclude establishments for special circumstances when documentation is provided by FSIS field 

personnel. 

Average frame size 

Generally, the frame is around 480 establishments. This value fluctuates monthly as new 

establishments become eligible and others become ineligible. Ineligibility may result from 

seasonal processing, closure, withdrawal of inspection, change in business practices and for other 

reasons. 

77 Please see the following website for more information: 

http://www.fsis.usda.gov/PDF/Baseline_Data_Domestic_Beef_Trimmings_Rev.pdf. 

42
 
 

 

 

 

 

 

 

Sample size 

FSIS selects between 200 and 250 establishments from the frame every month, depending upon 

the number of weeks in a month. Annually, this amounts to mailing 2,600 sample forms per 

year. This sample size is not adequate to detect practical changes from the national prevalence 

level as estimated by the 2007 baseline study. The choice of implementing 50 forms per week 

was the result of FSIS laboratory capacity at the time of implementation. 

Sampling methodology 

MT50 is a simple random sample without replacement. 

Collection methodology 

Inspectors were directed to collect an N60 sample weighing 325 grams where each piece 

matches a template (1‖ wide x 3‖ long x 1/8‖ deep) and the goal is collection of 60 pieces, per 

FSIS Directive 10,010.1, Revision 3, Ch. II, IV. The N60 sample is to be placed in one container 

and a second container is filled with small pieces. The purpose of an N60 sample is to gather a 

more representative sample consisting mostly of surface area, where E. coli O157:H7 is most 

likely to exist. In practical terms, however, it is nearly impossible for an inspector to collect an 

N60 sample that meets the number of pieces, piece dimension and total sample weight 

specifications. As of last year, the FSIS laboratories have redefined the analytical portion to 

consist of the analysis of up to 60 pieces (N60) weighing up to 715 grams (up to two 325 gram ± 

32.5 gram subsamples, rather than limit the sample to 325 grams. This decision was reached 

after the method was validated to process a single 325 gram sample (previously it was 5-65 gram 

subsamples). 

Mean response rate 

Since 2007, the mean annual response rate for collected samples, as compared to printed forms, 

is 40%. The low response rate may be due to a poorly defined frame; that is, not all slaughter 

establishments may produce this product or they produce them infrequently. Additionally, the 

collection methodology is N60, which is an onerous and resource-intensive method. This may 

also contribute to low collection rates. 

Mean analyzed samples 

Since 2007, FSIS laboratories have analyzed a mean of 1,092 samples per year. The necessary 

number of analyzed samples to be able to estimate a change in prevalence is between 3,000 and 

4,000 per year. As a result, FSIS cannot say with certainty that the results of the MT50 sampling 

project are statistically different from the baseline prevalence estimate. 

Routine testing of domestic components to raw ground beef – other than trim – at domestic 

establishments (MT54) 

Purpose 

The intended purpose of the MT54 sampling project is to verify HACCP. 

43
 
 

 

 

 

 

 

 

 

 

Sampling Frame definition 

The frame includes establishments that meet one of the following requirements: 1) Active, 

federally inspected beef and veal slaughter establishments and 2) Active, federally inspected 

ammoniated lean finely textured beef (LFTB) producing establishments (there are six of these 

known to be operating in the U.S.). If an MT54 sampling form is returned to the laboratories 

with code 60 (product not produced) selected, then the establishment is excluded from the frame 

for 12 months. An exclusion list is maintained to exclude establishments for special 

circumstances when documentation is provided by FSIS field personnel. 

Average sample frame size 

Generally, the frame is around 450 establishments. This value fluctuates monthly as new 

establishments become eligible and others become ineligible. Ineligibility may result from 

seasonal processing, closure, withdrawal of inspection, change in business practices or for other 

reasons. 

Sample size 

FSIS selects between 60 and 75 establishments from the frame every month, depending upon the 

number of weeks in a month. Annually, this amounts to mailing 780 sample forms per year. 

The choice of implementing 15 forms per week was due to laboratory contracting limitations of 

780 analyses per year at the time of implementation. 

Sampling methodology 

MT54 is a simple random sample without replacement, except for ammoniated beef 

establishments. The ammoniated LFTB establishments are selected with certainty every month. 

Collection methodology 

Inspectors are directed to collect two pounds of component product other than trim, per FSIS 

Directive 10,010.1, Rev. 3. How the inspector collects the sample depends upon the type of 

product being collected. For Advanced Meat Recovery (AMR) product and Low Temperature 

Rendered (LTR) product, IPP are to select randomly a sample consisting of no less than one 

pound, but not more than two pounds of product from a specific production lot. For other raw 

beef components (e.g., heart meat), IPP are to collect randomly one piece, or enough pieces, of 

the beef components to equal no less than one pound, but not more than two pounds of product 

from a specific production lot. If the component is very large, IPP are to collect an N60 sample 

where the goal is collection of 60 pieces, in the manner as described in Ch. II, IV. In practical 

terms, however, it is nearly impossible for an inspector to collect an N60 sample that meets the 

number of pieces, piece dimension and total sample weight specifications. As of last year, the 

FSIS laboratories have redefined the analytical portion to consist of the analysis of up to 60 

pieces (N60) weighing up to 715 grams (up to two 325 gram ± 32.5 gram subsamples) rather 

than limit the sample to 325 grams. This decision was reached after the method was validated to 

process a single 325 gram sample (previously it was 5-65 gram subsamples). 

Mean response rate 

Since 2008, the mean annual response rate of collected samples, as compared to printed forms, is 

27%. The low response rate may be due to a poorly defined frame; that is, not all slaughter 

establishments may produce this product. 

44
 
 

 

 

 

 

 

Mean analyzed samples 

Since 2008, FSIS laboratories have analyzed a mean of 224 samples per year. 

Routine testing of bench trim at domestic establishments (MT55) 

Purpose 

The intended purpose of the MT55 sampling project is to verify HACCP. This sampling project 

was implemented in September 2009. 

Sample frame definition 

The frame includes all active, federally inspected beef processing establishments that produce 

trim from purchased product. These establishments were initially identified from a combination 

of PBIS extension profile data and the 2007 FSIS E. coli checklist responses. If an MT55 

sampling form is returned to the laboratories with code 60 (product not produced) selected, then 

the establishment is excluded from the frame for 12 months. An exclusion list is maintained to 

exclude establishments for special circumstances when documentation is provided by FSIS field 

personnel. 

Average sample frame size 

Generally, the frame is around 1,100 establishments. This value fluctuates monthly as new 

establishments become eligible and others become ineligible. Ineligibility may result from 

seasonal processing, closure, withdrawal of inspection, change in business practices or for other 

reasons. 

Sample size 

FSIS selects 150 establishments from the frame every month. Annually, this amounts to mailing 

1,800 sample forms per year. The decision to select 150 forms per month was due to a desire to 

send one form to each establishment in the original frame within the first 12 months of project 

implementation. 

Sampling methodology 

MT55 is a simple random sample without replacement. 

Collection methodology 

Inspectors are directed to collect an N60 sample weighting 325 grams where each piece matches 

the template (1‖ wide x 3‖ long x 1/8‖ deep) and the goal is collection of 60 pieces, per FSIS 

Directive 10,010.1, Revision 3, Ch. II, IV. The N60 sample is to collect 60 pieces that weigh 

325 grams in one bag and to collect a second bag of small pieces. If the establishment produces 

trim derived from primals and subprimals resulting in large pieces, IPP are to sample the product 

using the N60 sampling procedures in Chapter II, IV. If the establishment produces trim derived 

from primals and subprimals resulting in trim too small to be sampled using the N60 sampling 

procedure or produces trim derived from steaks, roasts or other cuts designated for non-intact 

use, IPP are to collect enough pieces to equal two pounds of product for sampling. If the 

establishment produces both types of trim as described above, IPP are to sample only the product 

that can be sampled using the N60 sampling procedure. However, in practical terms, it is nearly 

impossible for an inspector to collect an N60 sample that meets the number of pieces, piece 

dimension, and total sample weight specifications. As of last year, the FSIS laboratories have 

45
 
 

 

 

redefined the analytical portion to consist of the analysis of up to 60 pieces (N60) weighing up to 

715 grams (up to two 325 gram ± 32.5 gram subsamples) rather than limit the sample to 325 

gram. This decision was reached after the method was validated to process a single 325 gram 

sample (previously it was 5-65 gram subsamples). 

Mean response rate 

Since September 2009, the mean annual response rate of collected samples, as compared to 

printed forms, is 29%. The low response rate may be due to a poorly defined frame; that is, not 

all establishments in the frame may produce this product or produce them infrequently. 

Mean analyzed samples 

Since September 2009, FSIS laboratories have analyzed a mean of 538 samples per year. 

Follow-up testing to a positive in trim or components at a domestic establishment (MT53) 

Purpose 

An MT53 sample follows an MT50, MT54, MT55, or MT52 positive. The purpose of the MT53 

sampling project is to follow-up in establishments that recently had a trim or components 

positive, providing more frequent, targeted sampling at these establishments as a means to verify 

that HACCP systems are back in control. 

Sample frame definition 

This project does not define a frame because it is not a statistical sampling project. Rather, 

establishments that receive MT53 sample request forms are those that have recently had a trim or 

components positive sample. 

Average sample frame size 

This project does not have an average frame size because MT53 is targeted sampling based upon 

positive trim or component results, which can include coarse raw ground beef. 

Sample size 

For each positive at an establishment, 16 follow-up sample request forms are automatically 

scheduled at that establishment. In the case of a low-volume producing establishment, then only 

eight samples are collected. The decision to collect 16 follow-up samples was made in 2008, 

when an FSIS analysis showed that establishments that test positive were five times more likely 

to receive another positive in the next 160 days than those that do not. At that time, the national 

average for grinders was approximately 0.17% positive in sampled lots. Under binomial 

distribution, 16 negative samples from 16 lots gives a 95% confidence that the establishment is 

less than 100 times above the national average. While FSIS performed these calculations, they 

were not seriously considered out of practicality as 1,750 follow-up samples over four months 

would be needed to verify that the establishment was at or below 0.17% positive. 

Sampling methodology 

Samples for the MT53 project are automatically scheduled following a trim or components 

positive. The follow-up samples are scheduled at the same establishment with the initial positive 

sample. 

46
 
 

 

 

 

 

 

 

 

Collection methodology 

Inspectors are to collect an N60 sample weighing 325 grams, where each piece matches the 

template (1‖ wide x 3‖ long x 1/8‖ deep) and the goal is collection of 60 pieces, per FSIS 

Directive 10,010.1, Revision 3, Ch. II, IV. The N60 sample is to collect 60 pieces that weigh 

325 grams in one bag and to collect a second bag of small pieces. If available, the product 

collected should be the same as the original positive. As discussed above, FSIS‘ laboratories 

have redefined the analytical portion to consist of the analysis of up to 60 pieces (N60) weighing 

up to 715 grams (up to two 325 gram ± 32.5 grams subsamples) rather than limit the sample to 

325g. This decision was reached after the method was validated to process a single 325 gram 

sample (previously it was a 5-65 gram subsamples). 

Mean response rate 

Since 2008, the mean annual response rate of collected samples, as compared to printed forms, is 

53%. Although 16 forms are sent to all establishments, inspectors are instructed only to collect 

eight samples in very small volume establishments. These forms are difficult to identify in the 

data structures, so they may artificially deflate the response rate. Additionally, some 

establishments choose to stop producing after a positive sample, so it would be impossible to 

collect a sample from them. 

Mean analyzed samples 

The annual mean of analyzed samples is 161 per year. This value is dependent upon the number 

of positive trim and component samples analyzed during the year. 

Follow-up testing at supplier establishments following a positive in raw ground beef and 

bench trim (MT52) 

Purpose 

An MT52 sample follows a MT43, MT44, or MT55 positive. MT52 samples are also taken for 

the Agricultural Marketing Service (AMS) School Lunch Program and of suppliers, when raw 

ground beef or bench trim are recalled. The purpose of the MT52 sampling project is to followup at originating slaughter establishments and ammoniated LFTB following an E. coli O157:H7 

positive, providing more frequent, targeted sampling at the implicated supplier establishments, as 

a means of verifying that HACCP systems are back in control. 

Sample frame definition 

This project does not define a frame because it is not a statistical sampling project. Rather, 

establishments that receive MT52 sample request forms are those that have supplied trim or 

components to an establishment that had a recent positive sample. Supplier establishments are 

identified by FSIS traceback to the originating slaughter establishments. These supplier 

establishments are documented and tracked in the FSIS Supplier Traceback to E. coli Positive 

System (STEPS). 

Average sample frame size 

This does not apply because MT52 is targeted sampling based upon positive E. coli O157:H7 

results. 

47
 
 

 

 

 

 

 

 

 

 

Sample size 

If an originating slaughter establishment was the only supplier, or if any of the originating 

slaughter establishments were suppliers identified in STEPS within approximately four months 

(or 120 days) of the current raw ground product positive result, then 16 follow-up sample request 

forms are automatically scheduled at that establishment. If the establishment is a low volume 

producer (less than 1,000 lbs. per day), only eight follow-up samples are collected. The decision 

to collect 16 follow-up samples was made in 2008, when an FSIS analysis showed that 

establishments that test positive were five times more likely to receive another positive in the 

next 160 days than those that do not. At that time, the national average for grinders was 

approximately 0.17% positive in sampled lots. Under binomial distribution, 16 negative samples 

from 16 lots gives a 95% confidence that the establishment is less than 100 times above the 

national average. While FSIS performed these calculations, they were seriously considered out 

of practicality as 1,750 follow-up samples over four months would be needed to verify that the 

establishment was at or below 0.17% positive. If a supplier is not a sole supplier or a repeat 

supplier in STEPS, FSIS will request a single follow-up sample from the supplier for each 

component used in the positive raw ground beef product. 

Sampling methodology 

Samples for the MT52 project are requested following traceback investigation. The follow-up 

samples are scheduled at the originating slaughter suppliers or ammoniated LFTB, not at other 

intermediate suppliers. 

