USDA Food Safety and Inspection Service 

Annual Sampling Summary Report 

Fiscal Year 2019 

United States Department of Agriculture 

Food Safety and Inspection Service 

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Table of Contents 

Introduction.............................................................................................................................. 2 

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

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

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

Pork Products ........................................................................................................................ 7 

Siluriformes Products.............................................................................................................. 8 

Poultry Products .................................................................................................................... 8 

Ready-to-Eat (RTE) Products ...................................................................................................10 

National Residue Program......................................................................................................12 

Domestic Scheduled Sampling Plan ......................................................................................12 

Inspector-Generated Sampling Plan......................................................................................14 

Imports Sampling..................................................................................................................16 

Import Residue Sampling ....................................................................................................16 

Imports Microbial Sampling ....................................................................................................18 

Whole Genome Sequencing (WGS) Initiatives............................................................................19 

NARMS................................................................................................................................19 

Other Sampling .....................................................................................................................22 

Conclusion...............................................................................................................................22 

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 FY19 Annual Sampling Summary Report, summarizes the activities and provides an 

overview of results for the products the agency inspected during fiscal year (FY) 2019 (October 1, 2018 

– September 30, 2019). 

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FSIS routinely evaluates sampling data, posts these data to the FSIS website, including establishment 

specific datasets, and shares data through quarterly letters directly with regulated establishments. 

These data include FSIS pathogen verification data, FSIS National Residue Program data, and import and 

export data. The results of these assessments are used in a variety of ways, including monitoring 

effectiveness, overall sanitation, and food safety systems, 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. 

FSIS analyzes sampling data and calculates either percent positive or prevalence. Percent positive is 

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. In FY 2019, FSIS concluded a comprehensive internal evaluation of all sampling 

projects called the Strategic Assessment of Sampling Resources (SASR). During this evaluation, FSIS 

developed several new tools to help optimize the benefits provided by each sampling project. 

FSIS looked for other areas to improve their sampling programs and implemented the following: 

• Microbiological Sampling Programs 

o A revised methodology for assessing whether establishments meet applicable Salmonella 

performance against the current performance standards for poultry products. 

o The implementation of a new Salmonella categorization methodology in response to public 

comments. 

o Calculating and publishing new estimates of the prevalence of Salmonella in pork products. 

o New collaborative work with USDA’s Agricultural Research Service to determine the 

presence of non-O157 Shiga toxin-producing Escherichia coli (STEC) in pork products. 

o The development of a new sampling plan for raw pork products to be implemented in FY 

2020. 

o Publishing new performance standards for Campylobacter in not ready-to-eat (RTE) 

comminuted chicken and turkey. 

• National Residue Program 

o Modernization of the FSIS residue annual sampling plan (formerly known as the Blue 

Book). 

o Updated residue methodology. 

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o Redefined the sampling of lamb and mature sheep. 

o Implemented liquid and dry egg products surveillance for pesticide residues. 

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. In coordination with the CDC, FSIS began using 

whole genome sequencing (WGS) as the primary characterization tool for Salmonella, Campylobacter, 

and E. coli in meat and poultry. 

Beef Products 

FSIS collects samples from federally inspected establishments and retail firms to verify products are not 

adulterated. These samples 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 samples all raw beef products for Escherichia coli (E. coli) 

O157:H7and Salmonella in raw beef product samples; in addition, a subset of raw beef products are 

sampled for non-O157 STEC (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, as well as for traceback to supplier establishments (Table 

1). The follow-up sample may or may not be from the same location as where the initial positive sample 

was collected (i.e., trace back to the supplier). 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. 

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 

Verification Code Sampling Code 

MT43 Raw ground beef MT53 or MT44/1/ 

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 retail MT06 

/1/ FSIS also conducts MT44T follow-up sampling for positive samples not from FSIS verification sampling (e.g., 

traceback related to recalls or from state testing results). 

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In FY 2019, there were a sufficient number of MT43 and MT60 samples to estimate the prevalence of 

STEC. The calculated E. coli O157:H7 prevalence (MT60) in FY 2018 was 0.15% and was 0.05% in FY 2019. 

