USDA Food Safety and Inspection Service 

Annual Sampling Summary Report 

Fiscal Year 2020 

United States Department of Agriculture 

Food Safety and Inspection Service 

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Table of Contents 

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

Background............................................................................................................................... 3 

Summary of Sampling................................................................................................................. 3 

Beef Products ........................................................................................................................ 4 

Pork Products ........................................................................................................................ 8 

Siluriformes Products.............................................................................................................. 9 

Poultry Products .................................................................................................................... 9 

Ready-to-Eat (RTE) Products ...................................................................................................12 

National Residue Program......................................................................................................15 

Domestic Scheduled Sampling Plan ......................................................................................15 

Surveillance Sampling Plan ..................................................................................................15 

Inspector-Generated Sampling Plan......................................................................................20 

Imports Sampling..................................................................................................................24 

Import Microbial Sampling ..................................................................................................24 

Import Residue Sampling ....................................................................................................25 

Whole Genome Sequencing (WGS) Initiatives............................................................................28 

National Antimicrobial Resistance Monitoring System (NARMS)...................................................28 

Other Sampling.....................................................................................................................29 

Conclusion...............................................................................................................................30 

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Introduction 

The U.S. Department of Agriculture’s (USDA) Food Safety and Inspection Service (FSIS) inspects meat, 

poultry, and egg products to ensure that the food produced is safe, wholesome, and properly labeled. 

Verification activities serve to protect the public from foodborne hazards. A key FSIS inspection 

verification activity is the sampling of product for microbiological contaminants or chemical residues. 

Each year, FSIS establishes sampling priorities and goals through its annual sampling plan. FSIS utilizes 

the Agency’s Strategic Plan goals, outcomes, objectives, and measures – as well as specific items of 

focus in the agency’s Annual Plan – to develop its Annual Sampling Plan. The Annual Sampling Plan 

identifies changes planned for the fiscal year to FSIS’ various sampling programs and describes the 

agency’s overall strategy for directing its sampling resources. In addition, the Annual Sampling Plan 

aligns goals and measures described in FSIS’ Strategic and Annual Plan with sampling activities and 

results. This report, the FY 2020 Annual Sampling Summary Report, summarizes the activities and 

provides an overview of results for the products the agency inspected during fiscal year (FY) 2020 

(October 1, 2019 – September 30, 2020). 

FSIS routinely assessessampling data, posts these data (including establishment-specific datasets)to the 

FSIS website, and shares data through quarterly letters directly with regulated establishments. These 

data include FSIS pathogen verification data, FSIS National Residue Program data, and import data. The 

results of these assessmentsare used in a variety of ways, including monitoring the effectiveness, where 

applicable, of Hazard Analysis and Critical Control Points (HACCP) plans, informing agency policy making, 

estimating public health impact, and advising strategic and performance planning. 

Background 

The agency historically used the Annual Sampling Plan to detail sampling results and related activities 

from the previous years, in addition to reporting the planned sampling allocations and activities for the 

current year. Effective FY 2019, FSIS began reporting only the prospective current year planned 

information in the annual sampling plan and developed this report to provide the retrospective 

information, including sampling results. 

Each sampling project has a unique description name and alpha-numeric data system code; both are 

commonly used when discussing sampling projects and are both included in this report. FSIS analyzes 

sampling data and calculates either percent positive or prevalence. Percent positive is the percentage of 

samples of a specific FSIS-regulated product with a specific pathogen detected by sampling. Prevalence 

is the estimated proportion, nationally, of a specific FSIS-regulated product with a specific pathogen. 

More information on the definitions for percent positive, volume-weighted percent positive, and 

prevalence can be found on the FSIS website sampling results data dictionary. 

Summary of Sampling 

FSIS continued to focus on its mission of protecting public health and preventing foodborne illness in 

several different ways. FSIS continued to implement and expand on efforts begun in FY 2019 in 

response to the Strategic Assessment of Sampling Resources (SASR). 

On October 28, 2019, FSIS proposed and requested public comment on an updated Salmonella 

performance standard for raw ground beef and a new Salmonella performance standard for beef 

manufacturing trimmings, a primary component of raw ground beef (80 FR 57688). FSIS proposed both 

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standards to ensure that establishments are consistently controlling or reducing Salmonella, a pathogen 

not ordinarily considered an adulterant in raw beef products. On August 6, 2019, FSIS announced new 

Campylobacter standards for comminuted poultry (84 FR 38203). 

FSIS modernized laboratory technologies for identifying Salmonella. For samples collected after January 

1, 2020, labs began to use whole genome sequencing (WGS)-derived serotyping to identify Salmonella 

strains in place of traditional methods. 

In June 2020, FSIS requested comments on the proposal to expand its routine verification testing for six 

non-O157 Shiga toxin-producing Escherichia coli (STEC) to ground beef, bench trim, and other raw 

ground beef components to further protect public health (84 FR 34397). Currently, FSIS analyzes all 

ground beef, bench trim, and other raw ground beef components for E. coli O157:H7, but only tests its 

beef manufacturing trimmings samples for the six non-O157 STEC. FSIS is currently reviewing the public 

comments. 

In September 2020, in conjunction with USDA’s Office of Food Safety (OFS), FSIS released the Roadmap 

to Reducing Salmonella: Driving Change through Science-Based Policy, which outlines programs and 

policies that are science-based, data-driven, and promote innovation to reduce Salmonella in meat, 

poultry, and egg products. The USDA FSIS Virtual Public Meeting: Salmonella - State of the Science 

meeting information and recordings are available for viewing. 

In August 2020, FSIS convened the National Advisory Committee on Meat and Poultry Inspection 

(NACMPI) to discuss the steps FSIS should take to ensure better control of artisanal, shelf-stable readyto-eat (RTE) fermented, salt-cured, or dried products that rely on multiple hurdles for lethality. In 

addition, NACMPI considered whether the Agency should continue not to test boxed beef primal and 

sub-primal products for Shiga toxin-producing E. coli (STEC), if they are intended for intact cuts (85 FR 

51674). The virtual NACMPI public meeting information is available for viewing. 

FSIS collaborated with U.S. Centers for Disease Control and Prevention (CDC) and the U.S. Food and Drug 

Administration (FDA) to meet the agency’s goal to improve coordination of Federal food safety efforts 

and address cross-cutting priorities for food safety data. FSIS also developed a triage team procedure to 

be initiated when one or more Listeria monocytogenes (Lm) positive food, food contact, or 

environmental FSIS samples are closely related to a historical clinical isolate. The triage team’s summary 

can inform the Public Health Risk Evaluation (PHRE) and any subsequent Food Safety Assessment (FSA) 

performed in response to the Lm positive. 

Beef Products 

FSIS collects samples from Federally inspected establishments and retail firms to verify that 

establishments’ food safety systems are addressing the pathogen effectively and that products are not 

adulterated. Samples from establishments are scheduled monthly by randomly selecting establishments 

from the current population that produce eligible products. The frequency of sampling at any 

establishment is based on the volume of eligible products. FSIS analyzes raw beef products from 

establishments for Escherichia coli (E. coli) O157:H7, non-O157 Shiga toxin-producing E. coli (STEC), and 

Salmonella and samples from retail for E. coli O157:H7 and Salmonella (Table 1). 

FSIS also collects raw beef follow-up samples that are scheduled in response to a positive finding from 

an initial routine verification sample positive at the establishment where FSIS found the positive. For 

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ground beef product or bench trim samples that are positive, FSIS also collects follow-up samples from 

suppliers, when suppliers provided source materials. (Table 1). Follow-up samples are a tool FSIS uses 

to verify whether the establishment has made effective corrective action in response to the initial 

positive detected through routine FSIS verification testing. Follow-up samples may also be collected at 

retail in response to a positive result. 