Collection methodology 

Inspectors are to collect an N60 sample weighing 325 grams, where each piece matches the 

template (1‖ wide x 3‖ long x 1/8‖ deep) and the goal is collection of 60 pieces, per FSIS 

Directive 10,010.1, Revision 3, Ch. II, IV. The N60 sample is to collect 60 pieces that weigh 

325 grams in one bag and to collect a second bag of small pieces. Collection depends on the 

type of product being collected—see FSIS Directive 10,010.1, Revision 3. Inspectors should 

collect the same component identified in traceback. As discussed above, FSIS‘ laboratories have

redefined the analytical portion to consist of the analysis of up to 60 pieces (N60) weighing up to 

715 grams (up to two 325 gram ± 32.5 gram subsamples) rather than limit the sample to 325 

grams. This decision was reached after the method was validated to process a single 325 gram 

sample (previously it was 5-65 gram subsamples). 

Mean response rate 

Since 2007, the mean annual response rate of collected samples, as compared to printed forms, is 

77%. IPP are only to submit eight samples and mail the remaining eight follow-up forms with 

the last sample collected. Response rates may also be influenced by production volume of 

scheduled establishments. 

Mean analyzed samples 

The annual mean of analyzed samples is 610 per year. This value is dependent upon the number 

of positive E. coli O157:H7 samples analyzed during the year. 

48
 
 

 

 

 

 

 

 

 

 

 

Limitations of Current Sampling Projects 

FSIS has identified several limitations to the Agency‘s current sampling projects, most of which 

influence FSIS‘ ability to compute estimates. 

1.	 Prior Notification 

It is possible that prior notification affects the ability of FSIS to collect representative 

samples. However, policy constraints require that notification be given to establishments so 

that they can plan for holding product until FSIS laboratory test results are to help prevent 

recalling product and posing a risk to the public‘s health. FSIS recently requested comments 

on a new Federal Register Notice that would change the Agency‘s procedures and withhold a 

determination as to whether meat and poultry products are not adulterated, and thus eligible 

to enter commerce, until all test results that bear on the determination have been received.78 

2.	 Sample Sizes for MT50, MT54, MT55 Programs 

Precision usually improves as sample sizes increase. In addition, the precision of the 

estimate may provide an indicator of its reliability. That is, larger sample sizes typically lead 

to smaller variances. In particular, rare event sampling requires large sample sizes to obtain 

reasonable precision. The MT50 program detected four positive trim samples out of 1,274 

analyzed samples in 2010, which gives an indication that this is rare event testing. Likewise, 

there were no positives out of the 169 analyzed MT54 samples in 2010 and no positives out 

of the 574 analyzed in MT55 samples in 2010. 

3.	 Representativeness of the Samples 

For MT50, MT54 and MT55, the sample scheduling is representative of establishments. 

Because the sample designs do not incorporate stratification or weighting by production 

volume, the samples may not be adequately representative of product from each production 

class. 

4.	 Industry Testing Affecting FSIS Estimates 

Industry test and divert practices may result in a lower percent positive estimate obtained by 

FSIS verification testing than would be obtained through baseline testing, because a portion 

of positive product would already be removed. 

Recent improvements to the domestic sampling 

FSIS recently stopped E. coli O157:H7 RTE sampling in dried/semi-dried, fermented sausages 

and cooked meat patties. This testing was discontinued after an analysis showed that testing over 

10,000 such products for E. coli O157:H7 over a nine-year period yielded no positive samples. 

Additionally, FSIS recently shifted from five 65 gram sub sample analyses per collected sample 

to one 325 gram analysis for raw ground beef samples and two 325 gram sub samples for N60 

samples or component samples, which should reduce the total number of analyses conducted by 

FSIS laboratories and release resources to conduct other analyses. 

E. coli O157:H7 Measures of Success 

As described above, there are several different E. coli O157:H7 sampling projects, each with 

slightly different goals. Yet, the overall purpose of the E. coli O157:H7 sampling projects is to 

provide verification of HACCP policy implementation and to assess, and minimize, the risk to 

public health from contaminated product. 

78 http://www.fsis.usda.gov/OPPDE/rdad/FRPubs/2005-0044.pdf 

49
 
 

 

 

 

 

 

Consequently, FSIS believes it is appropriate to measure the success of the different sampling 

projects in broad terms, rather than focusing solely on volume-weighted percent positives in raw 

ground beef. As such, to measure the success of the E. coli O157:H7 sampling program, FSIS 

evaluates its efforts in terms of three key metrics: 

1.	 Volume-weighted percent positives from FSIS‘ raw ground beef E. coli O157:H7 

sampling project and unweighted percent positives from other FSIS E. coli O157:H7 

testing projects. 

2.	 Estimated number of E. coli O157:H7 foodborne illnesses associated with FSIS-regulated 

products. 

3.	 Number of E. coli O157:H7 recalls. 

Volume-Weighted Percent Positives 

As described in this report, FSIS samples product regulated by the Agency to verify HACCP 

policy implementation and to assess, and minimize, the risk to public health from contaminated 

product. FSIS uses this sampling to calculate percent positives for many of the E. coli O157:H7 

sampling projects. FSIS believes that percent positives are a good measure of the effectiveness 

of the individual E. coli O157:H7 sampling projects maintained by the Agency, with declines in 

percent positives indicating greater control and prevention of E. coli O157:H7 in finished 

product. Table 2.1.3.4 displays the volume-weighted percent positives from FSIS sampling of 

raw ground beef over time. Figure 2.1.3.1 provides unweighted percent positives for four of 

FSIS‘ major E. coli O157:H7 sampling projects. The reason this metric is presented is because 

historically, FSIS has only calculated volume weighted percent positive for the raw ground beef 

verification sampling project (MT43). 

Table 2.1.3.4: Volume-Weighted Percent Positives from FSIS E. coli O157:H7 Sampling for 

Raw Ground Beef 

Year/Quarter 

Volume-Weighted Percent 

Positive (All FSIS MT43 

Samples) 

FY 2009 0.32% 

FY10Q3 0.23% 

FY10Q4 0.25% 

FY11Q1 0.16% 

FY11Q2 0.14% 

FY11Q3 0.08% 

50
 
 

 

 

 

 

 

 

Figure 2.1.3.1: Unweighted Percent Positives for Select Group of FSIS Sampling Projects 

for E. coli O157:H7 

Foodborne Illness Estimates: 

As FSIS‘ ultimate goal is to prevent foodborne illnesses from regulated products, it is important 

to measure reductions in foodborne illness as a result of FSIS inspections, sampling, policies and 

other activities. FSIS calculates a performance measure, known as the All-Illness Measure, 

which represents all foodborne Salmonella, Lm and E. coli O157:H7 illnesses from FSISregulated meat, poultry and processed egg product. FSIS updated the All Illness Measure in Q3, 

FY2011 to reflect the release of new illness burden estimates from the CDC79 and the Healthy 

People 2020 goals80, as well as to coincide with the release of the FSIS Strategic Plan for 2011­

2016. Objectives for the All-Illness measure were set using a combination of data from 

published CDC FoodNet case rates and outbreak data and are aligned with Healthy People 2020 

goals. For E. coli O157:H7, FSIS uses a rolling 12 month window of case rate data from the 

CDC, in addition to an attribution estimate, to estimate the total number of E. coli O157:H7 

illnesses from FSIS regulated products. Using this methodology, the illness measure is the 

estimate of the total annual illnesses for the fiscal year, rather than independent measures of 

illness for each quarter. 

79 Scallan E, Hoekstra RM, Angulo FJ, Tauxe RV, Widdowson M-A, Roy SL, et al. Foodborne illness acquired in the United 

States—major pathogens. Emerg Infect Dis [serial on the Internet]. 2011 Jan [November 2011].
 

http://www.cdc.gov/EID/content/17/1/7.htm.
 80 For more information please see the following website:
 

http://www.healthypeople.gov/2020/topicsobjectives2020/objectiveslist.aspx?topicId=14. 

51
 
 

 

 

 

 

 

 

 

 

 

 

Performance Measure 

Using the newly updated All Illness Measure data sources and methodology, FSIS set a target of 

reducing the estimated E. coli O157:H7 illnesses associated with FSIS regulated products to 

20,071 in Q3 FY 2011; FSIS achieved that target with 18,798 estimated illnesses. Figure 2.1.3.2 

illustrates the quarterly targets for E. coli O157:H7 illnesses and the estimated illnesses for the 

most recent four quarters. While it is difficult to interpret these trends with a great deal of 

statistical certainty, this data suggests that the E. coli O157:H7 testing projects are effective in 

reducing human illness. 

Figure 2.1.3.2: Estimated E. coli O157:H7 illnesses associated with FSIS regulated products 

Recalls 

The number of recalls FSIS supports is a good indication of the effectiveness of the E. coli 

O157:H7 sampling projects maintained by the Agency. Recalls occur when adulterated product 

is found in commerce. A recall is a firm‘s action to remove product from commerce (e.g., by 

manufacturers, distributors, or importers) to protect the public from adulterated or misbranded 

products. Although it is a firm‘s decision to recall product, FSIS coordinates with the firm to 

ensure the firm has properly identified and removed recalled product from commerce by 

verifying the effectiveness of the firm‘s recall activities. FSIS also notifies the public about 

product recalls.81 In general, the discovery of a positive sample in FSIS testing should prevent 

contaminated product from reaching the consumer marketplace. While FSIS does not currently 

mandate that establishments hold product until negative test results are received, the Agency 

recently requested comments on a new Federal Register Notice that would change the Agency‘s

procedures and withhold a determination as to whether meat and poultry products are not 

adulterated, and thus eligible to enter commerce, until all test results that bear on the 

determination have been received.82 

Therefore, when firms hold product pending FSIS test results, FSIS sampling projects can 

prevent recalls from occurring. The possibility of recalls has prompted industry to increase its 

capacity and willingness to hold product while it is being tested, to institute their own test and 

divert programs and to ultimately contribute to the lower estimate of E. coli O157:H7 in the food 

81 FSIS Directive 8080.1 http://www.fsis.usda.gov/OPPDE/rdad/FSISDirectives/8080.1.pdf 82 http://www.fsis.usda.gov/OPPDE/rdad/FRPubs/2005-0044.pdf 

52
 
 

supply. Therefore, evaluating the number of recalls due to positive E. coli O157:H7 results over 

time allow FSIS to, in part, evaluate the overall effectiveness of its policies, as Figure 2.1.3.3 

demonstrates. 

Figure 2.1.3.3: E. coli O157:H7 reported recalls, 1994-2010. 

Key: 

1996: HACCP rule published 

1. 1999-2000—HACCP implementation complete 

2: 2002—Industry to reassess HACCP with O157:H7 a hazard likely to occur, also industry started widespread test 

and divert programs 

3: 2007—Started MT50 and MT54 

4: 2008—Switched to risk (production volume) based sampling 

5: 2009—Started MT55 

53
 
 

 

 

 

 

 

 

 

2.1.4: RTE Meat and Poultry Products (Listeria monocytogenes (Lm) and Salmonella) 

Overview of Sampling Projects 

FSIS conducts microbiological testing of RTE meat and poultry products for Listeria monocytogenes (Lm) and Salmonella.83 Lm 

domestic sampling projects are summarized in Table 2.1.4.1. As the projects are different, they will be described separately. 

Table 2.1.4.1 FSIS RTE Domestic Sampling Projects 

Product class 

RTE Sampling 

Projects 

Pathogens 

Tested 

Number 

of 

FY2010 

samples 

Regulatory Purpose of 

Sampling Program 

Type of 

Sampling 

Program 

Both post-lethality exposed 

and non-post-lethality exposed 

RTE products 

ALLRTE Lm, 

Salmonella 2,990 Monitor industry performance Random 

Post-lethality exposed RTE 

products RTE001 Lm, 

Salmonella 8,700 Verify non-detectable standard Risk Based 

RLm product samples RLMPROD Lm 1,960 Monitor industry performance Risk Based 

RLm food contact surface 

samples RLMCONT Lm 6,600 Monitor industry performance Risk Based 

RLm non-food contact 

environmental samples 

(Composited 5-sample Units; 

Lm) 

RLMENVC Lm 690 Monitor industry performance Risk Based 

Intensified Verification 

Testing (IVT) product samples INTPROD Lm or 

Salmonella 225 Response to positive ALLRTE, RTE001, 

RLMPROD and/or RLMCONT sample Targeted 

IVT food contact surface 

samples INTCONT Lm or 

Salmonella 550 Response to positive ALLRTE, RTE001, 

RLMPROD and/or RLMCONT sample Targeted 

IVT non-food contact 

environmental samples INTENV Lm or 

Salmonella 275 Response to positive ALLRTE, RTE001, 

RLMPROD and/or RLMCONT sample Targeted 

In addition to Lm and Salmonella, testing for E. coli O157:H7 was performed for dry and semi-dry fermented sausages and fully cooked meat patties until April, 2011. FSIS 

officially announced the discontinuation of the program in a May 13, 2011 Constituent Update which can be found at: 

http://www.fsis.usda.gov/News_&_Events/Const_Update_051311/index.asp. This testing was discontinued after an analysis showed that testing over 10,000 such products for E. 

coli O157:H7 over a sixteen year period (1994-2011) yielded no positive samples. 

54 

83 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Historical Basis of Sampling Programs 

Lm has been implicated in illness outbreaks since the early 1980s. FSIS has conducted a 

regulatory microbiological testing program in RTE meat and poultry products since 1983. From 

1983 until 2004, establishments were randomly selected for regulatory samples from different 

sub-populations or from the total population of establishments producing RTE products.84 In 

1987, FSIS increased testing for Lm in regulated products, including domestic cooked meat and 

poultry and imported cooked products.85 In 1989, after a confirmed human listeriosis case was 

linked to cooked poultry, FSIS identified Lm as an adulterant subject to recall if found in 

86	 87 commerce. After the implementation of PR/HACCP regulations in 1996, FSIS organized Lm 

testing around the four HACCP processes of; 1) fully cooked, not shelf stable products, 2) heattreated, shelf stable products, 3) not heat-treated, shelf stable products and 4) products with 

secondary inhibitors that are not shelf stable. In addition to the material provided below, a 

timeline of FSIS activities related to Lm can be found on the Agency‘s website.88 

FSIS began random testing of RTE product samples in the 1990s, while risk-based testing of 

RTE products for Lm began in 2005. Since the inception of the Lm verification testing program 

for RTE meat and poultry products, FSIS has also sampled packaged RTE products for the 

presence of Salmonella. 