The calculated non-O157 STEC prevalence (MT60) in FY 2018 was 0.25% and was 0.51% in FY 2019. 

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

from FSIS inspected establishments was 3.36% in FY 2018 and 2.25% in FY 2019, and Salmonella 

prevalence in beef manufactured trimmings was 1.85% in FY 2018 and 1.44% in FY 2019. The number of 

samples allocated each year to other raw beef sampling 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 or Salmonella through routine testing. The 

elevated levels of STEC and Salmonella, when compared to routine projects, is not unusual. The results 

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

(Table 3). Effective February 4, 2019, FSIS started using a harmonized laboratory method for detection 

of both E. coli O157:H7 and non-O157 STEC in the first screen step. This method has been documented 

in the Microbiology Laboratory Guidebook, and stakeholders were informed of this through both a 

Federal Register Notice (84 FR 57688) and a February 1, 2019 Constituent Update. This change affected 

MT60 and all follow-up sampling codes. 

Table 2. FY 2019 Summary of FSIS’ Beef Verification Sampling Programs 

FY 2019 results for FSIS’ five verification sampling codes for detecting Escherichia 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 Type of or Percent 

Product Name Establishments Samples Number Calculation Positive 

and Project Code Pathogen Sampled Analyzed Positive /1/ Calculation 

Raw Ground Beef 

E. coli 

O157:H7 1,211 10,683 8 Prevalence <0.01% 

MT43 Salmonella 

spp. 1,211 10,683 162 Prevalence 2.25% 

Beef 

E. coli 

O157:H7 489 4,077 5 Prevalence 0.05% 

Manufacturing 

Trim 

non-O157 

STEC 477 3,983 34 Prevalence 0.51% 

MT60 Salmonella 

spp. 

489 4,076 75 Prevalence 1.44% 

Raw Ground Beef E. coli Percent 150 1,212 2 0.17% Components O157:H7 Positive 

other than Trim Salmonella Percent 150 1,213 75 6.18% MT64 spp. Positive 

Bench Trim 

E. coli 

O157:H7 466 1,350 1 Percent Positive 0.07% 

MT65 Salmonella 

spp. 

466 1,349 10 Percent 

Positive 0.74% 

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E. coli Percent Raw Ground Beef 531/2/ 531 1 0.19% O157:H7 Positive In Retail Salmonella Percent MT05 531/2/ 531 10 1.88% 

spp. Positive 

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

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. 

Table 3. FY 2019 Summary of FSIS’ Beef Follow-Up Sampling Programs 

FY 2019 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 

Number of of Percent 

Product Name and Establishments Samples Number Positive 

Project Code/1/ Pathogen Sampled Analyzed Positive Calculation 

Raw Ground Beef 

E. coli 

O157:H7 3 31 0 0.00% 

MT44 Salmonella 

spp. 

E. coli 

O157:H7 

3 

2 

32 

61 

0 

1 

0.00% 

1.64% 

Trim and Components 

MT52 

non-O157 

STEC 

2 43 0 0.00% 

Salmonella 

spp. 

E. coli 

O157:H7 

2 

43 

61 

515 

3 

2 

4.92% 

0.39% 

Beef Manufacturing Trim 

MT53 

non-O157 

STEC 41 469 7 1.49% 

Follow-up Testing to an E. 

coli Positive 

(Trim or Ground Beef) 

MT44T/2/ 

Salmonella 

spp. 

E. coli 

O157:H7 

non-O157 

STEC 

Salmonella 

spp. 

43 

9 

9 

9 

515 

31 

31 

31 

20 

0 

0 

0 

3.88% 

0.00% 

0.00% 

0.00% 

/1/ No MT06 samples were collected in FY 2019. 

/2/Traceback not at slaughter establishments and dependent on positive findings from other E. coli O157:H7 or 

non-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). Using the results of these 

exploratory sampling programs, FSIS narrowed its focus to products more likely to be contaminated with 

Salmonella. In October 2019, FSIS announced increased sampling of raw pork products. Raw 

comminuted pork products are sampled under the project code HC_PK_COM01 and raw intact and raw 

non-intact pork products are sampled under the project code HC_PK_CUT01 (FSIS Notice 41-19). 