For more information on source materials sampled, the sample project summary, sample method, and 

product sampled, see the FSIS Directive 10,010.1 Informational Dashboard and select the appropriate 

sample code for more information. 

Table 1. FSIS’ Raw Beef Verification Sampling 

FSIS has five verification sampling codes and corresponding follow-up sampling codes. 

Raw Beef Sampling Sample Project Description Corresponding Follow-Up 

Code Sampling Code 

MT43 Raw ground beef MT53 or MT441 

MT60 Beef manufacturing trimmings produced from MT53 

cattle slaughtered onsite 

MT64 Raw ground beef components other than trim, MT53 

produced from cattle slaughtered onsite 

MT65 Bench trim produced from cattle not MT52 or MT53 

slaughtered onsite 

MT05 Raw ground beef in commerce MT06 1

FSIS also conducts MT44T follow-up sampling for positive samples not from FSIS verification sampling (e.g., 

traceback related to outbreaks). 

In FY 2020, there were a sufficient number of MT43 and MT60 samples to estimate the prevalence of 

STEC in raw ground beef and beef manufacturing trimmings, respectively. Unlike percent positive, 

prevalence calculations incorporate the production volume of each establishment. Though the number 

of positives or percent positive may remain at similar levels each year, a positive from a high-volume 

producer will increase the prevalence more than a positive from a low volume producer. The calculated 

E. coli O157:H7 prevalence in raw ground beef (MT43) in FY2019 was <0.01% and in FY 2020 was 0.14%; 

one large raw ground beef producer with a single positive MT43 sample was a major contributing factor 

to the FY 2020 prevalence value. The calculated E. coli O157:H7 prevalence in beef manufacturing 

trimmings (MT60) in FY 2019 was 0.05% and 0.14% in FY 2020. The calculated non-O157 STEC 

prevalence (MT60) in FY 2019 was 0.51% and 0.13% in FY 2020. 

Salmonella analysis is performed on all raw beef samples. Salmonella prevalence in raw ground beef 

from FSIS-inspected establishments was 2.25% in FY 2019 and 2.89% in FY 2020, and Salmonella 

prevalence in beef manufactured trimmings was 1.44% in FY 2019 and 2.01% in FY 2020. The number of 

samples allocated each year to other raw beef sample projects does not allow FSIS to estimate 

prevalence; instead, those values are reported as percentage positive (Table 2). 

Follow-up samples are assigned based on detection of STEC through routine testing. The elevated levels 

of STEC and Salmonella in follow-up samples, when compared to routine projects, is not unusual. The 

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results are used by FSIS to support compliance determinations and enforcement actions, when 

necessary (Table 3). 

Table 2. FY 2020 Summary of FSIS’ Beef Verification Sampling Programs 

FY 2020 results for FSIS’ five verification sampling codes for detecting E. coli O157:H7 and/or non-O157 

STEC (including O23, O45, O103, O111, O121, and O145) and Salmonella in raw beef product samples. 

Number Prevalence 

Number of of or Percent 

Product Name Establishments Samples Number Type of Positive 

and Project Code Pathogen Sampled Analyzed Positive Calculation1 Calculation 

Raw Ground Beef 

E. coli 

O157:H7 1,200 10,539 7 Prevalence 0.14% 

MT43 Salmonella 

spp. 

1,200 10,540 166 Prevalence 2.89% 

Beef 

E. coli 

O157:H7 488 4,109 10 Prevalence 0.14% 

Manufacturing 

Trim 

non-O157 

STEC 481 4,028 23 Prevalence 0.13% 

MT60 Salmonella 

spp. 

488 4,108 88 Prevalence 2.01% 

Raw Ground Beef E. coli Percent 135 1,294 2 0.15% Components other O157:H7 Positive 

than Trim Salmonella Percent 135 1,294 95 7.34% MT64 spp. Positive 

E. coli Percent 470 1,386 0 0.00% Bench Trim O157:H7 Positive 

MT65 Salmonella Percent 470 1,386 14 1.01% 

spp. Positive 

E. coli Percent Raw Ground Beef 5242 524 0 0.00% O157:H7 Positive In-Commerce Salmonella Percent MT05 5242 525 16 3.05% 

spp. Positive 1Percent positive is 100*(the total number of positive samples divided by the total number of tested samples). Prevalence is a 

more complex, calculated percentage that takes into account establishment production volumes and the volume of 

contaminated product. See the sampling results data dictionary on the FSIS website for a detailed description of prevalence. 2 MT05 ground beef samples are collected from retail firms, not Federal establishments. 

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Table 3. FY 2020 Summary of FSIS’ Beef Follow-Up Sampling Programs 

FY 2020 follow-up testing results in raw beef product samples in response to samples positive for either E. coli O157:H7 or non-O157 STEC in the 

verification sampling projects are shown. 

Number of Number of 

Establishments Samples Number Percent Positive 

Product Name and Project Code1 Pathogen Sampled Analyzed Positive Calculation 

Raw Ground Beef E. coli O157:H7 4 42 0 0.00% 

MT44 Salmonella spp. 4 42 1 2.38% 

Trim and Components 

MT52 

E. coli O157:H7 

non-O157 STEC 

Salmonella spp. 

5 

5 

5 

11 

10 

11 

0 

0 

0 

0.00% 

0.00% 

0.00% 

Beef Manufacturing Trim 

MT53 

E. coli O157:H7 

non-O157 STEC 

Salmonella spp. 

54 

54 

54 

745 

711 

745 

1 

11 

24 

0.13% 

1.55% 

3.22% 

Follow-Up Testing to an E. coli E. coli O157:H7 4 34 3 8.82% 

Positive non-O157 STEC 4 27 0 0.00% 

(Trim or Ground Beef) 

MT44T2 Salmonella spp. 4 34 0 0.00% 

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No MT06, raw ground beef retail follow-up, samples were collected in FY 2020. 2Traceback not at slaughter establishments and dependent on positive findings from other E. coli O157:H7 or on-O157 STEC sampling projects. 

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Pork Products 

FSIS began exploratory sampling of raw pork products in May 2015 to test for pathogens of public health 

concern, as well as for indicator organisms (January 26, 2015, 80 FR 3940). In FY 2020, FSIS announced 

to inspection program personnel the expansion of raw pork sampling in FSIS Notice 41-19, Raw Pork 

Sampling Program (reissued in FY 2021 under FSIS Notice 65-20). This change expanded sampling across 

all eligible official establishments from the limited set of establishments in the FY 2019 exploratory 

phase and grouped non-intact and intact cuts into a single project based on the data collected in the 

exploratory projects. Beginning in November 2019, eligible establishments producing over 6,000 

pounds of not ready-to-eat (NRTE) comminuted pork products (HC_PK_COM01) and establishments 

producing more than 50,000 pounds a day of raw pork cuts (HC_PK_CUT01) receive 5 sample tasks per 

month. Establishments below these thresholds that produce more than 1,000 pounds daily are sampled 

randomly throughout the year. 

FSIS entered into a research collaboration with USDA’s Agricultural Research Service (ARS) to continue 

diagnostics related to STEC in raw pork products sampled by FSIS. As announced in the October 4, 2019, 

Constituent Update, for all raw pork products collected after October 7, 2019, FSIS sent enrichments 

with ARS for further analysis of STEC recovery. Low numbers of samples collected in Table 4 correlate 

with 6 days of sampling at the beginning of FY2020 from October 1 – 6 prior to implementing the change 

on October 7, 2019. 

Table 4. FY 2020 Results for FSIS’ Raw Pork Sampling Program 

FY 2020 exploratory sampling results for detecting E. coli (O157:H7 and non-O157 STEC) and Salmonella 

in raw pork product samples are shown. 