Type of Analysis 

All samples collected for analysis in the RTE product testing projects are evaluated using 

qualitative and quantitative methods. In 2006, FSIS initiated MPN analysis of positive RTE food 

products identified during follow-up testing. 

Volume Data 

Production volume data for the ALLRTE and RTE0001 sampling projects are obtained in two 

ways: 

1.	 For all establishments with post-lethality exposure (RTE001 and RLm sampling projects), 

volume information was provided on an annual basis using FSIS Form 10,240-1, as 

required under Federal Regulation 9 CFR 430. This form contained the establishment's 

annual production volume of post-lethality exposed RTE meat and poultry products for 

89	 90 each control Alternative in each of nine product categories.

2.	 For RTE establishments that produce RTE products with no post-lethality exposure 

(which are a part of the ALLRTE sampling projects), volume information is provided on 

a voluntary basis.91 

84 Please see the following website for more information: http://www.fsis.usda.gov/Science/Micro_Testing_RTE/index.asp.
 85 Federal Register, Volume 52, No. 47, March 11, 1987.
 86 Federal Register Volume 54, No. 98, Tuesday May 23, 1989.
 87 Pathogen Reduction/Hazard Analysis and Critical Control Point System final rule (61 FR 38806, July 25, 1996).
 88 Please see the following website for more information: http://www.fsis.usda.gov/PDF/Lm_Timeline.pdf
 89 For Alternative 1, the establishment uses a post-lethality treatment for its product and an antimicrobial agent or process that 

suppresses or limits of growth of Lm. For Alternative 2, the establishment uses either a post-lethality treatment for product 

(choice 1) or an antimicrobial agent or process that suppresses or limits the growth of Lm (choice 2). For Alternative 3 the 

establishment uses a sanitation program that controls Lm contamination in the processing environment and on the product.
 90	 th This form was discontinued as of September 30 , 2011. Moving forward, this information will be collected through PHIS. 91 This volume information will be collected in PHIS once it has been fully implemented. 

55
 
 

 

 

 

 

 

 

 

 

 

 

Thus, approximately 90% of establishments in the ALLRTE sampling project have volume 

information available from the RTE001 sampling project, the exceptions (prior to PHIS) being 

those establishments with no post-lethality exposure. 

Current Design of Sampling Plans 

FSIS conducts regulatory microbiological testing of RTE meat and poultry products for two 

microorganisms: Lm and Salmonella. Currently, there are three verification testing projects for 

the detection of Lm contamination: ALLRTE, RTE001 and RLm. ALLRTE and RTE001 

product samples also are concurrently tested for Salmonella. Intensified Verification Testing 

(IVT) is conducted in establishments with positive ALLRTE, RTE001, and RLMPROD and/or 

RLMCONT (product and food contact surface) samples. 

In general, all sampling projects for Lm in post-lethality exposed RTE products rely on 9 CFR 

430.4 ―Control of Listeria monocytogenes in post-lethality exposed ready-to-eat products‖, 

published on June 6, 2003 (68 FR 34207). Other relevant regulations/directives/notices for each 

sampling program are listed after each program description. 

Description of the FSIS RTE Domestic Sampling Projects for Lm and/or Salmonella 

A description of each domestic sampling project for RTE meat and poultry products, food 

contact surfaces and non-food contact environmental surfaces follows below. 

ALLRTE 

Purpose 

The ALLRTE sampling project began in January 2004 and was designed to obtain random 

samples across all RTE products and across all establishments producing a RTE product, 

regardless of risk or product type. The ALLRTE sampling program is structured with the intent 

of verifying compliance with zero tolerance for Lm in RTE products. Products are sampled for 

Lm and Salmonella. Both post-lethality exposed and non-post-lethality exposed products are 

tested. Currently, samples are randomly selected by FSIS. 

The following FSIS policy relates to ALLRTE: FSIS Directive 10,240.4 Revision 2 ―Verification 

Procedures for Consumer Safety Inspectors for the Listeria monocytogenes (Lm) Regulation and 

Lm Sampling Program‖, dated February 3, 2009. 

Any RTE products testing positive for Lm and Salmonella are considered to be adulterated and 

subject to regulatory control. FSIS recommends that establishments hold product pending FSIS 

confirmed test results so that adulterated products are not sold into commerce. If an 

establishment releases a product into commerce that later confirms positive Lm or Salmonella, 

FSIS recommends a recall to remove the product from commerce and requires the establishments 

to rework, re-cook or condemn the product in a manner validated to destroy the adulterant. As 

discussed above, FSIS recently requested comments on a new Federal Register Notice that would 

change the Agency‘s procedures and withhold a determination as to whether meat and poultry 

products are not adulterated, and thus eligible to enter commerce, until all test results that bear on 

the determination have been received.92 

92 Please see the following website for more information: http://www.fsis.usda.gov/OPPDE/rdad/FRPubs/2005-0044.pdf. 

56
 
 

 

 

 

 

 

 

 

 

 

 

 

 

Frame Definition, Frame Size, and Sample Size 

The ALLRTE frame contains approximately 2,400 active RTE establishments under Federal or 

Talmadge/Aiken (T/A) inspection authority,93 based on information available in PBIS. This 

value can fluctuate as new establishments become eligible and others become ineligible. 

Ineligibility may result from seasonal processing, closure, withdrawal of inspection or change in 

business practices. A total of 85 samples per week (4,420 per year) are selected from the frame, 

with the goal of each establishment being selected at least once per year, with a number of 

establishments being selected twice or more annually. 

Several establishments were excluded from the ALLRTE sampling project prior to 2009 because 

they produced excepted products, which include oils, shortening, lard, margarine, lard margarine, 

pork skins, pork rinds, dried soup bases and mixtures of rendered animal fats and products 

labeled ―for further processing,‖ among other products.94 FSIS Directive 10,240.4, Revision 2 

removed the exceptions for these products (excluding products for further processing) from the 

ALLRTE sampling project. However, FSIS Notice 10-10 stated that ―oils, shortening, lard, 

margarine, lard margarine, and mixtures of rendered animal fats are not to be collected for 

sampling under the ALLRTE or RTE001 sampling projects because there is no validated method 

for testing these products for Lm.‖

95 FSIS will continue to sample popped pork skins, pork rinds, 

dried soup bases, concentrated (high salt content) soup mixes, and pickled pig‘s feet under both 

RTE sampling projects. Because there is not enough information on which specific products are 

produced at a given establishment at any given time, it is not possible to automatically exclude 

establishments that produce such products from sample scheduling algorithms. However, FSIS 

anticipates that this issue will be addressed through full PHIS implementation. 

Sampling Methodology 

On a monthly basis, FSIS randomly selects the samples from the frame using simple random 

selection. The sample size is 85 per week. Establishments that have already been sampled once 

within a fiscal year are removed from the frame and then reinstated on a cyclic basis. Samples 

are selected so that all RTE establishments, regardless of HACCP size, production volume or 

process design have an equal chance of being sampled each fiscal year (e.g., no weighting is 

applied during sample selection). 

Collection Methodology 

Two pounds of product in its final packaged form are collected at the establishment and sent to 

FSIS laboratories for testing. 

Response Rate 

In fiscal year 2010, an average of 66% of scheduled ALLRTE samples were collected and 

analyzed for both Lm and Salmonella. 

93 Talmadge-Aiken establishments, formally known as Federal-State Cooperative Inspection Plants, are the approximately 250 

meat and poultry establishments in 10 states where USDA has contracted with state agency inspectors to conduct federal 

inspection activities. Even though state employees conduct the inspections in these establishments, they are considered to be 

under federal rather than state inspection Talmadge-Aiken (7 U.S.C. 450) 

94 FSIS Directive 10,210.1, Amendment 6 95 Please see the following website for more information: http://www.fsis.usda.gov/OPPDE/rdad/FSISNotices/10-10.pdf. 

57
 
 

 

 

 

 

 

 

RTE001 

Purpose 

The RTE001 sampling project is a risk-based verification testing project, implemented in 

January 2005. This sampling project is used primarily to verify that establishments producing 

post-lethality exposed meat and poultry products are controlling Lm and are in compliance with 

the zero tolerance requirements of 9 CFR 430. In this project, products are sampled for both Lm 

and Salmonella. This project is also used to calculate volume-adjusted percent positives for Lm. 

The following FSIS policy relates to the RTE001 sampling project: FSIS Directive 10,240.4 

Revision 2. 

Any RTE products testing positive for Lm or Salmonella are considered to be adulterated and 

subject to regulatory control. Currently, FSIS recommends that establishments hold product 

pending FSIS confirmed test results so that adulterated products are not sold into commerce. If 

an establishment releases product into commerce that later confirms positive for Lm or 

Salmonella, then FSIS recommends a recall to remove the product from commerce and requires 

the establishment to otherwise rework, re-cook or condemn the product in a manner validated to 

destroy the adulterant. As discussed above, FSIS recently requested comments on a new Federal 

Register Notice that would change the Agency‘s procedures and withhold a determination as to 

whether meat and poultry products are not adulterated, and thus eligible to enter commerce, until 

all test results that bear on the determination have been received.96 

Frame Definition, Frame Size, and Sample Size 

The RTE001 frame contains about 2,170 active RTE establishments with post-lethality exposure 

under Federal or T/A inspection authority, based on information available in PBIS. This value 

can fluctuate as new establishments become eligible and others become ineligible. Ineligibility 

may result from seasonal processing, closure, withdrawal of inspection and change in business 

practices, among other possibilities. A total of 200 samples per week (10,400 per year) are 

selected from the frame. 

Sampling Methodology 

Establishments are identified for sampling based on a risk-ranking algorithm, which takes into 

account the Lm control Alternative,97 the production volume, the type of product produced and 

the sampling history. An establishment is selected from the frame as little as once per year to, at 

most, once per month, depending on its position in the risk-ranking algorithm. 

Collection Methodology 

Two pounds of product in its final, packaged form are collected at the establishment, with higher 

risk products given priority for collection. The order of risk for the various types of products is 

provided in FSIS Directive 10,240.4, Revision 2. The current list of product types used for riskranking purposes is as follows: 

96 Please see the following website for more information: http://www.fsis.usda.gov/OPPDE/rdad/FRPubs/2005­

0044.pdf.
 97 Control Alternative refers to any one of four procedures used to prevent (control) the growth of Lm in postlethality exposed RTE products. See footnote 89 for a complete description of the Alternatives.
 

58
 
 

 

 

 

 

1) Deli-meats that are sliced in the federal establishment,
 

2) Deli-meats shipped whole from the federal establishment (this does not include cookin-bag products; only those exposed post-lethality),
 

3) Hotdog Products,
 

4) Deli salads, pâtés, and meat spreads,
 

5) Fully cooked type products (other than cooked products in 1-4 above),
 

6) Fermented products,
 

7) Dried products,
 

8) Salt-cured products, and
 

9) Products labeled as "Keep Frozen".
 

Response Rate 

In fiscal year 2010, the percent of RTE001 samples that were collected and analyzed for both Lm 

and Salmonella averaged 83%. 

RLm 

Purpose 

The RLm sampling project, implemented in April 2006, is a routine, risk-based sampling project, 

which consists of food contact samples, non-food contact environmental samples, and product 

samples taken during the production of RTE meat and poultry products exposed to the postlethality environment. Samples are analyzed only for Lm and are taken during the same day of 

production. In conducting the RLm project, FSIS assesses the compliance of establishments 

with regulation 9 CFR 430 regarding the control of Lm in post-lethality exposed RTE production 

areas and ensures that RTE products are safe for consumption at the end of the production 

process. 

RLm sampling, done in conjunction with an FSA, provides an in-depth evaluation of the 

effectiveness of the food safety practices employed by an establishment. The ability to use the 

product, contact and environmental data collected from the establishments can help identify 

possible risk factors that could be associated with positive results. 

The following FSIS policy relates to the RLm sampling project: FSIS Directive 10,240.5 

Revision 2. 

Frame Definition, Frame Size, and Sample Size 

The RLm frame is identical to that of RTE001. It contains about 2,170 active RTE 

establishments with post-lethality exposure under Federal or T/A inspection authority, based on 

information available in PBIS. This value can fluctuate as new establishments become eligible 

and others become ineligible. Ineligibility may result from seasonal processing, closure, 

withdrawal of inspection and change in business practices, among other possibilities. In 2009, 

FSIS policy was to require an RLm/FSA in every establishment with post-lethality exposure at 

least once every four years. Pursuant to an Office of the Inspector General (OIG) mandate, 

starting in August 2009, a sample size of 45 establishments per month (540 per year) is selected 

from the frame. 

59
 
 

 

 

 

 

 

 

 

 

 

 

 

Sampling Methodology 

RLm establishments are selected from the frame using the FSA prioritization model, which takes 

into account FSIS‘ public health decision criteria,98 control alternative and type of product 

produced. The RLm project consists of the following three concurrent sampling projects: 

1. RLMPROD—routine, risk-based testing of intact RTE food product samples throughout 

the selected production shift; three samples are collected per sampling unit. 

2. RLMCONT— routine, risk-based testing of surfaces that have direct contact with RTE 

products in the RTE production area (e.g., conveyor belts, storage racks, slicer blades, 

loaders and table tops). 

3. RLMENVC—routine, risk-based testing of environmental (non-food contact) surfaces in 

the RTE production areas (e.g., floors, drains, walls and floor mats). Starting in August 

2009, environmental samples were composited at the testing labs. 

Collection Methodology 

Microbiological samples are collected as units. A unit consists of 10 food contact surface swabs 

(RLMCONT), five environmental swabs, which are later composited at the testing laboratories 

(RLMENVC), and three intact product samples (RLMPROD). In establishments that use brine 

chillers, the FSIS Enforcement Investigations and Analysis Officers (EAIO) collect a sample of 

brine from each line using a brine chiller. Brine samples could be either RLMENVR 

(environmental/not composited) if the product package is impermeable or RLMCONT if the 

product package is permeable. The number of units per establishment is based on HACCP size. 