FSIS Notice 41-19 indicated FSIS schedules five (5) samples per month for eligible establishments 

producing >6,000 pounds per day of comminuted product and eligible establishments producing 

>50,000 pounds per day of pork cuts (intact and non-intact). Sampling is focused on larger 

establishments because they produce the most product and have the highest Salmonella levels. 

Establishments producing 1,001 to 6,000 pounds of comminuted pork products or 1,001 to 50,000 

pounds of pork cuts are randomly selected for sampling tasks. 

FSIS announced the FY 2019 results of the exploratory raw pork sampling program, as well as next steps, 

in an October 4, 2019 Constituent Update (Table 4). 

Table 4. FY 2019 Results for FSIS’ Exploratory Raw Pork Sampling Program 

FY 2019 exploratory sampling results for detecting E. coli (O157:H7 and non-O157 STEC) and Salmonella 

in raw pork product samples are shown. 

Product Name and 

Project Code Pathogen 

Number of 

Establishments 

sampled 

Number of 

Samples 

Analyzed 

Number 

Positive 

Percent 

Positive 

Calculation 

E. coli 

O157:H7 32 493 0 0.00% 

Intact Cuts 

EXP_PK_ICT02 

non-O157 

STEC 32 494 0 0.00% 

Salmonella 

spp. 125 1,345 137 10.19% 

E. coli 

O157:H7 15 362 0 0.00% 

Non-intact Cuts 

EXP_PK_NCT02 

non-O157 

STEC 15 361 0 0.00% 

Salmonella 

spp. 43 1,154 86 7.45% 

E. coli 

O157:H7 42 677 0 0.00% 

Comminuted 

EXP_PK_COM02 

non-O157 

STEC 42 678 3 0.44% 

Salmonella 

spp. 

140 1,667 363 21.78% 

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Siluriformes Products 

In FY 2019, FSIS collected exploratory samples in raw Siluriformes fish products that will inform the next 

steps for food safety verification through routine sampling in the future. 

Table 5. FY 2019 Siluriformes Sampling Results 

FY 2019 exploratory sampling results for FSIS raw Siluriformes product sampling are shown. 

Number of Number of Percent 

Product Name and Establishments Samples Number Positive 

Project Code Pathogen sampled Analyzed Positive Calculation 

Raw Siluriformes Salmonella 73 608 21 3.45% EXP_FI_MIC01 

Poultry Products 

In federally inspected slaughter and processing establishments, FSIS analyzes young chicken and turkey 

carcasses, comminuted chicken and turkey, and chicken parts samples for Salmonella and 

Campylobacter (Table 6). 

FSIS concluded the exploratory sampling for religious exempt and very low volume poultry slaughter 

establishments in FY 2019, as announced in the August 2, 2019 Constituent Update. FSIS increased 

sampling across several verification projects, including poultry carcass and parts sampling, to maximize 

the categorization of eligible establishments relative to the FSIS Salmonella performance standards. This 

change in sampling task assignments was announced in the July 26, 2019 Constituent Update. 

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. 

Table 6. FY 2019 Sampling Result Summary For FSIS’ Raw Poultry Sampling Programs 

FY 2019 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. 

Prevalen 

ce or 

Number Percent 

Product Name Number of of Positive 

and Establishments Samples Number Type of Calculati 

Project Code Pathogen Sampled Analyzed Positive Calculation on 

Salmonella Chicken Whole 207 8,985 415 Prevalence 3.62% 

spp. Carcasses /3/ 

Campylobacter Percent HC_CH_CARC01 207 8,961 1895 21.15% 

spp. /4/ Positive 

Salmonella Percent 63 89 6 6.74% 

spp. Positive 

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Chicken 

Quarter or Half Campylobacter Percent Carcasses /3/ 63 87 29 33.33% 

spp. /4/ Positive EXP_CPT_QH01 

/1/ 

Chicken Parts - Salmonella 478 9,393 859 Prevalence 8.77% Legs, Breasts, spp. 