Number of Number of Percent 

Product Name and Establishments Samples Number Positive 

Sampling Code Pathogen Sampled Analyzed Positive Calculation 

E. coli 

O157:H7 6 12 0 0.00% 

Intact Cuts 

EXP_PK_ICT021 

non-O157 

STEC 6 12 0 0.00% 

Salmonella 76 232 8 3.45% 

spp. 

E. coli 

O157:H7 5 14 0 0.00% 

Non-intact Cuts1 

EXP_PK_NCT02 

non-O157 

STEC 5 14 0 0.00% 

Salmonella 36 188 12 6.38% 

spp. 

E. coli 

O157:H7 5 10 0 0.00% 

Comminuted1 

EXP_PK_COM02 

non-O157 

STEC 5 10 0 0.00% 

Salmonella 87 264 60 22.7% 

spp. 

Comminuted 

HC_PK_COM012 

Salmonella 

spp. 

292 5,596 1,267 29.6% 

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Intact and Non-Intact Salmonella Cuts 87 1,826 205 6.75% 

spp. HC_PK_CUT012,3 

1 At the end of October 2019, exploratory (EXP) sampling ended. 2

Beginning in November2019, eligible establishments producing over 6,000 pounds of not ready-to-eat (NRTE) 

comminuted pork products (HC_PK_COM01) and establishments producing more than 50,000 pounds a day of raw 

pork cuts(HC_PK_CUT01) receive 5 sample tasks per month. 3 Beginning in November 2019, all raw pork cuts, 

whether intact or non-intact, are collected under the same sampling code. 

Siluriformes Products 

FSIS began sampling raw fish of the order Siluriformes in May 2016 (FSIS Directive 14,010.1 from eligible 

establishments. In FY 2020, FSIS collected exploratory samples for Salmonella in raw Siluriformes fish 

products that will inform the next steps for food safety verification through routine sampling in the 

future. 

Table 5. FY 2020 Siluriformes Sampling Results 

FY 2020 exploratory sampling results for FSIS raw Siluriformes product sampling are shown. 

Number of Number of Percent 

Product Name and Establishments Samples Number Positive 

Sampling Code Pathogen Sampled Analyzed Positive Calculation 

Raw Siluriformes 

EXP_FI_MIC01 Salmonella 75 599 23 3.8% 

Poultry Products 

FSIS samples Federally inspected establishments to verify whether eligible products meet applicable 

Salmonella performance standards 1. Eligible products were scheduled for sampling 2 to 5 times per 

month throughout the year based on product volume. This allows FSIS to place each product into a 

category based on 24 to 60 sample results. All samples are tested for Salmonella and Campylobacter 

using enrichment methods (Table 6). Other products (quarter or half chicken carcasses, other chicken 

parts (hearts, livers, gizzards; FSIS Notice 42-20), and mechanically separated chicken and turkey) were 

also sampled but at lower numbers per establishment (Table 6). Notably, Campylobacter results in 

Table 6 were derived from the enrichment method. The transition from direct plating to the more 

sensitive enrichment method was announced in the August 27, 2018 Constituent Update. FSIS 

announced new proposed Campylobacter standards for comminuted poultry (84 FR 38203) on August 6, 

2019. 

In FY 2020, FSIS concluded the exploratory sampling for livers, hearts, necks, and gizzards 2 and initiated 

an exploratory sampling program for fowl carcasses slaughtered under the New Poultry Inspection 

System (NPIS)3. 

1 Product eligibility described at https://www.fsis.usda.gov/sites/default/files/media_file/2020-08/10250.1-

Salmonella_Scheduling_Algorithm_Functions.pdf. 

2 As announced in the August 7, 2020 Constituent Update. 

3 As announced in FSIS Notice 25-20. 

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Table 6. FY 2020 Sampling Result Summary for FSIS’ Raw Poultry Sampling Programs 

FY 2020 sampling results for detecting Salmonella and Campylobacter in raw poultry product samples 

are shown. Follow-up samples from previous positives are not included in the calculations. 

Number 

Product Name Number of of Prevalence or 

and Establishments Samples Number Type of Percent Positive 

Sampling Code Pathogen Sampled Analyzed Positive Calculation Calculation 

Salmonella Chicken Whole 205 9,686 456 Prevalence 3.52% 

spp. Carcasses1 

Campylobacter Percent HC_CH_CARC01 205 9,648 1,937 18.42% 

spp.4 Positive 

Chicken Salmonella Percent 51 63 6 9.52% Quarter or Half spp. Positive 

Carcasses1 

Campylobacter Percent EXP_CPT_QH01 50 62 28 45.16% 

2 spp.

4 Positive 

Chicken Parts - Salmonella 479 13,909 1,160 Prevalence 7.62% Legs, Breasts, spp. 

Wings1 Campylobacter Percent 479 13,856 2,280 17.17% HC_CPT_LBW01 spp.

4 Positive 

Other Raw 

Chicken 

1,Parts1,5 

EXP_CPT_OT01 

2,6 

Salmonella Percent 75 145 90 62.07% 

spp. Positive 

Campylobacter Percent 75 146 55 37.67% 

spp. Positive 

Salmonella Comminuted 69 2,057 502 Prevalence 27.19% 

spp. Chicken Campylobacter Percent HC_CH_COM01 69 2,043 94 5.32% 

spp.4 Positive 

Mechanically Salmonella Percent 25 82 66 80.49% Separated spp. Positive 

Chicken2 Campylobacter Percent 25 82 61 74.39% EXP_CH_MSK01 spp.

4 Positive 

Salmonella Turkey Whole 43 1,731 19 Prevalence 0.92% 

spp. Carcasses3 

Campylobacter Percent HC_TU_CARC01 43 1,727 50 2.33% 

spp.

4 Positive 

Salmonella Comminuted 44 1,413 229 Prevalence 17.02% 

spp. Turkey Campylobacter Percent HC_TU_COM01 44 1,404 19 1.28% 

spp.

4 Positive 

Salmonella Percent 14 87 42 48.28% 

spp. Positive 

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Mechanically 

Separated Campylobacter Percent 14 87 29 33.33% Turkey2 spp.

4 Positive 

EXP_TU_MSK01 

1 This sampling uses a product rinse. 

2 Exploratory sampling projects. 

3 This sampling project uses sponge sampling. 

4 Campylobacter results are of samples analyzed using the enrichment method. FSIS began analyzing raw poultry samples using 

the enrichment method on August 27, 2018. 

5 Only Salmonella results are reported for Raw Chicken - Other Parts. 

6 Campylobacter results from the EXP_CPT_OT01 sampling project are based on the direct plating method because the limited 

sample collection volume prevents the use of the enrichment method. 

Table 7. FY 2020 Follow-Up Sampling Result Summary for FSIS’ Raw Poultry Sampling Programs 

FY 2020 follow-up sampling results for detecting Salmonella in raw poultry product samples are shown 

below. Follow-up sampling is assigned when an establishment does not meet a Salmonella performance 

standard. FSIS Salmonella follow-up sampling results provide a snapshot of a specific establishment’s 

performance based on intensified sample collection after the establishment implemented corrective 

actions, which can assist FSIS personnel during a Public Health Risk Evaluation or Food Safety 

Assessment. For this reason, the aggregated set of data reflects FSIS’ efforts to collect follow-up samples 

but does not provide overall information about individual establishment performance. 

Number 

Product Name Number of of Percent 

and Establishments Samples Number Type of Positive 

Sampling Code Pathogen Sampled Analyzed Positive Calculation Calculation 

Chicken Whole Salmonella Percent Carcasses1 40 623 73 11.72% 

spp. Positive F_CH_CARC01 

Chicken Parts - Percent 

Legs, Breasts, Salmonella Positive 95 1361 209 15.36% Wings1 spp. 