FSIS collects three sample units from large HACCP establishments, two sample units from small 

establishments and one sample unit from very small establishments.99 

Response Rate 

In fiscal year 2010, the average response rate for RLm samples (combined RLMPROD, 

RLMCONT and RLMENVR/RLMENVC units) was 93%. 

Intensified Verification Testing (IVT) 

Purpose 

IVT is a follow-up, targeted sampling project, where FSIS tests product, food contact surfaces, 

and environmental surfaces for either Salmonella or Lm. An IVT is initiated after an 

establishment has either a positive Salmonella or Lm result in either finished product (ALLRTE, 

RTE001 and RLMPROD) or on a food contact surface (RLMCONT). An IVT can also be 

initiated at the discretion of an FSIS District Manager, in response to continuing sanitation noncompliances at the establishment. The IVT is performed after the establishment has taken 

corrective and preventative measures in response to FSIS‘ findings. As described above for the 

RLm program, in an IVT, FSIS collects samples in units. As with RLm, IVTs are performed 

with a FSA to provide an in-depth evaluation of food safety systems at the establishment. 

However, the FSA is conducted for-cause, rather than being routine in nature. A maximum of 

five units in a given establishment are considered per IVT. 

98 FSIS‘ Public Health Decision Criteria can be found at: 

http://www.fsis.usda.gov/OPPDE/NACMPI/Sep2010/2010_Public_Health_Decsion_Criteria_Report.pdf. 99 HACCP Establishment Sizes are as follows: Large; 500 or more employees, Small: 10-499 employees, and Very 

Small: < 10 employees and annual sales >2.5 million. 

60
 
 

 

 

 

 

 

 

 

 

 

 

The following FSIS policy relates to the IVT sampling project: FSIS Directive 10,300.1 

―Intensified Verification Testing (IVT) Protocol for Sampling of Product, Food Contact Surfaces 

and Environmental Surfaces for Listeria monocytogenes,‖ dated February 3, 2009, which 

provides instructions for performing an IVT.
 

Frame Definition, Frame Size, and Sample Size
 

There is no sampling frame for IVT, as it is dependent on a positive Lm or Salmonella ALLRTE, 

RTE001, RLMPROD and/or RLMCONT sample from a given establishment.
 

Sampling Methodology 

IVTs are scheduled in accordance with FSA prioritization criteria from FSIS Directive 10,200.1, 

with all establishments with Lm or Salmonella-positive ALLRTE, RTE001, RLMPROD and 

RLMCONT samples requiring an IVT. The FSIS districts have 30 days in which to schedule the 

IVT. 

Collection Methodology 

As described above for the RLm project, IVT microbiological samples are collected in units. A 

sampling unit for Lm consists of ten food contact surface samples, five environmental samples 

and three product samples per RTE processing line in operation on the day of sampling, whereas 

a unit for Salmonella consists of eight food contact surface samples, five environmental samples 

and five product samples per processing line. If the establishment uses a brine chiller, FSIS will 

also collect one brine sample per line from the brine chiller. 

Response Rate 

In fiscal year 2010, the IVT response rates in response to Lm- and/or Salmonella-positive 

ALLRTE and RTE001 samples were 100% and 71%, respectively. IVT for positive RLMPROD 

and/or RLMCONT samples was not implemented until October 2009 with the issuance of FSIS 

Notice 62-09. The RLm response rate was 56% for the fiscal year. 

Limitations of Current Sampling Programs 

FSIS has identified several limitations to the current Lm sampling projects; namely sampling 

rates not being met for specific establishments, sampling frequency, project overlaps, sampling 

biases, volume-weighted percent positive results and regulatory considerations. These issues 

will be discussed in detail below. 

1. Sampling Rates for Establishments 

One objective of the ALLRTE and RTE001 sampling projects is to sample every RTE 

establishment (ALLRTE) and every RTE establishment with post-lethality exposure (RTE001) at 

least once each year. In FY 2011, virtually all of the approximately 2,400 active RTE producing 

establishments were scheduled for collection in one of the three RTE verification testing projects 

(ALLRTE, RTE001 and/or RLm). However, not every establishment is sampled annually and a 

small number of establishments were not sampled at all between 2005 and the present. The 

reasons for this are varied. In the case of ALLRTE, some establishments produce products such 

as popped pork skins, which were previously exempt from testing. In other instances, an 

establishment may be producing seasonally and could not be scheduled during a period of 

61
 
 

 

 

 

 

 

 

 

 

 

production. As of October 2011, approximately 98% of all RTE establishments were sampled at 

least once over the calendar year. 

2. Sampling Frequency 

For ALLRTE, the random monthly sampling of scheduled RTE product producing 

establishments, plus the inclusion of all establishments in the sampling frame, may permit a 

comparative annual Lm positive rate in FSIS inspected establishments for an aggregate of the 

RTE products collected. Because the specific product to be collected is determined by IPP, 

specific products may be either over or under-sampled in relation to national production. For 

RTE001, higher risk establishments are scheduled more frequently. Accordingly, positive rates 

may vary as a function of the samples collected and tested from the scheduled establishments, 

resulting in a different measure of aggregate positive rates. 

3. Project Overlaps 

FSIS acknowledges that the RTE001 and ALLRTE projects exhibit a high degree of overlap due 

to independent scheduling. As the ALLRTE is independent of RTE001, sampling results are not 

currently combined, even though a single establishment may be sampled in both projects in a 

given month. However, sampling of the same establishment in the ALLRTE and RTE001 

projects in the same month often results in only the risk-based (RTE001) sample being collected, 

which can cause a non-response bias.100 

4. Sampling Biases 

RTE001 data are biased towards high-risk products based on the program structure. There may 

be a similar, though less pronounced bias in the ALLRTE data, as historical instructions to the 

field allowed for sampling of higher-risk products in ALLRTE. Regardless, for both ALLRTE 

and RTE001, no mechanism exists for truly randomizing what products are collected at a given 

establishment over time. These issues may arise from such factors as samples not being 

collected, lack of random product selection at the establishment level and lack of randomness in 

sample selection from the frame (see also project overlaps above). 

5. Volume-Weighted Percent Positive Results 

The ALLRTE and RTE001 percent positive numbers were standard FSIS performance measures 

for the Agency‘s annual Performance and Accountability Report (PAR) for Lm until 2008; these 

have subsequently been replaced by volume-weighted positive rates. Such rates attempt to take 

into account the proportion of national volume represented by an individual sample, but do not 

adjust for missing establishments, missing, over or under-represented products or sampling bias 

not related to the design of the project. 

6. Regulatory Considerations 

RTE projects were developed as a result of regulatory activities. Consequently, changes to the 

current projects may require reissuance of existing policies or issuance of new policies. 

100 FSIS has attempted to reduce this bias by issuing instructions for the ALLRTE sampling program in Directive 10240.4 stating 

that ―Consumer Safety Inspectors (CSIs) should make every effort to sample all the RTE products produced at an establishment 

by rotating through the products when CSIs receive sample request forms.‖

62
 
 

 

 

 

 

 

Lm Sampling Program Measures of Success 

There are several different Lm sampling projects, each with slightly different goals. Yet, the 

overall purpose of Lm sampling program is structured with the intent of verifying compliance 

with zero tolerance for Lm and Salmonella in RTE products. 

Consequently, FSIS believes it is appropriate to measure the success of the different sampling 

projects in broad terms, rather than focusing solely on volume-adjusted percent positive rates. 

As such, to measure the success of the Lm sampling projects, FSIS evaluates its efforts in terms 

of three key metrics; 

1.	 Volume-weighted percent positives from Lm sampling projects, 

2.	 Estimated number of Lm foodborne illnesses associated with FSIS-regulated products, 

and 

3.	 Number of Lm recalls. 

Percent Positive Rates 

FSIS conducts pathogen verification testing for the Agency‘s sampling programs. As described 

in this report, FSIS samples product regulated by the Agency to verify HACCP policy and to 

assess, and minimize, the risk to public health from contaminated product. FSIS uses this 

sampling to calculate a positive rate for many of the Lm sampling projects. FSIS believes that 

positive rates are a good measure of the effectiveness or success of the Lm sampling projects 

maintained by the Agency, with declines in percent positives potentially indicating greater 

control and prevention of Lm in RTE and meat and poultry products. 

Table 2.1.4.2 provides the production category volume-weighted percent positive rate for the 

RTE001 project and the ALLRTE project. 

Table 2.1.4.2: Quarterly Volume-Weighted Percent Positive Rates for Lm Sampling 

Projects 

Year/Quarter 

Volume-Weighted 

Percent Positive 

(ALLRTE) 

Volume-Weighted 

Percent Positive 

(RTE001) 

FY 2009 0.10% 0.24% 

FY10Q3 0.01% 0.18% 

FY10Q4 0.00% 0.10% 

FY11Q1 0.00% 0.10% 

FY11Q2 0.03% 0.14% 

FY11Q3 0.04% 0.14% 

Foodborne Illness Estimates: 

As FSIS‘ ultimate goal is to prevent foodborne illnesses from regulated products, it is important 

to measure reductions in foodborne illness as a result of FSIS inspections, sampling, policies and 

other activities. FSIS calculates a performance measure, known as the All-Illness Measure, 

which represents all foodborne Salmonella, Lm and E. coli O157:H7 illnesses from FSISregulated meat, poultry and processed egg product. FSIS updated the All Illness Measure in Q3, 

63
 
 

 

 

 

 

 

 

FY2011 to reflect the release of new illness burden estimates from the CDC101 and the Healthy 

People 2020 goals102, as well as to coincide with the release of the FSIS Strategic Plan for 2011­

2016. Objectives for the All-Illness measure were set using a combination of data from 

published CDC FoodNet case rates and outbreak data and are aligned with Healthy People 2020 

goals. For Lm, FSIS uses a rolling 12 month window of case rate data from the CDC, in addition 

to an attribution estimate, to estimate the total number of Lm illnesses from FSIS regulated 

products. Using this methodology, the illness measure is the estimate of the total annual illnesses 

for the fiscal year, rather than independent measures of illness for each quarter. 

Performance Measure 

Using the newly updated All Illness Measure data sources and methodology, FSIS set a target of 

reducing the estimated Lm illnesses associated with FSIS regulated products to 866 in Q3 

FY2011; FSIS achieved that target with 718 estimated illnesses. Figure 2.1.4.1 illustrates the 

quarterly targets for Lm illnesses and the estimated illnesses for FY2010 and FY2011. 

Figure 2.1.4.1: Estimated Listeria monocytogenes illnesses from FSIS regulated products 

Recalls 

The number of recalls FSIS supports is a good indication of the effectiveness or success of the 

Lm sampling projects maintained by the Agency. Recalls occur when a FSIS regulated product 

is found in commerce. A recall is a firm‘s action to remove product from commerce (e.g., by 

manufacturers, distributors or importers) to protect the public from consuming adulterated or 

misbranded products. Although it is a firm‘s decision to recall product, FSIS coordinates with the 

firm to ensure it has properly identified and removed recalled product from commerce by 

101 Scallan E, Hoekstra RM, Angulo FJ, Tauxe RV, Widdowson M-A, Roy SL, et al. Foodborne illness acquired in the United 

States—major pathogens. Emerg Infect Dis [serial on the Internet]. 2011 Jan [November 2011]. 

http://www.cdc.gov/EID/content/17/1/7.htm 

102 Please see the following website for more information: 

http://www.healthypeople.gov/2020/topicsobjectives2020/objectiveslist.aspx?topicId=14. 

64
 
 

 

 

 

 

 

verifying the effectiveness of the firm‘s recall activities. FSIS also notifies the public about 

product recalls.103 In general, the discovery of a positive sample in FSIS testing prevents 

contaminated product from reaching the consumer marketplace. Consequently, FSIS sampling 

programs can prevent recalls from occurring. Additionally, FSIS recently announced a new 

Federal Register Notice to encourage establishments to hold product while testing is underway to 

prevent contaminated product from reaching the marketplace. Further, evaluating the number of 

recalls over time allows FSIS to evaluate, in part, the effectiveness of its policies, as Figure 

2.1.4.2 demonstrates. 

Figure 2.1.4.2: Reported FSIS recalls for Products Contaminated with Lm, 1994-2010. 

103 FSIS Directive 8080.1, Revision 6. http://www.fsis.usda.gov/OPPDE/rdad/FSISDirectives/8080.1.pdf 

65
 
 

 

 

 

 

 

Section 2.2: FSIS Microbiological Baseline Data Collection 

In 1992, FSIS began a concerted effort to identify the microbiological profile of various classes 

of inspected raw meat and poultry carcasses and ground product. The purpose was to use the 

data to establish both pathogen reduction performance standards (for carcasses and ground 

product) and process control performance criteria (for carcasses). The pathogen reduction 

performance standards were intended to spur industry to control the presence of pathogens of 

public health concern, particularly Salmonella. The process control performance criteria were 

designed to reflect the prevalence and levels of contamination of E. coli (Biotype 1) on 

carcasses, as an indicator of process control for fecal contamination. In designing the baselines, 

FSIS intended to capture microbiological profile data for microorganisms of varying degrees of 

public health concern, and organisms or groups of organisms of value as indicators of general 

hygiene or process control. In addition, FSIS stated its expectation to repeat the baseline studies 

over time to document changes. Although microbiological data were collected by FSIS prior to 

1992, these earlier efforts were not conducted as part of anticipated rulemaking. A more 

complete description of the various microbiological baseline data collection efforts and their 

design considerations can be found in the preambles to the proposed and final rules associated 

with the PR/HACCP system rulemaking effort.104 

The carcass baselines, conducted periodically, were specifically designed to identify nationwide 

changes in the prevalence of Salmonella, expressed as a percentage of contaminated carcasses. 

Enough samples were taken to describe the annual distribution of test results and to account for 

possible seasonal variation, as well as provide for missing samples and incomplete data. These 

baselines were targeted at the major classes of livestock and poultry slaughtered, comprising 

approximately 95 percent of all livestock slaughtered, and approximately 99 percent of domestic 

birds slaughtered. The carcass baselines were originally designated as data collection 

―programs‖ because of the scope and length of time for the data collection effort, generally 

comprising at least one year. By contrast, the ground product baselines were originally 

designated as data collection ―surveys.‖ The surveys reflected the prevalence of Salmonella 

(expressed as a percentage of positive samples) as a snapshot over a short period of time, 

generally limited to a six month data collection effort. In the preamble to the PR/HACCP final 

rule, FSIS referred to both data collection efforts, collectively, as FSIS baseline surveys. 