Wings /3/ Campylobacter Percent 478 9,374 1650 17.60% HC_CPT_LBW01 spp. /4/ Positive 

Other Raw Salmonella Percent 93 286 145 50.70% Chicken Parts /3/ spp. Positive 

/5/ 

Campylobacter EXP_CPT_OT01 spp. /1,6/ 

Salmonella Comminuted 73 2,027 509 Prevalence 27.64% 

spp. Chicken Campylobacter Percent HC_CH_COM01 73 2,016 103 5.11% 

spp. /4/ Positive 

Mechanically 

Separated 

Chicken 

EXP_CH_MSK01 

/1/ 

Salmonella Percent 29 118 89 75.42% 

spp. Positive 

Campylobacter Percent 29 116 79 68.10% 

spp. /4/ Positive 

Salmonella Turkey Whole 46 1,841 12 Prevalence 0.38% 

spp. Carcasses /2/ 

Campylobacter Percent HC_TU_CARC01 46 1,842 29 1.57% 

spp. /4/ Positive 

Salmonella Comminuted 56 1,490 290 Prevalence 21.63% 

spp. Turkey Campylobacter Percent HC_TU_COM01 56 1,477 41 2.78% 

spp. /4/ Positive 

Mechanically 

Separated 

Turkey 

EXP_TU_MSK01 

/1/ 

Salmonella Percent 16 102 48 47.06% 

spp. Positive 

Campylobacter Percent 16 102 31 30.39% 

spp. /4/ Positive 

/1/ Exploratory sampling projects. 

/2/ This sampling project uses sponge sampling. 

/3/ This sampling project uses a product rinse. 

/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 generated using the direct plating method instead of 

the enrichment method because there is a limited sample collection volume. 

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

FY 2020 follow-up sampling results for detecting Salmonella and Campylobacter in raw poultry product 

samples are shown. FSIS Salmonella follow-up sampling results provide a snapshot of a specific 

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establishment’s performance based on intensified sample collection after the establishment 

implemented corrective actions. For this reason, the aggregated set of data reflects FSIS’ efforts to 

implement follow-up samples but does not provide overall information about performance without 

additional context. 

Number 

Product Name Number of of Percent 

and Establishments Samples Number Type of Positive 

Project Code Pathogen Sampled Analyzed Positive Calculation Calculation 

Chicken Whole 

Carcasses /3/ 

F_CH_CARC01 

Salmonella 

spp. 29 552 68 Percent Positive 12.32% 

Chicken Parts - Percent 

Legs, Breasts, 

Wings /3/ 

F_CPT_LBW01 

Salmonella 

spp. 80 1327 194 Positive 14.62% 

Comminuted 

Chicken 

F_CH_COM01 

Salmonella 

spp. 12 169 51 

Percent 

Positive 30.18% 

Turkey Whole 

Carcasses /2/ 

F_TU_CARC01 

Salmonella 

spp. 0 0 0 

Percent 

Positive --

Comminuted 

Turkey 

F_TU_COM01 

Salmonella 

spp. 13 199 47 

Percent 

Positive 23.62% 

Ready-to-Eat (RTE) Products 

FSIS conducts microbiological testing of post-lethality exposed (PLE) and not PLE-exposed RTE meat, 

poultry, and egg products for Lm and Salmonella in domestically produced RTE and egg products. 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. 

Table 8: FY 2019 Ready-to-Eat Product Sampling Results by Project 

FY 2019 sampling results for all FSIS domestic RTE microbiological sampling programs are reported for 

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

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Number of Number of Percent 

Product Name and Establishments Samples Number Positive 

Project Code Pathogen Sampled Analyzed Positive Calculation 

PLE and non-PLE Listeria 2,211 6,973 16 0.23% products selected monocytogenes 

randomly Salmonella spp. 2,211 6,986 4 0.06% RTEPROD_RAND 

PLE products 

selected by risk 

Listeria 

monocytogenes 1,688 7,558 14 0.19% 

RTEPROD_RISK Salmonella spp. 1,689 7,571 3 0.04% 

Intensified 

Verification Testing 

(IVT/for-cause) 

Listeria 

monocytogenes 

53 1,016 6 0.59% 

product 

INTCONT 

Salmonella spp. 6 55 0 0.00% 

IVT non-food 

contact 

Listeria 

monocytogenes 

53 515 14 2.72% 

environmental 

INTENV Salmonella spp. 6 88 1 1.14% 

IVT product 

INTPROD 

Listeria 

monocytogenes 

Salmonella spp. 