F_CPT_LBW01 

Comminuted Percent Salmonella Chicken 13 143 42 Positive 29.37% 

spp. F_CH_COM01 

Turkey Whole Percent Salmonella Carcasses2 1 1 0 Positive 0.00% 

spp. F_TU_CARC01 

Comminuted Percent Salmonella Turkey 15 178 13 Positive 7.30% 

spp. F_TU_COM01 

1 This sampling uses a product rinse. 

2 This sampling uses sponge sampling. 

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Ready-to-Eat (RTE) Products 

FSIS conducts microbiological testing of RTE meat, poultry, and egg products for Lm and Salmonella. Lm 

and Salmonella are adulterants in RTE products. Under various RTE sampling programs, FSIS collects RTE 

product samples and swab samples. More information can be found on the FSIS website: RTE Meat and 

Poultry Products Microbiological Sampling Programs. 

FSIS did not identify notable changes in the percent positive for Lm or Salmonella for RTE sampling 

programs (Table 8). There were fewer Routine Listeria monocytogenes (RLm) samples collected due to 

restrictions put in place due to the CoViD-19 pandemic making it difficult to compare trends although 

the percent positive was still within typical rates. 

In FY 2020, FSIS evaluated Salmonella and Lm percent positive in egg products (Tables 9 and 10). 

Table 8: FY 2020 Ready-to-Eat Product Sampling Results 

FY 2020 sampling results for all FSIS domestic RTE microbiological sampling programs are reported for 

Listeria monocytogenes (Lm) and Salmonella (if applicable). 

Number of Number of Percent 

Product Name and Establishments Samples Number Positive 

Sampling Code Pathogen Sampled Analyzed Positive Calculation 

Listeria 

Post-Lethality Exposed monocytogenes 2,162 6,609 8 0.12% 

(PLE) and non-PLE (Lm) 

products selected 

randomly RTEPROD_RAND Salmonella spp. 2,162 6,609 2 0.03% 

PLE products selected by 

risk 

RTEPROD_RISK 

Listeria 

monocytogenes 

(Lm) 

Salmonella spp. 

1,674 

1,674 

7,517 

7,520 

17 

0 

0.23% 

0.00% 

Intensified Verification 

Testing (IVT/for-cause) 

product 

INTCONT 

Listeria 

monocytogenes 

(Lm) 

Salmonella spp. 

31 

3 

558 

15 

9 

0 

1.61% 

0.00% 

IVT non-food contact 

environmental 

INTENV 

Listeria 

monocytogenes 

(Lm) 

Salmonella spp. 

31 

3 

305 

23 

17 

0 

5.57% 

0.00% 

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IVT product 

INTPROD 

Listeria 

monocytogenes 

(Lm) 

Salmonella spp. 

31 

3 

270 

15 

1 

0 

0.37% 

0.00% 

Routine risk-based Lm 

(RLm/risk-based) food 

contact surfaces 

RLMCONT 

Listeria 

monocytogenes 

(Lm) 

124 1,634 6 0.37% 

RLm non-food contact 

environmental (composite 

of 5-swabs) 

RLMENVC/1/ 

Listeria 

monocytogenes 

(Lm) 

124 164 11 6.71% 

RLm product (composite 

of five 25-gram products 

from same lot) 

RLMPRODC 

Listeria 

monocytogenes 

(Lm) 

125 165 0 0.00% 

/1/ Includes one RLMENVR noncomposited brine sample that was negative. 

In FY 2020, FSIS updated egg products sampling (FSIS Notice 22-20, FSIS Directive 10,230.3). Previously, 

FSIS sampled egg products under seven different project codes. Plants received one sample task per 

month for each sample code for which the plant produced eligible product, regardless of the plant’s 

production volume. For the revision, FSIS condensed the seven sample codes down to two. Inspectors 

at egg product plants now receive up to three sample tasks per month based on the plant’s overall 

production volume. 

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Table 9. RTE Egg Products FY 2020 Salmonella Sampling Results 

FY 2020 microbiological sampling of liquid and dried domestic pasteurized egg products tested for Salmonella are shown. 

Product 

Salmonella (Oct - May) Salmonella (Jun – Sep) 

Sampling 

Code Positive 

Total Percent Positive 

Calculation Code/Product Positive Total 

Percent 

Positive 

Calculation 

EM31 Egg Whites 0 224 0.00% 

EGG_LQ_MIC01– 

Liquid / Frozen Egg 

Products 

1 377 0.26% 

EM32 Whole Egg or Yolks 0 293 0.00% 

EM33 Whole Eggs with Added 

Yolks or Whole Egg Blends 0 155 0.00% 

EM34 Whole Eggs or Yolks with > 

2% Salt or Sugar Added 0 215 0.00% 

EM35 Dried Yellow Egg Products 0 105 0.00% EGG_DY_MIC01– 

Dried Egg Products 0 97 0.00 EM36 Dried Egg Whites 0 76 0.00% 

EM37 Pan Dried Egg White 0 8 0.00% 

Table 10. RTE Egg Products FY 2020 Sampling Listeria monocytogenes Results 

FY 2020 microbiological sampling of liquid and dried domestic pasteurized egg products tested for Listeria monocytogenes are 

shown. 

Product 

Listeria monocytogenes (Lm) 

(Oct - May) 

Listeria monocytogenes (Lm) 

(Jun – Sep) 

Sampling 

code Positive Total 

Percent 

Positive 

Calculation Sampling Code/Product Positive Total 

Percent 

Positive 

Calculation 

EM31 Egg Whites 0 224 0.00% 

EGG_LQ_MIC01– Liquid / 

Frozen Egg Products 0 377 0.00% 

EM32 Whole Egg or Yolks 0 293 0.00% 

EM33 Whole Eggs with Added 

Yolks or Whole Egg 

Blends 0 155 0.00% 

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I 

EM34 Whole Eggs or Yolks 

with > 2% Salt or Sugar 

Added 0 215 0.00% 

EM35 Dried Yellow Egg 

Products 0 105 0.00% EGG_DY_MIC01– Dried 

Egg Products 0 97 0.00 

EM36 Dried Egg Whites 0 76 0.00% 

EM37 Pan Dried Egg White 0 8 0.00% 

National Residue Program 

The U.S. National Residue Program (NRP) sampling plan guides the collection of domestic and imported meat, poultry, and egg product samples. 

Information on the NRP can be found on the FSIS website: Residue Chemistry. 

Domestic Scheduled Sampling Plan 

The domestic sampling plan includes surveillance sampling, inspector-generated, and special project sampling in both Federal and stateinspected slaughter establishments. The NRP requires the cooperation and collaboration of other agencies (Food and Drug Administration (FDA) 

and Environmental Protection Agency (EPA)) for its successful design and implementation. Each year, representatives from FSIS, FDA, EPA, USDA 

Agricultural Research Service (ARS), USDA Agricultural Marketing Service (AMS), and the U.S. Centers for Disease Control and Prevention (CDC), 

convene for a meeting of the Surveillance Advisory Team to evaluate chemical compounds for inclusion in the NRP for the following fiscal year. 

Surveillance Sampling Plan 

Surveillance sampling is the scheduled sampling of specified slaughter subclasses at the time of slaughter after a carcass has passed antemortem 

inspection. In FY 2020, 10 analytical methods were used by FSIS to detect approximately 250 different veterinary drugs, pesticides, and 

environmental contaminants. Of the 7,726 samples analyzed by FSIS (7,304 from U.S. Federal plants and 422 from U.S. State inspected plants), 

31 samples contained violative chemical residues. In total, more than 1,000,000 chemical residues were evaluated in the 7,726 samples 

analyzed under the scheduled sampling plan. 