From the FSIS baseline surveys, the prevalence for Salmonella was used for setting the 

qualitative pathogen reduction performance standards. However, for the process control 

performance criteria, a statistical procedure known as a ―3-class attributes sampling plan‖ 

applied in a moving window was used. Consequently, the ―m‖ and ―M‖ criteria were set at the 

th th closest power of 10 to the actual numbers estimated for the 80 and 98 percentiles from the 

FSIS baseline surveys. These criteria are quantitative (colonies per square centimeter of carcass 

surface area). 

The data generated from FSIS baseline surveys continue to be used to set pathogen reduction 

performance standards, and to inform design of FSIS regulatory testing programs, as well as in 

guidance to industry related to effective process control. Since the time that the PR/HACCP 

final rule was implemented, FSIS has also used FSIS baseline survey data in risk assessments to 

predict the public health impact of risk mitigation strategies. During the most recent poultry 

104 60 FR Federal Register 6774, February 3, 1995, and 61 Federal Register 38806, July 25, 1996. 

66
 
 

 

 

 

 

carcass baseline surveys, a method for isolating Campylobacter was developed and validated and 

has since been adopted by the agency. Some of the commodities for which baseline surveys have 

been conducted since the original FSIS baseline surveys supporting the PR/HACCP final rule 

include: beef trim, young chicken carcasses and young turkey carcasses. The most recent FSIS 

baseline surveys underway include market hogs and chicken parts. A second FSIS baseline 

survey of unpasteurized liquid egg product is underway with the intent of using the data to 

establish lethality performance standards for pasteurized egg product. 

Section 2.3 Chemical Residues 

Overview of Sampling Projects 

FSIS conducts testing for chemical residues in regulated meat, poultry and processed egg 

products. Domestic sampling projects are summarized in Table 2.3.1. 

Table 2.3.1: Residue Sampling Projects 

Residue 

Sampling 

Projects 

Number of 

Residue 

Analyzed 

samples 

FY2010 

Regulatory 

Purpose of 

Sampling 

Program 

Routine-NRP1 14,929 

Chemical 

Residue 

Exposure 

AssessmentRandom 

KISTM Test-Field 157,524 Targeted 

KISTM Test –Lab2 8,041 Targeted 

FAST-Field 47,676 Targeted 

FAST-Lab 291 Targeted 

1. National Residue Program samples for meat, poultry and processed egg products, as well as residue monitoring 

and inspector generated samples. 

2. Verification/confirmation sampling conducted by the FSIS Laboratories. Includes confirmatory KISTM tests on 

field positives. 

Background Information 

Since 1967, FSIS has administered the United States National Residue Program (NRP). FSIS 

collects samples of raw meat, poultry and processed egg products, as well as imported product 

and analyzes the samples at one of the three FSIS laboratories. The NRP is designed to detect 

contamination of meat, poultry and processed egg products with residual veterinary drugs, 

pesticides and heavy metals. Under this program, FSIS inspectors sample meat, poultry and 

processed egg products in slaughter and processing establishments for chemical residues and 

compare, when applicable, the results with tolerances established by the Food and Drug 

Administration (FDA) and the Environmental Protection Agency (EPA) to prevent adulterated 

meat, poultry and processed egg products from entering into commerce. The NRP is an 

interagency program operating under a 1984 Memorandum of Understanding. There are three 

interagency workgroups that coordinate residue sampling operations: 1) the Interagency Residue 

67
 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Control Group (IRCG), 2) the Surveillance Advisory Team (SAT), and most recently, 3) the 

Senior Executive Council (SEC). 

The IRCG meets about once a month to discuss all pertinent residue testing issues and is 

attended by chemical residue subject matter experts from the USDA (FSIS, AMS and ARS), 

FDA and EPA. The SAT meets once a year and identifies the priority public health residues of 

concern. FSIS then develops specific sampling plans, which guide the allocation of FSIS‘ 

laboratory and inspection resources. In response to a 2010 OIG recommendation to have a 

process for elevating issues and resolving broader policy issues, the SEC was formed to ensure 

that senior level management meet regularly to resolve long-standing chemical residue issues. 

Each year, FSIS publishes the ―National Residue Program Scheduled Sampling Plans‖ (the Blue

Book) as a means of informing stakeholders about the sampling program and ―National Residue

Program Data‖ (the Red Book) as a means of reporting the results of the Agency‘s NRP testing. 

The Blue Book provides a description of the principles and methods used to design the sampling 

plans for the NRP and summarizes the planned domestic and import sampling plans on a 

calendar year basis. The Red Book presents details on the testing results of the various NRP 

sampling projects conducted throughout the calendar year. The Blue Book also includes a 

summary of adjustments to the previous year‘s NRP. 

105 Taken together, these books provide a 

comprehensive view of the program and the analyses of the data. 

An important component of the NRP is to provide verification of chemical residue control in 

HACCP systems. As part of the HACCP regulation, slaughter and production establishments are 

required to identify all chemical residue hazards that are reasonably likely to occur and develop 

systems that prevent, eliminate or minimize these hazards. A vigilant chemical residue 

prevention program is essential to ensure the prudent use of veterinary drugs and pesticides in 

food animals and is a complement to the NRP. 

A violation occurs when a FSIS laboratory detects the presence of a chemical compound or a 

given compound level in excess of an established tolerance or action level in a sample. FSIS 

shares violation findings with FDA through the Residue Violation Information System (RVIS). 

To assist FDA in investigating producers at an on-farm level, FSIS obtains the names of 

producers and other parties involved in offering the animals for sale. FSIS informs producers 

through certified letters that a product from their animal tested positive for violative chemical 

residues and that they will be considered repeat violators if associated with more than one 

violation. FSIS also maintains Residue Repeat Violator Lists for FSIS field personnel, 

establishments and livestock markets to help identify producers with more than one residue 

violation in the last 12 months either in the same establishment or different establishments.106 

Intent of Sampling Program 

The NRP is designed to: 1) provide a structured process for identifying and evaluating chemical 

compounds of concern in food animals; 2) analyze chemical compounds of concern; 3) collect 

105 Information on the National Residue Program can be obtained from the FSIS website at: 

http://www.fsis.usda.gov/Science/Chemistry/index.asp#nrp.
 106 Please see the following website for more information: http://www.fsis.usda.gov/science/chemistry/index.asp.
 

68
 
 

 

 

 

 

 

 

 

 

 

 

 

 

and report results and 4) provide appropriate regulatory follow-up when violative levels of 

chemical residues are found. 

Current Design of Sampling Program 

Domestic chemical residue sampling consists of scheduled and inspector-generated sampling. 

Scheduled sampling plans consist of random sampling of tissue from food animals that have 

passed ante-mortem inspection. The development of scheduled sampling plans is a process that 

proceeds in the following manner: 1) determine which compounds are of food safety concern; 2) 

use algorithms to rank the selected compounds; 3) pair these compounds with appropriate 

production classes and 4) establish number of samples to be collected. The annual SAT provides 

an interagency forum to discuss prioritization of chemical hazards, as well as to determine the 

compound/production class pairs to be sampled. Inspectors receive the scheduled requests for 

sampling from FSIS headquarters. 

Inspector-generated sampling is conducted by in-establishment Public Health Veterinarians 

(PHVs) or a designated and trained IPP. If the PHV/IPP believes an animal may contain 

violative levels of chemical tissue in any of its edible tissues, the inspector may use his/her own 

judgment in collecting a sample, including guidance from FSIS Directives 10,800.1 and 

10,220.3. When an inspector-generated sample is collected, a residue quick test (Kidney 

Inhibition Screen (KIS)TM test or Fast Antimicrobial Screen Test (FAST)) is performed on tissue 

collected from the suspect animal. If the KISTM or FAST is positive, muscle, liver and kidney 

tissue from the positive animal is sent to the FSIS laboratory and the carcass is held pending 

confirmation from the laboratory. If a carcass or parts of the carcass is found to contain violative 

levels of chemical residues, the carcass, parts or both are condemned. 

Objectives of Sampling 

The NRP consists of two different types of projects. First, the FSIS chemical residue control 

projects seek to: 1) Monitor the occurrence of meat, poultry and processed egg products 

contaminated with chemical residues; 2) Document the use, non-use or misuse of certain 

compounds and 3) Maintain equivalency status with international trading partners. Second, the 

NRP conducts exploratory assessments, which seek to determine the identity and the 

concentrations of a particular chemical residue that may be in meat, poultry and processed egg 

products, such as melamine in baby food or dioxin in chicken products. 

Statistical or Policy Basis for Current Sampling Programs 

The FSIS domestic scheduled sampling program consists of random sampling of tissue from 

food animals that have passed ante-mortem inspection. Since 2006, FSIS has selected 300 

samples for each compound/production class pair to provide a 95 percent assurance that with 

zero violations in the samples, the violation rate in the entire population for a particular chemical 

or chemical compound is less than one percent. If one or more violations are found in the 300 

samples for each compound/production class pair, then the violation rate is one percent or more. 

Description of the FSIS Residue Sampling Projects 

Fast Antimicrobial Screen Test (FAST) 

Historical Basis 

When FSIS suspects, based on herd history or ante-mortem or post-mortem examination, that 

animals may have illegal levels of antimicrobial drug residues, the Agency conducts an in69
 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

establishment screening test to determine whether IPP will need to submit a sample to an FSIS 

laboratory for further testing. The FAST is one of the biological screening tests used for the 

detection of antimicrobial residues in animal tissues. FAST has been validated for use in testing 

swine and cattle for antimicrobial residue levels and is performed by a veterinarian or a 

designated food inspector in a slaughtering establishment. FAST is an adaptation of the 

antimicrobial screening test that was used in FSIS laboratories for many years. FAST replaced 

the Swab Test on Premises (STOP) in-establishment screen for testing in livestock, including 

sheep, goat and horses. 

Purpose/Intent of the Project 

FAST is an in-establishment screen performed by in-establishment personnel as part of a 

targeted testing project. FAST testing is necessary in problematic slaughter classes or 

subpopulations of these classes (those with a high prevalence of antimicrobial residue violations) 

and helps to detect carcasses with violative antimicrobial residues so they cannot enter the food 

supply. It is also used to more closely monitor producers and others who are known historically 

to have marketed animals with violative concentrations of antimicrobial residues. Further, the 

FAST is used to determine whether establishment noncompliances have been corrected and to 

verify the performance of an establishment‘s HACCP system in preventing or eliminating 

chemical (residue) hazards. 

Statistical or Policy Basis 

Targeted testing in establishments allows FSIS to verify that establishments have adequate 

residue control projects. FSIS IPP are instructed to perform in-establishment screening when 

they suspect animals (ante-mortem inspection) or carcasses (post-mortem inspection) have 

violative levels of chemical residues in their tissues. FSIS Directive 10,220.3 provides a list of 

pathologies and conditions warranting sampling and retention for in-establishment testing. As 

this screen is intended to target animals suspected of having violative residue levels and testing is 

at the discretion of field personnel, the FAST project is not statistically based. 

Limitations of Sampling 

FAST materials are no longer being produced, and FSIS laboratories are maintaining supplies 

until the Agency has completely phased in the KISTM Test. 

Functionally, FAST will screen for approximately 20 antibiotics and is not as sensitive for many 

of these drugs as the KISTM Test, which is described below. For example, FAST does not detect 

Non-Steroidal Anti-Inflammatory Drugs (NSAIDS), a common class of pharmaceuticals used in 

cattle. 

Kidney Inhibition Screen (KISTM) Test 

Historical Basis 

In mid-2007, the only company supplying the FAST kits discontinued its contract with FSIS. 

FSIS thus had to seek other options to continue in-establishment screening for residues and 

selected the KISTM test produced by Charm Sciences, Inc. A pilot trial was successfully 

completed in six bovine establishments simulating real-life situations and the FSIS Midwest 

laboratory confirmation validated this new test. The Charm KISTM Test is an antibiotic detection 

test for kidney tissue and the principle of detection is microbial inhibition. Bacteria, cultured in 

70
 
 

 

 

 

 

 

 

 

 

 

 

 

 

agar with purple pH indicator media and kidney extract, generate acid that produces a yellow 

color. In the presence of antibiotic, the bacterial growth is inhibited, and the test remains 

blue/purple. KISTM Test screening was implemented in the highest slaughter volume cattle 

establishments in July 2009 and expanded to cover all bovine slaughter establishments in 2010. 

Purpose/Intent of the Project 

The KISTM Test is an in-establishment screen performed by IPP as part of a targeted testing 

program. KISTM testing is necessary in problematic slaughter classes or subpopulations of these 

classes (those with a high prevalence of antimicrobial residue violations) and helps to detect 

carcasses with violative antimicrobial residues so they cannot enter the food supply. It is also 

used to more closely monitor producers and others who are known historically to have marketed 

animals with violative concentrations of antimicrobial residues. Further, KISTM testing can be 

used to determine whether establishment noncompliances have been corrected and to verify the 

performance of an establishment‘s HACCP system in preventing, eliminating or minimizing 

chemical (residue) hazards. 

Statistical or Policy Basis 

Targeted testing in establishments is a means for FSIS to verify that establishments have 

adequate residue control projects. FSIS field personnel are instructed to perform inestablishment screening when they suspect animals (ante-mortem inspection) or carcasses (postmortem inspection) to have violative levels of chemical residues in tissues. Directive 10,220.3 

provides a list of pathologies and conditions warranting sampling and retention for inestablishment testing.107 As in-establishment field screen tests are intended to target animals 

suspected of having violative residue levels and testing is at the discretion of field personnel, the 

KISTM testing program is not statistically based. 

Limitations of Sampling 

Similar to the FAST sampling program, the KISTM program does not screen for NSAIDS. 