53 

6 

489 

55 

5 

0 

1.02% 

0.00% 

Routine risk-based 

Lm (RLm) food 

contact surfaces 

Listeria 

monocytogenes 190 2,637 5 0.19% 

RLMCONT 

RLm non-food 

contact 

environmental 

(composite of 5-

Listeria 

monocytogenes 

190 267 25 9.36% 

swabs) 

RLMENVC 

RLm product 

(composite of five 

25-gram products 

from same lot) 

Listeria 

monocytogenes 190 264 2 0.76% 

RLMPRODC 

Table 9. RTE Egg Products FY 2019 Sampling Results by Project 

FY 2019 microbiological sampling of liquid and dried domestic pasteurized egg products 

regulated by FSIS are shown. More information can be found on the FSIS website: 

Quarterly Sampling Reports on Ready-to-eat Products and Egg Products. 

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Product Name Number of Number of 

and Project Establishments Samples Number Percent Positive 

Code Pathogen Sampled Analyzed Positive Calculation 

Listeria 

Egg Whites 36 351 0 0.00% monocytogenes EM31 Salmonella spp. 36 354 1 0.28% 

Whole Egg or 

Yolks 

Listeria 

monocytogenes 45 433 0 0.00% 

EM32 Salmonella spp. 45 442 1 0.23% 

Whole Eggs 

with Added 

Listeria 

monocytogenes 26 235 0 0.00% 

Yolks or Whole 

Egg Blends Salmonella spp. 26 241 0 0.00% 

EM33 

Whole Eggs or 

Yolks with > 2% 

Listeria 

monocytogenes 

40 345 2 0.58% 

salt or sugar 

added Salmonella spp. 40 348 0 0.00% 

EM34 

Dried Yellow 

Egg Products 

Listeria 

monocytogenes 16 139 0 0.00% 

EM35 Salmonella spp. 16 139 0 0.00% 

Dried Egg 

Whites 

Listeria 

monocytogenes 11 116 0 0.00% 

EM36 Salmonella spp. 11 116 0 0.00% 

Pan Dried Egg 

White 

Listeria 

monocytogenes 1 12 0 0.00% 

EM37 Salmonella spp. 1 12 0 0.00% 

National Residue Program 

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

Domestic Scheduled Sampling Plan 

Scheduled sampling is the sampling of specified slaughter subclasses at the time of slaughter after a 

carcass has passed antemortem inspection. Of the 7,767 samples analyzed by FSIS, (7,312 from 

federally regulated plants and 455 from State inspected plants), 21 chemical residue violations were 

found. 

In comparison to previous years’ domestic scheduled sampling (FY 2016 – FY 2019), the number of 

samples collected has remained the same, but the violation rate (below 0.4%) has been declining since 

2016. In FY 2019, the detected residue violations consisted of the following residues: piperonyl 

butoxide (2), moxidectin (2), carbadox (3), florfenicol (2), atrazine (2), metolachlor (3), and one each for 

doramectin, salbutamol, ceftiofur, clothianidin, heptachloraobenzene, and tetracycline. 

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In FY 2019, FSIS sampled and analyzed egg products and did not report any violations. 

Overall, the violation rate for the domestic scheduled sampling plan has remained below 0.4% for the 

last 4 years. In the cattle class, there was a decline in violation rate for heifers. All swine violations 

reported in FY 2019 were from violative residues of carbadox in roaster swine. For species considered 

minor class, such as lamb/sheep and goats, the increase in violation in sheep was not significant (Table 

10). 