In comparison to NRP Surveillance sampling from previous years (FY 2016 -- FY 2020), the number of samples collected has remained about the 

same. The violation rate (no. of violations/no. of samples collected) for Surveillance sampling was 0.27% in FY 2019 and 0.40% in FY 2020. In FY 

2020, the detected residue violations consisted of the following residues: moxidectin (4), piperonyl butoxide (3), DDT and metabolites (3), 

atrazine (3), diclofenac (3), lasalocid (3), metolachlor (3), metronidazole (3), tilmicosin (2), and one instance each for bifenthrin, carbadox, 

15 
 

 

ciprofloxacin, enrofloxacin, imidacloprid, pentachlorobenzene, permethrin, and ractopamine. In some cases, sample violations were associated 

with multiple residues in a single sample. 

Table 11: Summary of FY 2020 Surveillance Sampling Residue Results 

FY 2020 summary of surveillance sampling results from FSIS inspector-collected muscle, kidney, and liver tissue from carcasses and parts is 

shown. 

Number of Samples Analyzed by Animal Class 

Animal 

Category 

Animal 

Category 

Number of Samples 

Planned Total 

Samples 

Number of NonDetect Samples 

Number of NonViolative Positives 

Samples 

Number of 

Violative Samples 

Beef Cows 800 850 843 5 2 

Bob Veal 400 420 413 7 --

Dairy Cows 800 863 858 4 1 

Bovine Formula-Fed Veal 75 64 63 -- 1 

Heifers 400 509 483 24 2 

Non-Formula-Fed Veal 75 63 61 1 1 

Steers 400 477 455 22 --

Feral Swine 75 57 56 -- 1 

Porcine Market Swine 

Roaster Swine 

800 

300 

869 

312 

861 

311 

7 

--

1 

1 

Sows 800 715 708 1 6 

Young Chickens 400 397 395 2 --

Poultry Whole Chickens 400 219 218 1 --

Young Turkeys 800 656 649 7 --

Goats 300 298 294 -- 4 

Lambs 100 127 123 4 -- Other Mature Sheep 100 105 103 -- 2 Species Siluriformes (Catfish) 650 564 547 10 7 

Egg Products 400 161 158 1 2 

Annual Total 8,075 7,726 7,599 96 31 

16 
 

 

Table 12: FY 2020 Residue Surveillance Sampling Summarized by Chemical Methods 

FY 2020 residue surveillance collection summary is shown reflecting the number of samples (carcasses) analyzed per chemical method per 

animal class. 

Number of Samples Analyzed per Chemical Method 

Animal 

Category 

Samples 

Collected Aminoglycosides Antifungal 

Dyes Avermectins βeta-Agonists Carbadox Metals 

MultiResidue 

Method 

Nitrofurans Pesticides 

Beef Cows 850 850 -- 91 430 -- 118 850 -- 433 

Bob Veal 420 419 -- 48 208 -- 99 420 -- 212 

Dairy Cows 863 863 -- 100 436 -- 120 863 -- 441 

Formula-Fed Veal 64 64 -- 6 24 -- 1 64 -- 24 

Heifers 509 508 -- 55 253 -- 114 509 -- 256 

Non-Formula Fed Veal 63 63 -- 7 27 -- -- 63 -- 28 

Steers 477 476 -- 55 232 -- 110 477 -- 233 

Feral Swine 57 -- -- -- -- -- -- 7 -- 57 

Market Swine 869 867 -- 94 464 -- 127 869 -- 465 

Roaster Swine 312 -- -- -- -- 311 -- 1 -- --

Sows 715 714 -- 85 350 -- 106 715 -- 351 

Young Chickens 397 396 -- -- -- -- 90 396 169 191 

Whole Chickens 219 219 -- -- -- -- -- 219 213 219 

Young Turkeys 656 654 -- -- -- -- 132 656 315 320 

Goats 298 298 -- 40 -- -- -- 298 -- 145 

Lambs 127 127 -- 24 -- -- -- 127 -- 20 

Mature Sheep 105 105 -- 12 47 -- -- 104 -- 57 

Siluriformes 564 -- 299 -- -- -- 283 563 218 263 

Egg Products 161 -- -- -- 103 -- -- 126 -- 161 

Annual Total 7,726 6,623 299 617 2,574 311 1,300 7,327 915 3,876 

17 
 

 

Table 13. Summary FY 2020 Surveillance Sampling Residue Violations by Animal Class 

List of FY 2020 surveillance sampling residue violations, including specific compound, concentration, tolerance, and regulatory citation by animal 

class is shown. 

Animal Tolerance Authority Tissue Compound Concentration Units Category Level Value (CFR Citation) 

Beef Cow Muscle p,p'-DDE (4,4') * * * CPG Sec. 575.100 

Beef Cow Muscle Diclofenac * * * Not Approved1 

Dairy Cow Muscle Piperonyl Butoxide 0.162 PPM 0.100 40 CFR 180.127 

Eggs -- Lasalocid * * * 21 CFR 556.347 

Eggs -- Lasalocid * * * 21 CFR 556.347 

Feral Swine Muscle DDT and Metabolites * * * CPG Sec. 575.100 

Enrofloxacin 0 * * 21 CFR 556.226 Formula-fed Veal Muscle Ciprofloxacin 0 * * 21 CFR 530.41 

Goat Muscle Moxidectin 40.40 PPB 0.00 21 CFR 556.426 

Goat Muscle Moxidectin 43.10 PPB 0.00 21 CFR 556.426 

Goat Muscle Moxidectin 32.10 PPB 0.00 21 CFR 556.426 

Goat Muscle Moxidectin 35.90 PPB 0.00 21 CFR 556.426 

Heifer Liver Ractopamine 0.114 PPM 0.090 21 CFR 556.570 

Heifer Muscle Diclofenac * * * Not Approved1 

Market Swine Muscle DDT and Metabolites * * * CPG Sec. 575.100 

Mature Sheep Muscle Diclofenac * * * Not Approved1 

Mature Sheep Muscle Pentachlorobenzene * * * Not Approved1 

Non-Formula-fed Liver Tilmicosin 23.30 PPM 1.200 21 CFR 556.735 

Veal Muscle Tilmicosin 3.080 PPM 0.100 21 CFR 556.735 

Roaster Swine Liver Carbadox 130.0 PPB 30 21 CFR 556.100 

Siluriformes Muscle Imidacloprid 

Lasalocid 

0.433 

* 

PPM 

* 

0.050 

* 

40 CFR 180.472 

21 CFR 556.347 

Siluriformes Muscle Atrazine and Metabolites * * * 40 CFR 180.220 

Siluriformes Muscle Atrazine and Metabolites * * * 40 CFR 180.220 

Muscle Metolachlor * * 0.00 40 CFR 180.368 Siluriformes Muscle Atrazine and Metabolites * * * 40 CFR 180.220 

18 
 

 

Animal 

Category Tissue Compound Concentration Units Tolerance Level Value 

Authority 

(CFR Citation) 

Siluriformes Muscle Metolachlor * * 0.00 40 CFR 180.368 

Siluriformes Muscle Metolachlor * * 0.00 40 CFR 180.368 

Siluriformes Muscle Bifenthrin 0.693 PPM 0.500 40 CFR 180.442 

Permethrin (Cis and Trans) 0.089 PPM 0.050 40 CFR 180.378 Sow Muscle Piperonyl Butoxide 0.169 PPM 0.100 40 CFR 180.127 

Sow Muscle Piperonyl Butoxide 0.174 PPM 0.100 40 CFR 180.127 

Sow Muscle Metronidazole * * * Not Approved1 

Sow Muscle Metronidazole * * * Not Approved1 

Sow Muscle Metronidazole * * * Not Approved1 

Sow Muscle p,p'-DDE (4,4') * * * CPG Sec. 575.100 

* Violative residue results were detected but not quantified. 