Overall Limitation of Current Residue Sampling 

The current algorithm for the annual sampling plan has been unchanged for approximately ten 

years and contains variables (measured qualitatively) that may no longer be appropriate measures 

for prioritizing hazards. In addition, the scheduling algorithm is a ―one size fits all‖ strategy that 

determines the number of samples collected, regardless of product class/compound pairing, 

geographical area or seasonal trends. In an attempt to reduce oversampling issues, several ad 

hoc rules have been created to manage the scheduling algorithm, which reduces the random 

nature of the program. Finally, there are continual complaints that the NRP is a resource 

intensive sampling program that provides FSIS with minimal information on the true chemical 

residue burden in Agency regulated products and is structured in such a manner that the program 

is slow to respond to emerging residue issues. 

107 FSIS is in the process of revising Directive 10,220.3 to incorporate the implementation of KISTM testing.

71
 
 

 

 

 

 

 

 

 

 

 

3.0 Imports
 

Section 3.1: Microbiological Sampling Programs 

Overview of Sampling Programs 

The U.S. imports over three billion pounds of meat, poultry and egg products annually.108 All 

shipments of meat and poultry and processed egg products that enter the U.S. must be presented 

to an FSIS inspector at one of the approximately 130 official FSIS import facilities located at 

major ocean ports and land border crossings. One hundred percent of imported product entering 

the U.S. is reinspected by FSIS at the point-of-entry (POE) for that product and every shipment 

is examined for proper documentation and box count, general condition, labeling and 

transportation damage. 

In addition to these POE verifications, FSIS performs random reinspections on shipments of 

meat, poultry and processed egg products. The POE random reinspection activities include 

physical product examinations, condition-of-container reinspections and laboratory testing (e.g., 

microbiological sampling, food chemistry analysis, species verification and chemical residue 

testing). This process is assisted by FSIS‘ Automated Import Inspection System (AIIS), a 

centralized computer database that generates and stores reinspection results. Acceptable products 

are marked as ―Inspected and Passed‖ and released into U.S. commerce. Non-compliant 

products are marked as ―Refused Entry‖ and prohibited from entering U.S. commerce. More 

intensive reinspection is automatically applied to subsequent product shipments from a foreign 

establishment that produces products failing reinspection. 

FSIS‘ POE verifications and reinspections involve evaluation of products that have first been 

inspected under an equivalent food safety system established by the exporting country. Thus, 

FSIS‘ POE activities are intended to monitor the effectiveness of exporting countries‘ inspection 

systems and overall food safety programs. Reinspections are one component of FSIS' 

comprehensive quality assurance/quality control process designed to ensure the equivalence of 

exporting country‘ food safety systems. 

Sections 3.1, 3.2, and 3.3 describe FSIS‘ POE pathogen testing programs. Section 3.4 describes 

FSIS‘ chemical residue testing in imported regulated products.

Please see the following website for more inforamation: 

http://www.fsis.usda.gov/factsheets/importing_meat_poultry_egg_products/index.ASP. 

72
 

108 
 

 

 

3.1.1: Salmonella 

FSIS maintains a formal sampling project for Salmonella in imported processed egg products. This program is described in Table 

3.1.1.1 below. FSIS also tests for Salmonella in RTE products as part of the IMVRTE program—this project is described in Section 

3.3. 

Table 3.1.1.1: FSIS Sampling for Salmonella in Imported Product 

Product 

Type/Class 

Sampling 

Project 

Total 

Number 

of 

Samples 

Analyzed 

(Failures) 

Average 

Number of 

Samples 

Collected Per 

Establishment 

Number of 

Establishments 

Included in 

Sampling 

Population 

Regulatory 

Purpose of 

Sampling 

Program 

Type of 

Sampling 

Program 

Pasteurized 

imported 

liquid, 

frozen or 

dried 

products 

(POE 

Sampling) 

EGGIMP 74 (0) Not 

Applicable Not Applicable 

Component 

of FSIS' ongoing 

equivalence 

verification 

program 

Performance 

-Based 

73
 
 

 

 

EGGIMP—Processed Egg Products 

Historical Basis and Overview: 

The imported processed egg products sampling program is a carry-over from when the AMS 

administered the program. Up until October 1, 2006, whenever a lot of pasteurized dried, liquid 

or frozen egg product was presented for import reinspection, a product examination and a 

Salmonella sample were assigned. After that date, a policy decision was made that processed 

egg products examinations would be consistent with the meat and poultry testing requirements. 

Volume Data 

Import volumes (number of lots presented for reinspection and presented net weights) are 

reported and tracked by exporting country, foreign establishment, species, process category and 

process sub-category within AIIS. When PHIS is implemented, process subcategories will be 

expanded and replaced with product category and product group. FSIS compiles this 

information and utilizes it in determining sample sizes for the various import sampling programs. 

Statistical or Policy Basis 

The current processed egg product sampling project utilizes the same approach that FSIS uses to 

determine the required number of product examinations to be performed in imported meat and 

poultry products. Under this program, the number of product examinations performed annually 

is based on the number of lots of product imported annually. When the meat and poultry 

procedures were implemented for processed egg products, a product examination and a 

Salmonella sample were randomly assigned in advance of the processed egg products shipment 

arrival at a FSIS regulated import facility. Thus, this was the beginning of ―Skipped‖ lot 

sampling in imported processed egg products. 

Sample Sizes 

Annual sample sizes for the various import reinspection programs are based on the average 

number of lots presented in the previous two years and the country history by each eligible 

country for the applicable species/process category combination. 

Limitations of Current Sampling 

Currently, imported processed egg product sampling is not a part of the AIIS and is not based on 

a statistical methodology specifically related to processed egg products food safety. 

74
 
 

3.1.2: E. coli O157:H7 

There are two primary E. coli O157:H7 sampling projects for imported products; 

1) Raw ground beef (MT08) 

2) Raw, non-intact beef (MT51) 

Please see Table 3.1.2.1 for more details. 

Table 3.1.2.1: FSIS E. coli O157:H7 Sampling Projects for Imported Products 

Product 

Type/Class 

Sampling 

Project 

Total 

Number 

of 

Samples 

Analyzed 

(Failures) 

Average 

Number of 

Samples 

Collected Per 

Establishment 

Number of 

Establishments 

Included in 

Sampling 

Population 

Regulatory 

Purpose of 

Sampling 

Program 

Type of 

Sampling 

Program 

Component 

Imported raw of FSIS' onground beef 

(POE MT08 23 (1) Not Applicable Not Applicable going equivalence 

PerformanceBased 

Sampling) verification 

program 

Trim and other Component 

raw ground of FSIS' onbeef 

components MT51 695 (2) Not Applicable Not Applicable going equivalence 

PerformanceBased 

(POE verification 

Sampling) program 

75
 
 

 

 

 

 

 

 

 

 

 

Ground Beef (MT08) 

Current Design 

The current sampling project is based on a desired number of Normal level samples to be 

assigned and analyzed over a given calendar year for each country. The samples are divided and 

allocated based on the amount of raw ground beef/veal product the country has exported to the 

U.S. over the past 24 months. This approach results in approximately 25 samples scheduled 

annually for MT08, a number that was calculated by FSIS in 2008. Because of the small number 

of lots of raw ground beef imported annually, this number has remained approximately static. 

When the FSIS identifies a foreign establishment as a ―Multi-source‖ positive E. coli O157:H7 

supplier in STEPS, FSIS management places the foreign establishment on Increased inspection. 

Foreign establishments may also be placed on Increased inspection as a result of a management 

decision triggered by other concerns, such as failure to present.109 Under Increased inspection, 

the AIIS is programmed to assign samples for E. coli O157:H7 to a minimum of the next 15 

consecutive lots of applicable beef/veal product. If all samples are negative, the Increased level 

is removed from the AIIS and sampling returns to Normal. 

Similarly, when a foreign establishment or country is identified during a U.S. audit as having 

issues, FSIS may place the country or establishment on Increased inspection. The sampling rate 

is determined by FSIS. The Increased level is removed when the objective has been met, or by 

management decision and sampling returns to Normal. 

When a positive E. coli O157:H7 sample is reported, the AIIS is programmed to place the 

foreign establishment that produced the product on an Intensified level of inspection. This 

means that, at a minimum, the next 15 consecutive lots of raw ground beef/veal and 15 times the 

weight of the failed lot are assigned E. coli O157:H7 sampling. If all samples are negative, the 

Intensified level is removed from the AIIS and sampling returns to Normal. 

Limitations of Current Sampling 

The statistical power of the MT08 project is limited by the small number of lots of raw ground 

beef imported into the U.S. annually. 

Non-Intact Beef (MT51) 

Current Design 

The project is based on a desired number of Normal level samples to be assigned and analyzed 

over a given calendar year for each country. The samples are divided up and allocated based on 

the amount of beef/veal trimmings a country has exported to the U.S. over the past 24 months. 

This resulted in 356 samples annually, a number calculated by FSIS in 2008. This sample size 

remained approximately static in 2009 and 2010. In 2011, the number of normal samples 

scheduled to be collected was increased to reflect the large number of lots of non-intact beef 

presented for reinspection at U.S. POE. 

Beginning CY2010, because the AIIS was incapable of assigning only to beef/veal, a decision 

was made to pro-rate the samples by import region and have them assigned. Based on the 

109 Failure-to-Present (FTP) is when product has not been presented to the FSIS inspector for an AIIS assignment 

and enters commerce. Failure to present for FSIS inspection may result in penalties. 

76
 
 

 

 

 

 

 

 

 

number of lots presented in the past, a set number of samples were provided to each import 

region to assign throughout the year for each country. Import regions were given time periods in 

which they should sample based on number of positive samples and where the producing country 

is located geographically. When FSIS identifies a foreign grinding establishment as a ―multisource‖ supplier of E. coli O157:H7 positive beef/veal, FSIS management will place the foreign 

establishment on Increased inspection. 

The designation of a ―multi-source‖ or ―sole-source‖ positive E. coli O157:H7 supplier 

notification result is reported in STEPS. The AIIS is programmed to assign samples for E. coli 

O157:H7 to a minimum of the next 15 consecutive lots for a ―multi-source‖ supplier notification 

of applicable beef/veal product. In the case of a ―sole-source‖ supplier notification, the next 15 

consecutive lots of applicable beef/veal product and 15 times the weight of the lot (if known) are 

sampled. If all samples are negative, the Increased level is removed from the AIIS and sampling 

returns to Normal. 

FSIS conducts periodic audits of those countries certified to export meat, poultry and processed 

egg products to the U.S. The audits focus on ensuring that the country maintains a food safety 

system equivalent to that of the U.S.. Audit findings that result in a food safety concern, such as 

inadequate government oversight, will be brought to FSIS headquarters attention. Based on the 

health risks associated with the food products and the nature of the failure, FSIS management 

may decide to place the country or establishment on Increased inspection for the product 

exported by that country. 

When a positive sample is reported, the AIIS is programmed to place the foreign establishment 

that produced the product on an Intensified level of inspection. This means that, at a minimum, 

the next 15 consecutive lots of applicable beef/veal product and 15 times the weight of the failed 

lot are assigned E. coli O157:H7 sampling. If all samples are negative, the Intensified level is 

removed from the AIIS and sampling returns to Normal. 

Statistical or Policy Basis 

The current E. coli O157:H7 import sampling project is based on the number of positive 

samples. 

Limitations of Current Sampling 

The current MT51 sampling project relies on implementation by the FSIS field supervisors to 

ensure that amenable product subcategories (e.g., boneless cuts) are sampled at the correct 

intervals. As a result, the MT51 project is more time-consuming to administer and monitor than 

the import sampling projects, such as MT08, that are fully implemented through the AIIS. 

77
 
 

3.1.3 RTE Meat and Poultry Products 

Overview of Sampling Programs 

FSIS maintains one sampling project for RTE products from importing countries. This project is listed below in Table 3.1.3.1 and 

described in more detail below. 

Table 3.1.3.1: FSIS RTE Sampling for Imported Products, FY 2010 

Pathogen Product 

Type/Class 

Sampling 

Project 

Total 

Number 

of 

Samples 

Analyzed 

(Failures) 

Average 

Number of 

Samples 

Collected Per 

Establishment 

Number of 

Establishments 

Included in 

Sampling 

Population 

Regulatory 

Purpose of 

Sampling 

Program 

Type of 

Sampling 

Program 

Salmonella 

and Lm 

Imported 

Intact RTE 

Product 

IMVRTE 

(POE 

Sampling) 

4,512 (3) Not 

Applicable Not Applicable 

Component 

of FSIS' ongoing 

equivalence 

verification 

program 

PerformanceBased 

78
 
 

 

 

 

 

 

IMVRTE—Imported Intact RTE Product 

Current Design 

The current project is based on a desired number of Normal level samples to be assigned and 

analyzed over a given calendar year. The samples are divided up and allocated based on the 

amount of RTE product a country has exported to the U.S. over the past 24 months, and then 

further subdivided and allocated by HACCP process category to each country. Consequently, 

approximately 3,000 total samples should be analyzed, as calculated by FSIS in 2008. Based on 

the way the AIIS is programmed for the import RTE sampling (IMVRTE) project, the AIIS 

assigns analyses for both Lm and Salmonella for a given sample unit. This results in more than 

6,000 sample analyses for Lm and Salmonella. However, this number is beyond FSIS‘ current 

capacity. Therefore, the sampling target was reduced to approximately 1,500 to 2,000 samples 

annually and each sample submitted to the lab is analyzed for the applicable pathogens. 

When a foreign establishment or country is identified as having issues during a U.S. audit or by 

some other means, FSIS management may place the country or establishment on Increased 

inspection. The sampling rate is determined by FSIS management, in accordance with 

guidelines developed by the Agency, and monitored to ensure that the specific management 

objective is met. The Increased level is removed when the defined management objective has 

been met, or by management decision, and sampling returns to Normal. 

When a positive sample is reported, the AIIS is programmed to place the foreign establishment 

that produced the product on an Intensified level of inspection. This means that, at a minimum, 

the next 15 consecutive lots or 15 times the weight of the failed lot are assigned sampling in the 

same HACCP process category for the pathogen that tested positive. If all samples are negative, 

the Intensified level is removed from the AIIS and sampling returns to Normal. 