Table 10: FY 2019 Scheduled Residue Sampling Results Summary 

FY 2019 sampling results for FSIS chemical residue sampling are shown. FSIS inspectors collect muscle, 

kidney, and liver tissue from carcasses and parts for laboratory analysis. Annual totals are included in 

the figure below to provide complete information typically found in the National Residue Program 

(NRP) sampling plan. FSIS has harmonized and incorporated the NRP sampling plan into the FSIS 

Annual Sampling Plan and is no longer publishing them separately. 

Number of Samples Analyzed by Animal Class 

Number 

of NonViolative Number of 

Animal Total Number of Non- Positives Violative 

Category Animal Class Samples Detect Samples Samples Samples 

Beef Cows 808 799 6 3 

Bob Veal 391 387 3 1 

Bulls 87 87 - -

Dairy Cows 808 802 3 3 

Formula-Fed Veal 56 56 - - Bovine Heavy Calves 64 64 - -

Heifers 516 513 3 -

Non-Formula-Fed 

Veal 64 63 - 1 

Steers 500 497 2 1 

Feral Swine 99 98 - 1 

Porcine Market Swine 

Roaster Swine 

823 

396 

822 

391 

1 

2 

-

3 

Sows 731 729 2 -

Young Chickens 733 732 1 - Poultry Young Turkeys 647 647 - -

Goats 282 281 - 1 

Other Lambs/Sheep 161 157 2 2 

Species Siluriformes Fish 582 567 10 5 

Egg Products 19 19 - -

Annual 7,767 7,711 35 21 Total 

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Inspector-Generated Sampling Plan 

FSIS inspectors conduct inspector-generated sampling when they suspect that animals presented for 

slaughter inspection may have violative levels of chemical residues. In FY 2019, 174,308 Kidney 

Inhibition Swab (KISTM) tests were conducted (Table 11). Of those, 3,569 samples were submitted to 

FSIS field laboratories for further analysis and 606 chemical residue violations were reported in 523 

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 (179), penicillin (141), and sulfadimethoxine (59), which account for 30%, 23%, and 9.7% of 

total violative residues, respectively. 

Dairy cows (71%) and bob veal (14%) accounted for 85% of the 606 violations reported under the 

inspector-generated sampling plan. 

• In FY 2019, dairy cow percent violation rates (violations/number of samples screened) using the 

KISTM test decreased significantly. Of the 2,294 dairy cow samples, desfuroylceftiofur (the 

primary metabolite of ceftiofur) and penicillin account for 6.8% and 4.9% of the violations 

reported, respectively. 

• In FY 2019, of the 247 bob veal samples analyzed at FSIS labs, neomycin accounts for greater 

than 10% of the violations reported. 

• In FY 2019, IPP performed a total of 20,360 KISTM tests in swine slaughter classes (market swine, 

sows, roaster swine, boar swine, and feral swine), resulting in only 8 violative samples (0.03%). 

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Table 11. Summary of FY 2019 Inspector-Generated Sampling (KISTM) Test and Confirmatory Tests 

FY 2019 sampling results for FSIS inspector-generated KISTM Residue Tests. Annual totals are included in the figure below to provide complete 

information typically found in the NRP sampling plan. FSIS has harmonized and incorporated the NRP sampling plan into the FSIS Annual 

Sampling Plan and is no longer publishing them separately. 

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 9,323 9,057 275 24 

Bison 1 1 0 0 

Bob Veal 30,709 30,462 247 73 

Bulls 1,335 1,293 44 3 

Bovine Dairy Cows 

Heavy Calves 

96,608 

225 

94,371 

206 

2,294 

19 

371 

1 

Formula-fed Veal 345 334 11 0 

Heifers 3,816 3,690 129 10 

Non-Formula-Fed Veal 255 208 43 12 

Steers 8,783 8,538 255 18 

Boar/Stag Swine 92 91 1 0 

Porcine Feral Swine 

Market Swine 

6 

15,116 

6 

14,951 

0 

166 

0 

1 

Roaster Swine 1,437 1,428 9 1 

Sows 3,709 3,654 56 6 

Goats 672 666 8 2 

Other Species Mature Sheep 565 562 5 0 

Lambs 1,311 1,307 7 1 

Annual Total 174,308 170,825 3,569 523 

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Imports Sampling 

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 3,501 product samples were analyzed under this program in FY 2019, of which, seven samples were violative. Those violative samples 

originated from the following countries: Costa Rica (1), Netherlands (1), Mexico (2), and Vietnam (3). The results are summarized in Table 12. 