1Not Approved: the residue detected is not approved for the animal class. 

PPB – parts per billion (μg/kg) 

PPM – parts per million (mg/kg) 

19 
 

 

 

 

 

 

 

 

Inspector-Generated Sampling Plan 

FSIS inspectors may generate non-scheduled samples when they suspect that animals presented for 

slaughter inspection may have violative levels of chemical residues. If an inspector suspects that there is 

misuse of drugs that cannot be detected by the KISTM test, the samples are sent directly to the laboratory 

for appropriate analysis. These samples are reported under the Collector-Generated program. 

In FY 2020, 166,306 Kidney Inhibition Swab (KISTM) tests were conducted on animals selected by FSIS 

(Table 14). In total, 2,783 samples were submitted to FSIS field laboratories for further analysis and, of 

these, 507 chemical residue violations were reported in 419 samples. Due to multiple analyses per 

sample submitted, multiple residue violations may be found in the same sample. The predominant 

violative residues in the inspector-generated samples were ceftiofur (152), penicillin (100), and 

neomycin (37), which account for 30%, 20%, and 7.3% of total violative residues, respectively. 

Dairy cows (63%) and bob veal (18%) accounted for 81% of the 419 violations reported under the 

inspector-generated sampling plan. 

• In FY 2020, desfuroylceftiofur (the primary metabolite of ceftiofur) and penicillin account for 49% 

and 26% of the violations reported in dairy cows, respectively. 

• In FY 2020, of the 180 bob veal samples analyzed at FSIS labs, neomycin accounts for greater than 

49% of the violations reported. 

• In FY 2020, IPP performed a total of 23,297 in-plant KISTM test in swine slaughter classes (market 

swine, sows, roaster swine, boar swine, and feral swine), resulting in only six violative samples 

(0.03%). 

20 
 

Table 14. Summary of FY 2020 Inspector-Generated Sampling (KISTM) Test and Confirmatory Tests 

FY 2020 summary of in-plant screening tests performed using the KISTM test, number of in-plant screens with negative results, number of 

carcasses sent to FSIS laboratory for confirmation, and the number of carcasses (i.e., samples) with violations for each animal class. 

KISTM Test 

Number of Number of 

Total Number of Number of In-plant Samples Samples with 

In-plant Negative Analyzed in FSIS Confirmed Lab 

Animal Category Animal Class Carcasses Carcasses Labs Violations 

Beef Cows 10,284 10,002 276 30 

Bison 2 2 0 0 

Bob Veal 26,880 26,700 180 76 

Bulls 1,382 1,342 41 10 

Bovine Dairy Cows 

Heavy Calves 

87,899 

290 

86,128 

277 

1,779 

13 

263 

4 

Formula-fed Veal 238 231 7 0 

Heifers 4,490 4,385 112 4 

Non-Formula-fed Veal 224 210 14 3 

Steers 9,356 9,164 197 15 

Boar/Stag Swine 78 78 0 0 

Porcine Feral Swine 

Market Swine 

2 

18,227 

2 

18,122 

0 

99 

0 

0 

Roaster Swine 1,575 1,571 4 0 

Sows 3,415 3,383 36 6 

Goats 593 583 12 8 

Other Species Mature Sheep 404 399 2 0 

Lambs 967 957 11 0 

Annual Total 166,306 163,536 2,783 419 

21 
 

 

Table 15. Summary of FY 2020 Inspector-Generated Sampling Residue Violation Results by Chemical Residue and Animal Class 

FY 2020 summary of chemical residue violations reported within the inspector-generated sampling. 

Animal Class 

Chemical Residue 

Beef 

Cow 

Bob 

Veal 

Bull/ 

Stag 

Dairy 

Cow Goat 

Heavy 

Calf Heifer 

Lamb 

NonFormulafed Veal Sow 

Steer 

Total 

Ampicillin -- -- -- 15 -- -- -- -- -- -- -- 15 

Ciprofloxacin 1 5 1 2 -- -- 1 -- -- -- 1 11 

Desethylene Ciprofloxacin -- 4 -- -- -- -- -- -- -- -- -- 4 

Desfuroylceftiofur 6 7 1 129 -- -- 1 -- 1 2 5 152 

Dihydrostreptomycin -- -- -- 1 -- -- -- -- -- -- -- 1 

Dimetridazole -- -- -- 1 -- -- -- -- -- -- -- 1 

Doramectin 2 -- 2 -- -- -- -- -- -- -- -- 4 

Doxycycline -- 1 -- -- -- -- -- -- -- -- -- 1 

Enrofloxacin -- 4 -- -- -- -- -- -- -- -- -- 4 

Florfenicol 3 1 1 1 -- -- 2 -- -- -- 2 10 

Florfenicol Amine -- 1 -- -- -- -- -- -- -- -- -- 1 

Flunixin 1 5 -- 22 -- 1 -- -- -- 2 3 34 

Gentamycin Sulfate 1 2 -- 2 -- -- -- 1 1 -- -- 7 

Ketoprofen -- -- -- 2 -- -- -- -- -- -- -- 2 

Lincomycin 1 -- -- -- -- -- -- -- -- -- -- 1 

Meloxicam -- -- -- 7 -- 1 -- -- -- -- -- 8 

Neomycin -- 37 -- -- -- -- -- -- -- -- -- 37 

Oxytetracycline 1 -- -- 3 8 -- -- -- -- -- -- 12 

Penicillin 12 6 3 70 2 1 1 -- -- 2 3 100 

Phenylbutazone -- -- -- -- -- -- -- -- 1 -- -- 1 

Sulfadimethoxine 1 4 1 30 -- -- -- -- -- -- -- 36 

Sulfadoxine -- -- -- 1 -- -- -- -- -- -- -- 1 

Sulfamethazine 6 1 3 11 -- -- -- -- -- -- 2 23 

22 
 

 

Sulfamethoxazole -- 13 -- -- -- -- -- -- -- -- -- 13 

Sulfathiazole -- 10 -- -- -- -- -- -- -- -- -- 10 

Tetracycline -- -- -- 4 -- -- -- -- -- -- -- 4 

Tilmicosin 1 2 1 3 -- 3 -- -- -- -- 3 13 

Tylosin -- 1 -- -- -- -- -- -- -- -- -- 1 

Annual Total 36 104 13 304 10 6 5 1 3 6 19 507 

Table 16. Summary of FY 2020 Collected-Generated Sampling 

FY 2020 summary of suspect carcass samples sent directly to any FSIS laboratory (collected-generated sampling) for appropriate analysis. 

Number of Non- Number of Non-Detect Number of Violative Animal Category Animal Class Violative Positives Total Samples Samples Samples Samples 

Beef Cow 18 3 1 22 

Bob Veal 2 -- 2 4 

Bull/Stag 1 -- -- 1 Bovine Dairy Cow 39 3 5 47 

Heifer 4 5 1 10 

Steer 52 9 2 63 

Market Swine 27 2 -- 29 

Porcine Roaster Swine 3 -- -- 3 

Sow 1 -- -- 1 

Poultry Young Turkey 1 -- -- 1 

Goat 4 -- -- 4 

Other Species Mature Sheep 1 -- -- 1 

Lamb 8 1 1 10 

Annual Total 161 23 12 196 

23 
 

 

 

 

 

 

 

 

Imports Sampling 

Import Microbiological Sampling 

FSIS conducts port-of-entry reinspection of imported meat, poultry, and egg products. This activity is a reinspection of products that have 

already been inspected and passed by an equivalent foreign inspection system. Thus, imported product reinspection is a means of verifying the 

equivalence of a foreign country’s inspection system on an ongoing basis. Sampling for imported product depends on the volume of shipments 

received by country and product. 