Limitations of Current Sampling 

Increased sampling is manual, and comes with the same difficulties Intensified sampling does, 

namely that while targeting is a good practice, it is not always one hundred percent accurate. 

Additionally, product sampling following a positive is limited to the same process category. 

Consequently, other products may be produced in the same area/line, but under a different 

HACCP process, which means that Intensified sampling does not take it into account. 

Imports Measures of Success 

POE reinspections, including pathogen and residue testing, are one component of a 

comprehensive, ongoing verification process designed to ensure equivalence of exporting 

countries‘ food safety systems. POE reinspections help to ensure that imported FSIS-regulated 

products are safe and wholesome by supporting FSIS‘ overall equivalence program through: 

Identifying shipments that do not meet FSIS requirements and refusing entry of these 

products into the U.S. 

Providing detailed information to support FSIS‘ equivalence verification audit programs.

Providing detailed information to support FSIS‘ performance-based sampling programs. 

Providing detailed information to support the NRP. 

79
 
 

 

In addition, POE reinspection findings are used to identify foreign establishments warranting 

increased/intensified reinspection, such as more frequent reinspection of subsequent shipments 

following presentation of a shipment that failed reinspection. 

To measure the success of the import sampling programs, FSIS evaluates its efforts in terms of 

four key operational metrics, as described in Table 3.1. Operational measures are included here 

as it is not currently possible to estimate the number of foodborne illnesses that come from 

imported products, as the number of samples collected do not warrant a measure of prevalence 

and the CDC does not differentiate illnesses acquired from eating contaminated imported food, 

as opposed to domestically produced food. 

Table 3.1: Measures of Success for FSIS Import Sampling Program 

Measure Goal 

Operational Performance 

Measure FY 2009 FY 2010110 FY 2015 

Percent of AIIS assigned E. coli 

samples that are collected. > 99 % >98% 95 % 

Percent of AIIS assigned E. coli 

samples that are not analyzed due to 

inspector error. 

< 1% <1% 5 % 

Percent of AIIS assigned E. coli 

foreign establishment-follow-up 

samples (e.g., establishment under 

intensified inspection status) that are 

collected. 

100 % 100% 95 % 

Percent of AIIS assigned E. coli 

foreign establishment-follow-up 

samples (e.g., establishment under 

intensified inspection status) that are 

not analyzed due to inspector error. 

[none] <5% 5 % 

110 The performance measure is calculated by using a 12 month rolling window, so the measure reflects the most recent 12 

months of data up to and including the current year. 

80 
 

 

 

 

 

 

Section 3.2: Chemical Residues 

Overview: 

Imported meat, poultry and processed egg products are sampled at U.S. POE to detect chemical 

residues as part of a POE reinspection. POE reinspection is a monitoring program conducted to 

verify the equivalence of inspection systems in exporting countries. The chemical residue 

sampling program is one of several Types of Inspection (TOI) conducted during FSIS 

reinspection of imported products. The following are the three levels of chemical residue 

reinspection: 

Normal sampling, defined as random sampling from a lot;
 

Increased sampling, defined as above the normal sampling as the result of an FSIS
 

management decision; and 

Intensified sampling, defined as occurring when a previous sample for a TOI failed to 

meet U.S. requirements. 

For both normal and increased sampling, the importer may choose to retain the lot pending the 

laboratory results, but it is not required. However, the lot is subject to recall if it is not retained 

and is found to contain violative levels of chemical residue. For Intensified sampling, the lot 

must be retained pending laboratory results. The data obtained from laboratory analyses are 

entered into the AIIS. 

Fresh and Processed 

Current Design 

The current program is based on a desired number of Normal level samples to be assigned and 

analyzed by compound over a given calendar year for each country, product (fresh or processed) 

and species. When the import volume of a particular product class is less than one percent of the 

total amount of meat, poultry and processed egg products imported, then eight samples are 

assigned to each country. The sample numbers come from the NRP SAT and are programmed 

into the AIIS. Please see Table 3.2.1 for fresh and processed samples analyzed in FY2010. 

Residue 

Sampling 

Total Number of 

Samples Analyzed 

Regulatory Purpose of 

Sampling Program 

Fresh and 

Processed 3,408 Component of FSIS' on-going equivalence verification program 

Table 3.2.1: FSIS Residue Sampling for Imported Products, FY 2010 

Statistical or Policy Basis 

The allocation of samples under the import program is based on several factors including: 

country of origin, product type, volume imported and chemical tested. The FSIS NRP Blue 

Book provides the algorithms used to prioritize reinspection sampling. 

Limitations of Current Sampling 

The current sampling program is based primarily on compounds known to be used domestically, 

and may exclude compounds of concern in the foreign country or compounds which exporting 

countries may use, but are prohibited for use in the United States. FSIS is currently evaluating 

its protocol for prioritizing hazards from chemical exposure, which may impact both 

domestically produced products, as well as those imported. 

81
 
 

 

 

 

4.0 In-Commerce Activities
 

Overview 

FSIS Compliance Investigators (CI) conduct surveillance to protect the health and welfare of 

consumers by ensuring that meat, poultry and processed egg products in-commerce are safe, 

wholesome, correctly labeled and packaged and secure from intentional acts of contamination. 

These activities are carried out at in-commerce locations such as warehouses, distribution centers 

and retail establishments, as well as POE and U.S. borders, to verify that persons and firms, 

whose business activities involve FSIS-regulated products, prepare, store, transport, sell or offer 

for sale or transportation such products in compliance with FSIS statutory and regulatory 

requirements. These activities require data collection and analysis that differs from that required 

for the domestic inspection activities covered by this report. 

Current Design of Sampling Plan 

FSIS has the following sampling projects currently in place at retail: 

1) E. coli O157:H7 testing in raw ground beef at businesses operating under a retail 

exemption (MT05). 

2) Follow-up testing for E. coli O157:H7 in raw ground beef products (MT06) scheduled 

only when an MT05 sample tests positive. 

Table 4.1: FSIS E. coli O157:H7 Sampling Projects for In-Commerce Surveillance 

Products Sampling 

Projects 

Number of 

E. coli 

O157:H7 

samples 

analyzed in 

CY2010 

Regulatory 

Purpose of 

Sampling 

Program 

Type of Sampling 

Program 

Raw ground 

beef at retail 

stores 

MT05 905 

Verify 

compliance 

with 

regulatory 

standard 

Targeted 

Follow-up 

testing to a 

MT05 

sample 

MT06 0 

Verify 

corrective 

measure 

Targeted, Consecutive 

Objectives of Retail Sampling: 

Retail sampling is an important part of FSIS‘ overall E. coli O157:H7 sampling activities. The 

retail sampling program addresses several objectives for FSIS: 

1.	 Helps ensure hazard controls at retailers are adequate to prevent product from becoming 

adulterated. 

82
 
 

 

 

 

 

 

 

 

 

 

Statutory provisions requiring inspection do not apply to the types of operations 

traditionally and usually conducted at retail stores. However, FSIS‘ adulteration and 

misbranding provisions do apply to exempt retail businesses. Retailers have the potential 

to adulterate product in the absence of adequate hazard controls. FSIS testing of retail 

samples for E. coli O157:H7 gives the Agency additional assurances that products are not 

being adulterated at retail facilities operating under a retail exemption. 

2.	 Encourages industry to adopt complete and accurate product tracing systems for food. 

Retail facilities should consistently maintain adequate records concerning suppliers of 

source material for raw ground beef products, as required by regulations and the Federal 

Meat Inspection Act (FMIA). With regard to investigations associated with raw ground 

beef consumption, product lot coding, production date and beef manufacturing 

establishment information are required to successfully conduct product traceback. 

In many circumstances, however, investigators are provided with only purchase 

information, such as date and location of purchase or type of ground beef. FSIS CI then 

must rely heavily on grinding records kept in retail stores, meat markets and other 

operations to gather the information needed to undertake traceback actions. 

Unfortunately, CI frequently find these grinding records to be incomplete or inaccurate, 

thereby delaying or preventing the traceback of potentially adulterated products, which 

could result in additional illnesses. 

When FSIS collects samples of raw ground beef from retail businesses, the Agency 

collects the relevant information using the FSIS Form 8010-1, Retail Ground Beef 

Sampling Worksheet, which is used if an E. coli O157:H7 positive finding is later 

identified. FSIS has stated it expects retail facilities to consistently maintain complete 

and adequate records, as required by the regulations (9 CFR part 320) and the Section 

202 of the FMIA (21 U.S.C. 601 et seq.). 

3.	 Encourage industry to conduct testing programs for E. coli O157:H7. 

FSIS considers product sampling to be one of several activities conducted to verify 

supplier claims and the effectiveness of hazard controls at retail facilities. Since the 

adoption of the FSIS E. coli O157:H7 testing program, many grinders and suppliers of 

raw ground beef components have instituted programs to routinely test their raw ground 

beef products or raw materials used in raw ground beef products for E. coli O157:H7. 

4.	 Serves as an indicator of the overall trend of the presence of E. coli O157:H7 in raw ground 

beef. 

Although FSIS views results from verification samples from Federal establishments as 

the best indicator of the overall trend of the presence of E. coli O157:H7 in raw ground 

beef, the test results from retail sampling gives the Agency another indicator of trends in 

the presence of E. coli O157:H7 in raw ground beef products. 

83
 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

MT05 and MT06—Raw Ground Beef at Retail 

Historical Basis and Background Information 

Although most microbiological samples are collected at federally inspected establishments, FSIS 

collects samples from retail stores in accordance with criteria listed in FSIS Directive 8010.1, 

Rev. 2, Methodology for Conducting In-Commerce Surveillance Activities, dated June 25, 2008. 

―Retailers‖ are one of more than a dozen business types in the FSIS In-Commerce Surveillance 

System (ICS) and constitute about 60% of businesses in the system. FSIS samples at retail 

when: 1) the retail store produces raw ground beef using whole muscle or trimmings from a 

cutting/boning operation conducted at the store, 2) the retail store does not maintain records of 

raw beef suppliers or records documenting clear and accurate grinding logs or 3) the retail store 

is not cleaning and sanitizing the grinder between the use of different source materials. 

Retail samples are not scheduled from an existing list of businesses producing raw ground beef. 

Rather, CI are instructed to collect a one-pound sample of raw ground beef for E. coli O157:H7 

testing at every retail business they visit for a surveillance review, if the business has raw ground 

beef it prepared under the retail exemption and the business meets one of the criteria listed 

above. Whether a raw ground beef sample will be collected depends on what the CI observes 

during a surveillance review at a retail business. 

Of the approximately 29,000 surveillance activities that FSIS has conducted since October 1, 

2008, over one-third (about 11,000) were performed at retailers and 2,627 ground beef samples 

were collected by the Agency. In FY 2011, CI collected 1,280 verification samples at retail 

businesses. Of the retail samples collected since October 1, 2008, 0.11% tested positive for E. 

coli O157:H7. 

In September 2011, as a result of a formal review of FSIS in-commerce activities by the National 

Academies of Science (NAS), the Agency shifted retailers from Tier 2 to Tier 3 facilities, 

111,112 making them lower priority for Agency surveillance. Tier 3 businesses are surveilled only 

―for cause.‖113 Therefore, while the number of retail surveillances FSIS will likely perform ―for 

cause‖ next year and in future years is unknown, it is unlikely to be high enough to generate 

comparable numbers of retail ground beef samples. Indeed, it is possible that the number of 

samples collected will be fewer than one hundred each year. 

Statistical or Policy Basis 

Approximately 75,000 retail businesses grind beef in the U.S. The MT05 sampling project for E. 

coli O157:H7 in raw ground beef at retail venues was started in 1994 to monitor compliance with 

regulatory standards and continues with that intent today. Neither the MT05 nor the MT06 

projects are conducted using a random method. Rather, they are targeted sampling projects to 

verify corrective actions that have been conducted as a result of a previous positive test and are 

therefore not statistically based. Present targeting criteria for sample selection are described in 

111Please see the following website for more information: http://www.nap.edu/openbook.php?record_id=12786.
 112 Please see the following website for more information: http://www.fsis.usda.gov/OPPDE/rdad/FSISNotices/53-11.pdf.
 113 Tier 1 and Tier 2 businesses, generally, have significant inherent hazards, handle large volumes of meat, poultry, and egg 

products, and receive minimal scrutiny by other regulatory authorities and accordingly are considered higher priority by FSIS. 

Tier 3 businesses, on the other hand, generally receive significant scrutiny from other regulatory authorities and therefore are 

considered lower priority by FSIS. 

84
 
 

 

 

 

 

 

 

FSIS Directive 8010.1. There is no set, required sample collection frequency or sample size, 

though the sample size is generally one pound. Samples are collected by a CI when a retail 

business meets at least one of the criteria described in FSIS Directive 8010.1. The number of 

samples collected and the percent positive have varied widely over time. Collection criteria also 

have varied over time. These issues, and other concerns regarding the representativeness of 

samples, make it inappropriate to extrapolate findings to all products sold at retail. Starting in 

October 2011, the sampling program was modified to collect a purposive sample of 

approximately 460 samples per year to provide a 99% probability of detecting one or more 

positive samples, if the actual percent positive rate reaches as high as 1%, with 90% probability 

of detecting one or more positives if the true percent positive is 0.5%. If every FSIS CI collects 

approximately one sample quarterly, this will produce about 460 samples per year, distributed 

evenly through the year and around the country. 

Not all retailers produce ground beef and not all of those produce it under the conditions 

specified in Appendix 1 of Directive 8010.1. Historically, FSIS CI has collected ground beef for 

E. coli O157:H7 testing during one out of four retail surveillances. However, CI will have to 

surveil- on average- only three retailers to identify a retailer eligible for sampling. Nationally, 

this would mean about 1,380 surveillances to generate about 460 samples. While this constitutes 

about 14% of FSIS‘ surveillances, these surveillances would be ―for cause.‖

Limitation of Current Sampling 

Past sampling objectives and strategies cannot be confirmed, but appear to vary. However, the 

present sampling strategy as outlined in Directive 8010.1 would result in samples that would not 

accurately represent the prevalence of E. coli O157:H7 in raw ground beef processed at retail. 