Table 12. Summary of FY 2019 Residue Sampling of Imported Products 

FY 2019 import residue samples by inspection level, per exporting country and production type. The number of violations are given in 

parentheses. Annual totals are included in the figure below to provide complete information typically found in the National Residue Program 

(NRP) sampling plan. FSIS has harmonized and incorporated the NRP sampling plan into the FSIS Annual Sampling Plan and is no longer 

publishing them separately. 

Number Samples by Inspection Level and Product Type (Violations) 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Country Normal Increased/1/ Intensified/2/ 

Raw Processed Raw Raw Processed Total 

Argentina 109 -- -- -- -- 109 

Australia 131 -- -- -- -- 131 

Brazil 48 125 -- 3 11 187 

Canada 416 57 -- -- -- 473 

Chile 122 -- 1 -- -- 123 

China 75 -- -- -- -- 75 

Costa Rica 50 (1) -- -- -- -- 50 (1) 

Denmark 22 2 -- -- -- 24 

Finland 22 -- -- -- -- 22 

France 41 1 -- -- -- 42 

Germany -- 3 -- -- -- 3 

Honduras 16 -- -- -- -- 16 

Iceland 2 -- -- -- -- 2 

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Number Samples by Inspection Level and Product Type (Violations) 

Country Normal Increased/1/ Intensified/2/ 

Raw Processed Raw Raw Processed Total 

Ireland 41 -- -- -- -- 41 

Israel -- 21 -- -- -- 21 

Italy -- 11 -- -- -- 11 

Japan 15 -- -- -- -- 15 

Korea, Republic Of -- 1 -- -- -- 1 

Lithuania -- 11 -- -- -- 11 

Mexico 101 (1) 7 1 14 (1) -- 123 (2) 

Namibia 20 -- 22 -- -- 42 

Netherlands 64 (1) 5 -- 12 -- 81 (1) 

New Zealand 203 1 -- -- -- 204 

Nicaragua 22 -- -- -- -- 22 

Northern Ireland 34 -- -- -- -- 34 

Poland 19 2 -- -- -- 21 

Spain 20 -- -- -- -- 20 

United Kingdom 39 -- -- -- -- 39 

Uruguay 47 2 14 -- 5 68 

Vietnam 1,414 (3) -- 12 64 -- 1,490 (3) 

Annual Total 3,093 (6) 249 50 93 (1) 16 3,501 (7) 

/1/Increased 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. 

/2/Intensified 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. 

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Imports Microbial Sampling 

Lab sampling for imported product, through product or rinsate sample collection, depends on the number of shipments received by country and 

product. 

Table 13. Summary of FY 2019 Import Microbiology Sampling Results by Project 

FY 2019 microbiological sampling results for FSIS imported products by inspection level. The values 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 Increased/1/ Intensified/2/ 

Number of Number of Number of 

Product Name and Project Samples Number Samples Number Samples Number Total 

Code Pathogen Analyzed Positive Analyzed Positive Analyzed Positive Samples 

Imported Raw Beef E. coli O157:H7 840 2 22 0 61 0 923 

Manufactured Trimmings or 

Components for use in Ground non-O157 STEC 800 2 22 1 60 0 882 

Beef or Beef Products 

MT51 Salmonella spp. 840 4 22 0 61 0 923 

Imported Raw Ground or 

Comminuted Beef or Veal 

Product 

MT08 

E. coli O157:H7 

Salmonella spp. 