Table 17. Summary of FY 2020 Microbiological Sampling of Imported Products 

FY 2020 microbiological sampling results for imported products by inspection level. The values shown here summarize results over all countries 

and do not reflect the percent positive for individual countries. Additionally, no direct comparisons should be made to domestic sampling. 

Normal Increased1 Intensified2 

Number of Number of Number of 

Product Name and Sampling Samples Number Samples Number Samples Number 

Code Pathogen Analyzed Positive Analyzed Positive Analyzed Positive Total 

Imported Raw Beef 

Manufactured Trimmings or 

Components for use in Ground 

E. coli O157:H7 

non-O157 STEC 

1,411 

1,371 

2 

5 

862 

829 

1 

3 

189 

185 

3 

2 

2,462 

2,385 

Beef or Beef Products 

MT51 

Salmonella spp. 1,410 11 862 5 189 3 2,461 

Imported Raw Ground or E. coli O157:H7 68 1 2 0 -- -- 70 

Comminuted Beef or Veal 

Product 

MT08 

Salmonella spp. 68 0 2 0 -- -- 70 

Micro Pathogen Sampling of RTE 

Products 

Listeria 

monocytogenes 2,727 4 5 0 83 0 2,815 

IMVRTE Salmonella spp. 2,726 0 5 0 83 0 2,814 

Listeria 

Imported Egg Products 111 0 -- -- -- -- 111

monocytogenes EGGIMP 

Salmonella spp. 111 0 -- -- -- -- 111 

Imported Raw and NRTE Poultry Salmonella spp. 766 150 -- -- -- -- 766 

Products 

Campylobacter 765 72 -- -- -- -- 765 IMP_Poultry 

Imported Raw Pork Product Salmonella spp. 329 7 -- -- -- -- 329 
 

 

 

 

 

 

 

 

IMP_Pork 

Imported Siluriformes 

Microbiology Sampling Salmonella spp. 652 2 -- -- -- -- 652 

IMPFISH_MI 1Increased is a level of reinspection above the normal level that is directed by a FSIS management decision. Under increased reinspection, FSIS may hold, on a case-by-case basis, 

lots of imported meat, poultry, or egg products pending receipt of a laboratory analysis. If FSIS does not place the product on hold, the importer of record is still required to hold 

product tested for adulterants by FSIS and is not to allow such product to enter commerce unless and until negative results are received. 

2Intensified is a level of reinspection that is implemented automatically by the Public Health Information System (PHIS) when a Type of Inspection PHIS task is reported as “Fail.” 

Under intensified reinspection, FSIS holds the sampled lot at the official import inspection establishment pending receipt of laboratory analysis. The sampled lot is not allowed to 

move off-site to be held. 

Import Residue Sampling 

Imported meat, poultry, and egg products are sampled through the point-of-entry Import Reinspection Sampling Plan, a chemical residue 

monitoring program, that is conducted to verify whether foreign inspection systems in exporting countries are equivalent to U.S. standards. A 

total of 6,661 samples were analyzed under this program in FY 2020, of which, six samples were violative. Those violative samples originated 

from the following countries: Argentina (2), Canada (2), and Vietnam (2). The results are summarized in Table 18. 

Table 18. Summary of FY 2020 Residue Sampling of Imported Products 

FY 2020 import residue samples by inspection level and production type. 

Normal Increased1 Intensified2 

Number Non-Violative Number of Non-Violative Number of Non-Violative Sampling Code Analytical Method of Violative Violative Annual Positives Samples Positives Samples Positives Samples Samples Samples Total Samples Analyzed Samples Analyzed Samples Analyzed 

Imported Fish 

Products- Antifungal Dyes, Eastern 656 -- -- -- -- -- -- -- 656 Metals, MRM Laboratory 

IMPFISH_CH_E 

Imported Fish Nitrofurans, 609 -- 1 -- -- 31 -- 1 640 Products- Pesticides 
 

 

 

 

 

 

 

Western 

Laboratory 

IMPFISH_CH_W 

Imported -

Metals Metals 357 ---- 597 -------- 954 

IMPMETALS 

Imported -

Pesticide 

IMPPESTICIDE 

Pesticides 807 1 2 574 3 ---- 1,381 

Imported Egg 

Products -

Chemistry 

IMPRESEGG 

Pesticides 37 -------------- 37 

Imported Fresh 

Products -

Residue Eastern 

Lab 

Aminoglycosides, 

Avermectins, 

MRM 

844 3 -- 603 4 5 ---- 1,452 

IMPRESFR_EL 

Imported Fresh 

Products -

Residue 

Western Lab 

IMPRESFR_WL 

Aminoglycosides, 

Beta Agonists, 

MRM, 

Nitrofurans 

742 5 1 579 2 26 5 1 1,347 

Imported 

Processed 

Products -

Residue Eastern Avermectins 107 7 

------------ 107 

Lab 

IMPRESPR_EL 

Imported 

Processed 

Products 

- Sulfonamides 87 

-------------- 87 

Residue 
 

 

 

 

 

Midwestern Lab 

IMPRESPR_MWL 

Annual Total 4,246 16 4 2,353 9 62 5 2 6,661 1Increased is a level of reinspection above the normal level that is directed by a FSIS management decision. Under increased reinspection, FSIS may hold, on a case-by-case basis, 

lots of imported meat, poultry, or egg products pending receipt of a laboratory analysis. If FSIS does not place the product on hold, the importer of record is still required to hold 

product tested for adulterants by FSIS and is not to allow such product to enter commerce unless and until negative results are received. During FY 2020, there were no violative 

samples at increased level of inspection. 2Intensified is a level of reinspection that is implemented automatically by the Public Health Information System (PHIS) when a Type of Inspection PHIS task is reported as “Fail.” 

Under intensified reinspection, FSIS holds the sampled lot at the official import inspection establishment pending receipt of laboratory analysis. The sampled lot is not allowed to 

move off-site to be held. 

Table 19. FY 2020 Import Residue Sampling Violations by Foreign Country/Animal Class 

List of FY 2020 import residue sampling violations (foreign country, specific compound, concentration, tolerance, and regulatory citation) by 

animal class. 

Tolerance Level Authority (CFR Foreign Country Animal Class Compound Concentrations Units Value Citations) 

Argentina Beef Ethion * * * Not Approved1 

Argentina Beef Ethion * * * Not Approved1 

Canada Beef Abamectin 73.8 PPB 20.0 40 CFR 180.449 

Canada Beef 

Doramectin 

Abamectin 

30.9 

49.2 

PPB 

PPB 

30.0 

20.0 

21 CFR 556.222 

40 CFR 180.449 

Vietnam Siluriformes Fipronil * * * Not Approved1 

Vietnam Siluriformes Fipronil * * * Not Approved1 

* Violative residue results were detected but not quantified. 

1Not Approved: the residue detected is not approved for the animal class. 

PPB – parts per billion (μg/kg) 
 

 

 

 

 

 

 

 

 

 

 

 

Whole Genome Sequencing (WGS) Initiatives 

FSIS engaged with Federal partners to establish, advance, and implement the application of whole 

genome sequencing (WGS) data for regulatory purposes. FSIS works to ensure that WGS-related 

projects: (1) align with the goals and objectives of the FSIS Strategic Plan and other policies and (2) 

disseminates information about the use of WGS data analyses to FSIS personnel and stakeholders. 