FSIS collects ground beef for testing from a very small proportion of retail businesses processing 

ground beef and virtually none are collected on a non-risk basis. Without further understanding 

of the situation, it would be difficult to compare yearly results from the retail program, with 

results from Federal establishments, or to all ground beef in-commerce. 

In-Commerce Measures of Success 

Though the in-commerce E. coli O157:H7 sampling program differs in purpose and intent from 

the Federal establishment sampling programs, the overall purpose of the program is to assess, 

and minimize, the risk to public health from contaminated product. As such, to measure the 

success of the E. coli O157:H7 sampling projects, FSIS can evaluate its efforts in terms of the 

percent positives from the in-commerce E. coli O157:H7 sampling program. 

Percent Positives 

FSIS believes that percent positives are a good measure of the effectiveness of the E. coli 

O157:H7 individual sampling projects maintained by the Agency, with declines in percent 

positives indicating greater control and prevention of E. coli O157:H7 in finished product. In FY 

2011, CI collected 1,280 samples. Of these samples, only 0.08% tested positive for E. coli 

O157:H7. 

85
 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

5.0 Foodborne Illness Investigation and Consumer Complaint 

Sampling Programs 

Domestic Programs 

Current Design of Sampling Program 

FSIS regulated products are collected during foodborne illness and consumer complaint 

investigations. 

Statistical or Policy Basis for Current Sampling Plan 

A foodborne illness investigation is defined as an investigation of the possible association 

between human illnesses and FSIS-regulated product that includes epidemiologic, laboratory and 

environmental assessments. Foodborne illness investigations are conducted as described in FSIS 

Directive 8080.3 and internal Standard Operating Procedures (SOPs). A consumer complaint is 

any complaint reported to FSIS that is initiated by or on behalf of a consumer and that is directly 

related to a meat, poultry or processed egg product. Consumer complaint investigations are 

conducted as described in FSIS Directive 5610.1 and internal SOPs. 

Purpose of Program 

During the course of foodborne illness and consumer complaint investigations, previously 

opened (non-intact) products consumed by case-patients (e.g., individuals identified by an illness 

investigation) or complainants may become available for investigative sampling and analysis by 

FSIS. Similarly coded intact products may be collected directly from the identified individuals 

at a point of purchase or at the producing establishment. These samples can provide the best 

opportunity for detecting foodborne hazards, including microbial pathogens, extraneous 

materials and chemicals. The data obtained from outbreak and consumer complaint sampling 

supplements available epidemiologic and environmental findings and assists with determining 

the type and extent of product contamination. Collectively, the information provides rapid 

results for timely and informed risk management decisions. 

Sampling Frame Definition 

To determine whether to sample and test potentially implicated products, FSIS investigators 

consider the following questions: 

1.	 Do the epidemiologic investigation data, including the reported food history, support a link 

between the illness or other described hazard and FSIS-regulated product? 

2.	 Do the laboratory findings support a link between the illness or other described hazard and 

FSIS-regulated product? 

3.	 Does the environmental assessment support a link between the illness or other described 

hazard and FSIS-regulated product? 

4.	 Is there product available to test that meets FSIS criteria for product identity, chain of 

custody and product handling? If not, are there reasons for testing product that may not meet 

all of these criteria? 

5.	 Has product already been tested by a non-FSIS laboratory with reliable methodology?114 

6.	 Can testing be carried out by or in association with FSIS? 

114 See FSIS Directive 10,000.1 Policy On Use Of Results From Non-FSIS Laboratories. 

86
 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

To determine whether to sample and test a non-intact product, FSIS investigators consider the 

following questions: 

1.	 Was the non-intact product directly handled by the case-patient or complainant? 

2.	 Was the non-intact product stored properly to avoid cross-contamination and temperature 

abuse? 

3.	 Are packaging materials and product labels that identify the non-intact product available? 

If not, was traceback successful in determining the product identity? 

Sampling size and methodology 

After determining whether to collect an investigative sample, FSIS drafts a sampling plan that 

takes into account the product available for sampling and the available laboratory resources and 

capacity. Potential sampling plans are described below: 

1.	 When a limited amount of product is available (e.g., if a few packages and lots are 

available for sampling): 

a.	 FSIS may request that all intact packages be submitted to the FSIS laboratory. 

2.	 When an un-manageable number of product packages are available: 

a.	 FSIS will provide guidance on sampling procedures consistent with available 

resources. FSIS has identified the following procedures when a unmanageable 

number of packages are available: 

i.	 Sampling by perceived relative risk. If evidence indicates that product of 

one lot/code is more suspect than another potentially implicated lot/code, 

FSIS may propose to stratify and allocate random sampling either 

proportionally or in tiers. For example, the FSIS laboratory determines it 

can analyze 50 samples per day. Lot A product appears to be of greater 

risk or concern compared to Lot B, but there is some reason to believe that 

the latter lot may be at risk as well. Both production lots are identified and 

under regulatory control. If the priority for the investigation is to 

determine status for both lots as quickly as possible, FSIS may propose 

weighted stratified sampling for each lot. For example, 30 samples from 

Lot A and 20 from Lot B. 

ii.	 Sequential sampling over time. If time is available for multiple analyses, 

FSIS may propose sequential sampling over time. For example, 50 

samples of Lot A may be analyzed initially and an additional 50 samples 

may be analyzed at a later date, as resources allow. 

iii.	 Sampling by relative volume. For sampling product from one or more lots 

or consignments of different size, FSIS may propose proportional random 

sampling by total volume. For example, Consignment A is 500 pounds, B 

is 1500 pounds and C is 3000 pounds. For 50 total sample analyses, 5, 15 

and 30 samples for Consignments A, B and C, respectively, would be 

selected. 

Sampling Weights, Ceilings, and Floors 

Not applicable to foodborne illness and consumer complaint investigation related sampling. 

87
 
 

 

 

 

 

 

 

 

Collection methodology 

If product sampling and testing is warranted, FSIS will follow procedures in FSIS Directive 

8080.3, Section IX or FSIS Directive 5610.1. FSIS staff would be directed to collect product 

samples using Domestic Laboratory Report Form 10,000-2 to document chain of custody, as 

described in FSIS Directive 8010.3 and to use sample seals as described in FSIS Directive 

7355.1. Samples are delivered to an FSIS Field Service Laboratory or another laboratory with 

available capacity and expertise. Results from foodborne illness and consumer complaint 

investigation related sampling is reported by email to FSIS management and other designated 

recipients, but are not reported through Biological Information Transfer and E-mail System 

(BITES) and Laboratory Electronic Application for Results Notification (LEARN). Results are 

also available in the FSIS Laboratory Information Management Systems (LIMS). Non-microbial 

test results are reported through the Consumer Compliant Monitoring System II (CCMS II). 

Mean Response Rate, Mean Analyzed Sample, and Percent Positive Rate for Samples 

Analyzed 

Not applicable to foodborne illness and consumer complaint investigation related sampling. 

Limitations of Current Sampling 

Testing should be performed within the context of available resources 

Testing cannot guarantee that a sampled lot is free from targeted hazard(s). 

Foodborne illness and consumer complaint investigation related testing is often 

performed outside the scope of the ISO 17025115 accreditation maintained by the FSIS 

laboratory system. 

FSIS laboratories may not have the expertise or capacity to test for certain analytes.116 

In some situations, FSIS may arrange for outbreak samples to be tested by other 

laboratories, such as FDA-Center for Food Safety and Applied Nutrition (CFSAN), ARS, 

the Food Emergency Response Network (FERN) or state laboratories of agriculture. 

. 

115 ISO/IEC 17025 is the main standard used by testing and calibration laboratories.
 116 A summary of routine FSIS laboratory analyses is available at http://dchqintra/learn/docfile/analyses.htm. 

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6.0 Appendices
 

89 
 

 

 

 

 

 

 

 

 

 

 

 

 

Appendix A: Definition of Terms 

Data Warehouse: FSIS collects numerous types of data from a variety of different sources. This 

data is stored in an electronic ―warehouse,‖ known as the FSIS Data Warehouse (DW).

Exclusion Criteria: Exclusion criteria are the standards FSIS uses to determine whether an 

establishment should be included in the sampling frame. For example, establishments that 

produce a very low volume of product may be excluded from the sampling frame. Therefore, 

producing low volume is the exclusion criterion. 

Percent Positive: The percentage of positive samples is expressed as a percentage, determined as 

the number of positive samples for the pathogen per the total number of samples tested, 

multiplied by 100. The expected value of this percentage in this document is called ―the percent 

positive.‖117 

Performance Based Sampling: A sampling plan in which establishments are sampled at a greater 

or lesser frequency based on their performance. For example, establishments that have fewer 

positive pathogen test results might be considered to be high performers and are therefore 

sampled less frequently than establishments that have more positive pathogen test results. 

Random Sampling: A random sample is one chosen by a method involving an unpredictable 

component. Random sampling can also refer to taking a number of independent observations 

from the same probability distribution, without involving any real population. 

Replacement: When a sampling unit is drawn from a finite population and is returned to that 

population, after its characteristic(s) have been recorded, but before the next unit is drawn, the 

sampling is said to be ―with replacement.‖ In the contrary case, the sampling is ―without 

replacement.‖ A different usage occurs in sample surveys when samples are taken on successive 

occasions. If the same members are used for successive samples there is said to be no 

replacement; but if some members are retained and others are replaced by new individuals there 

is said to be ―partial replacement‖.118 

Risk Based Sampling: A sampling plan in which establishments are sampled at a greater or lesser 

frequency based on the risk the establishment poses. For example, establishments that have 

fewer positive pathogen test results might be considered to be low risk and are therefore sampled 

less frequently than establishments that have more positive pathogen test results. 

Sampling Frame119: Sampling frame is the actual set of units from which a sample has been 

drawn. In the case of a simple random sample, all units from the sampling frame have an equal 

chance to be drawn and to occur in the sample. In the ideal case, the sampling frame should 

coincide with the population of interest. 

117Please see the following website for more information: 

http://www.fsis.usda.gov/PDF/Draft_Guidelines_Sampling_Beef_Trimmings_Ecoli.pdf. 118 Please see the following website for more information: http://stats.oecd.org/glossary/detail.asp?ID=3835. 119 Please see the following website for more information: www.statistics.com. 

90
 
 

 

 

 

 

 

 

 

Sample Size: The sample size of a statistical sample is the number of observations that constitute 

it. It is typically denoted n, a positive integer. The sample size is an important feature of any 

empirical study in which the goal is to make inferences about a population from a sample. In 

practice, the sample size used in a study is determined based on the cost of data collection, and 

the need to have sufficient statistical power. In a census, data are collected on the entire 

population; hence the sample size is equal to the population size. Larger sample sizes lead to 

increased precision when estimating unknown parameters. For example, to know the proportion 

of cattle that is infected with a pathogen, a more accurate estimate of this proportion will result 

from a sample of 200, rather than 100 cattle. 

Sample Ceiling: The maximum number of samples in a sampling frame. 

Sample Floor: The minimum number of samples in a sampling frame. 

Time Series: A time series is a set of regular, time-ordered observations of a quantitative 

characteristic of an individual or collective phenomenon taken at successive, in most cases 

equidistant, periods/points of time. Breaks in statistical time series occur when there is a change 

in the standards for defining and observing a variable over time. Such changes may the result of 

a single change or the combination of multiple changes at any one point in time of observation of 

the variable.120 For example, changes to the way in which the E. coli O157:H7 sampling frame 

is constructed over time disrupts the time series and makes it difficult to compare results from 

year to year. 

Please see the following website for more information: http://stats.oecd.org/glossary/search.asp. 

91
 

120 
 

Appendix B: E. coli O157:H7 Sampling Program Description and Features 

Average Sampling Mean Mean Project Frame Sampling Collection Sampling Sampling Purpose Frame Sample Size Ceilings/Fl Response Samples Code Definition Method Method Weights Frequency Size oors Rate Analyzed 

Ceilings: 4/ 

month for 

large 

volume 

producers, 

3/month for 

medium, Verification Federally Weighted Production 2/month for 1 lb sample of HACCP inspected random 11,482 1300 per month 1 lb of raw volume and small of raw 72% MT43 and assess beef 1300 sampling samples (15600 per year) ground beef historical volume, ground collected risk to grinding with per year test results and beef public health estab. replacement 1/month for 

very small 

Floor: 3 

analyzed 

samples per 

year per 

estab. 

Federally 

Follow-up to inspected NA 16 (or 8) follow- Targeted 1 lb of raw 56% MT44 MT43 beef up samples per samples sampling ground beef collected positives grinding MT43 positive per year 

estab. 

92
 

254 
MT50 

To track rate 

of O157:H7 

in manufact. 

trimmings 

over time as 

compared to 

the 2007 

prevalence 

estimate. 

Federally 

inspected 

beef and 

veal 

slaughter 

estab. 

480 50 per week 

(2600 per year) 

Simple 

random 

sampling 

without 

replacement 

N60 sample 

weighting 325 

g 

40% 

collected 

1092 

samples 

per year 

MT53 

Follow-up to 

positive trim 

or 

component 

sample 

Federally 

inspected 

slaughter 

estab. 

NA 

16 (or 8) follow-

up samples/ 

initial positive 

Targeted 

sampling 

N60 sample 

weighing 325 g 

or 2 lbs of 

component 

52% 

collected 

161 

samples 

per year 

Federally 

MT54 Verification 

of HACCP 

inspected 

beef 

slaughter, 

veal 

slaughter, 

and 

ammoniate 

d beef 

estab. 

450 15 per week (780 

per year) 

Simple 

random 

sampling 

without 

replacement 

2 lb collection 27% 

collected 

224 

samples 

per year 

Federally Simple 

random N60 sample 538 Verification inspected 150 per month 29% MT55 1100 sampling weighting 325 samples of HACCP estab. (nonslaughter) 

(1800 per year) without 

replacement 

g 

collected 

per year 

1 sample at each 

MT52 

Follow-up at 

suppliers to 

positive 

sample 

Federally 

slaughter 

inspected 

estab. 

N/A 

supplier if there 

are multiple 

suppliers OR 16 

(or 8) samples if 

there is only one 

Targeted 

sampling 

N60 sample 

weighing 325 g 

or 2 lbs of 

component 

77% 

collected 

610 

samples 

per year 

supplier 

93