FSIS laboratories performed WGS on all positive sample isolates for all pathogens from FSIS-regulated 

products. In FY 2020, this equated to ~14,000 bacterial isolate sequences uploaded to National Center 

for Biotechnology Information (NCBI). FSIS modernized Salmonella serotype determination and moved 

to using WGS data to routinely determine the serotype. FSIS laboratories additionally began inputting 

antimicrobial resistance genes, adaptability genes and E. coli virulence genes into the Data Warehouse 

in Quarter Four of FY 2020. The goal of this work is to provide the analyzed WGS data to Agency 

analysts for risk assessment purposes. 

National Antimicrobial Resistance Monitoring System (NARMS)

The National Antimicrobial Resistance Monitoring System (NARMS) is an interagency, collaborative 

partnership with state and local public health departments, the U.S. Food and Drug Administration 

(FDA), the Centers for Disease Control and Prevention (CDC), and the U.S. Department of Agriculture 

(USDA). This national public health surveillance system tracks changes in antimicrobial susceptibility of 

select foodborne enteric bacteria found in ill people (CDC), retail meats (FDA), and food animals (USDA 

FSIS). The NARMS program at FSIS historically focused on two sampling points: samples collected from 

intestinal (cecal) content; and carcass, food commodity or product samples. Until the first quarter of FY 

2020, food animals’ cecal content samples were taken from young chickens, young turkeys, dairy cattle, 

beef cattle, market hogs, and sows and analyzed for pathogens (Salmonella and Campylobacter) and 

indicator bacteria (E. coli and Enterococcus). In February 2020, FSIS implemented cecal content sampling 

for veal, lamb, sheep, and goats and these samples were analyzed for the same NARMS bacteria as the 

other cecal samples. In addition, lymph node sampling was included for dairy and beef cattle with a 

focus only on Salmonella analysis, and the new analysis of E. coli and Enterococcus was included into the 

Siluriformes fish sampling program. As shown in Table 20, in FY 2020, the NARMS program analyzed a 

total of 6,414 NARMS samples. From NARMS sampling in FY 2020, a total of 5,908 bacterial isolates were 

recovered. Antimicrobial Susceptibility Tests (AST) are routinely conducted on all NARMS isolates, and 

WGS is conducted on a selected number of isolates. AST information provides the phenotypic resistance 

information, which is determined using epidemiological cut-off values or clinical breakpoints to interpret 

data. WGS information provides the genotypic resistance information, which is the presence of acquired 

genes and mutations known to enable a bacterium to grow in the presence of higher antimicrobial 

concentrations. These data may be accessed at the FDA NARMS Integrated Data Dashboards. 

Table 20. Summary of FY 2019 NARMS Cecal Sampling Program 

FY 2020 NARMS samples analyzed, isolates recovered, and further characterized. 
 

 

Total Samples Samples Sampling Code Isolates Isolates Characterized Scheduled Analyzed Retrieved 

Salmonella Campylobacter E. coli Enterococcus 

NARMS_YC 

Young Chicken 617 560 914 

WGS - 233 

AST - 236 

WGS - 211 

AST - 222 

WGS - 91 

AST - 227 

WGS - 68 

AST - 219 

NARMS_YT 

Young Turkey 337 349 580 

WGS - 44 

AST - 44 

WGS - 149 

AST - 157 

WGS - 107 

AST - 189 

WGS - 59 

AST - 183 

NARMS_DC 

Dairy Cow 848 769 851 

WGS - 172 

AST - 173 

WGS - 195 

AST - 203 

WGS - 91 

AST - 257 

WGS - 54 

AST - 211 

NARMS_BC 

Beef Cow 416 393 245 

WGS - 31 

AST - 31 

WGS - 51 

AST - 55 

WGS - 39 

AST - 88 

WGS - 15 

AST - 68 

NARMS_ST 

Steer 1076 1001 403 

WGS - 103 

AST - 107 

WGS - 115 

AST - 120 

WGS - 40 

AST - 89 

WGS - 17 

AST - 82 

NARMS_HF 

Heifer 470 410 336 

WGS - 48 

AST - 49 

WGS - 109 

AST - 116 

WGS - 47 

AST - 84 

WGS - 26 

AST - 82 

NARMS_MS 

Market Swine 727 681 824 

WGS - 220 

AST - 224 

WGS - 156 

AST - 162 

WGS - 119 

AST - 224 

WGS - 63 

AST - 207 

NARMS_SW 

Sow 330 304 641 

WGS - 172 

AST - 172 

WGS - 69 

AST - 76 

WGS - 102 

AST - 199 

WGS - 62 

AST - 190 

NARMS_BV 

Bob Veal 150 138 207 

WGS - 44 

AST - 44 

WGS - 7 

AST - 7 

WGS - 38 

AST - 78 

WGS - 22 

AST - 76 

NARMS_FFV WGS - 3 WGS - 3 WGS - 20 WGS - 18 

Formula-Fed 

Veal 

76 73 65 

AST - 3 AST - 3 AST - 30 AST - 29 

NARMS_NFFV WGS - 5 WGS - 11 WGS - 6 WGS - 8 

Non-Formula 

Fed Veal 

72 56 59 AST - 5 AST - 11 AST - 26 AST - 20 

NARMS_GO 

Goat 92 75 84 

WGS - 14 

AST - 14 

WGS - 15 

AST - 16 

WGS - 9 

AST - 26 

WGS - 5 

AST - 24 

NARMS_LB 

Lamb 82 78 110 

WGS - 18 

AST - 18 

WGS - 30 

AST - 30 

WGS - 8 

AST - 33 

WGS - 7 

AST - 28 

NARMS_SH 

Sheep 71 62 81 

WGS - 17 

AST - 17 

WGS - 17 

AST - 17 

WGS - 8 

AST - 24 

WGS - 7 

AST - 23 

Siluriformes N/A1 1264 471 

WGS - 25 

AST - 25 

WGS – N/A 

AST – N/A 

WGS - 38 

AST - 211 

WGS - 58 

AST - 216 

Cattle Lymph 

Nodes 230 201 37 

WGS - 37 

AST - 37 

WGS – N/A 

AST – N/A 

WGS – N/A 

AST – N/A 

WGS – N/A 

AST – N/A 

N/A – not applicable 1Siluriformes NARMS samples are sourced from the Siluriformes microbiology sampling project, EXP_FI_MIC01, and not scheduled 

independently. 

Other Sampling 

FSIS conducts other sampling programs and special projects, in addition to microbiological and chemical 

residue sampling, in response to investigations or other rapidly evolving events to protect consumers 
 

 

 

and ensure food safety. These projects may include for-cause and inspector-generated sampling, such 

as: 

• Advanced meat recovery (AMR) sampling to verify that industry is preventing beef spinal cord 

material from entering the food supply and being misrepresented as meat; 

• Sampling in support of other outbreak or natural disaster investigations; 

• Animal species identification sampling to verify species named in labeling of meat, poultry, and 

egg products; 

• Food chemistry sampling to identify economic fraud or other chemical hazards; 

• Compliance testing to evaluate products in commerce that are suspected to be adulterated or 

misbranded; 

• Pathology testing to identify diseases, parasites, and related conditions in response to in-plant 

public health veterinarian findings from meat and poultry carcasses and parts; and 

• Abnormal container testing when inspection program personnel observe an abnormal container 

being used for thermally processed products. 

These projects may also include routine sampling, such as: 

• Label verification sampling to identify mislabeling, economic fraud, and adulteration of meat, 

poultry, and egg products. 

Conclusion 

In FY 2020, FSIS conducted meat, poultry, and egg products sampling verification to ensure that the food 

produced is safe, wholesome, and properly labeled to protect the public from foodborne hazards. As a 

science-based agency, FSIS uses data to inform decision making and drive continuous improvement of 

processes. FSIS evaluates these sampling data and shares the data, including analyses, on the FSIS 

website. Data sharing and transparency are critical steps to ensure public awareness of the food safety 

measures implemented.