43 

43 

0 

0 

--

--

--

--

--

--

--

--

43 

43 

Micro Pathogen Sampling of RTE 

Products 

Listeria 

monocytogenes 2,765 3 53 0 65 0 2,883 

IMVRTE Salmonella spp. 2,766 0 53 0 65 0 2,884 

Imported Egg Products 

EGGIMP 

Listeria 

monocytogenes 

Salmonella spp. 

131 

131 

0 

0 

--

--

--

--

--

--

--

--

131 

131 

Imported Raw and NRTE Poultry Salmonella spp. 687 137 -- -- -- -- 687 

Products Campylobacter 686 70 -- -- -- -- 686 IMP_Poultry 

Imported Raw Pork Product 

IMP_Pork Salmonella spp. 338 8 -- -- -- -- 338 

Imported Siluriformes 

Microbiology Sampling Salmonella spp. 745 1 -- -- -- -- 745 

IMPFISH_MI 

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/1/Increased 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. 

/2/Intensified 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. 

Whole Genome Sequencing (WGS) Initiatives 

FSIS engages with Federal partners to establish, advance, and implement the application of whole genome sequencing (WGS) data for regulatory 

purposes. FSIS: (1) works to ensure that WGS related projects 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 samples for all pathogens from FSIS-regulated products. In FY 2019, this equated to 15,240 sequences 

uploaded to National Center for Biotechnology Information (NCBI). In addition, FSIS implemented updated software for all pathogen 

bioinformatic analysis and modernized Campylobacter speciation via species determination through WGS. 

In FY 2019, FSIS partnered with USDA Agricultural Research Service (ARS) to evaluate the utility of long-read sequencing technology to 

complement FSIS’s current short-read approach. FSIS also collaborated with ARS and the Centers for Disease Control and Prevention (CDC) to 

capture emerging antimicrobial resistance genotypes of Salmonella. 

FSIS initiated real-time WGS result reporting for Lm to help District Offices and field inspectors to evaluate multiple findings of Lm in the same 

establishment. Such findings can indicate Lm harborage or cross-contamination events. 

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 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 USDA focuses on two sampling points—samples collected from intestinal (cecal) 

content and carcass or food commodity samples. Food animals cecal content samples are taken from young chickens, young turkeys, dairy 

cattle, beef cattle, market hogs, and sows and analyzed for pathogens, including Salmonella and Campylobacter, and the bacterial indicators 

Escherichia coli (E. coli) and Enterococcus. 

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In FY 2019, there were 6,206 NARMS cecal content samples analyzedwith 9,122 total bacterial isolates recovered, as summarized in Table 14. 

All the isolates were further characterized for antimicrobial resistance/susceptibility. All 1,636 Salmonella and 2,664 Campylobacter isolates, 

1,023 of the 2,466 E. coli, and 653 of the 2,296 Enterococcus recovered isolates were subject to WGS (Table 14). 

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Table 14. Summary of FY 2019 NARMS Cecal Sampling Program 

FY 2019 NARMS samples analyzed, isolates recovered, and further characterized. 

Further Isolates Characterized 

Sampling Samples Total Isolates Characteristics 

Code Analyzed Retrieved Analysis Salmonella Campylobacter E. coli Enterococcus 

Young Chicken WGS 427 540 148 106 856 1635 NARMS_YC AST 430 548 323 326 

Young Turkey WGS 66 215 131 62 434 718 NARMS_YT AST 66 216 218 214 

Dairy Cow WGS 261 487 145 102 1264 1656 NARMS_DC AST 261 483 451 445 

Beef Cow WGS 52 109 67 49 510 524 NARMS_BC AST 52 111 182 177 

Steer WGS 120 628 190 110 1203 1647 NARMS_ST AST 120 627 483 402 

Heifer WGS 61 323 92 64 640 863 NARMS_HF AST 62 328 250 216 

Market Swine 1610 WGS 475 286 199 124 1026 NARMS_MS AST 480 288 434 402 

Sow WGS 165 63 51 36 273 469 NARMS_SW AST 165 63 125 114 

The total numbers of isolates as well as whole genome sequencing (WGS) and antimicrobial susceptibility testing (AST) isolates do not match because: 

• The “Total Isolates Retrieved” column reflects the number of isolates logged from positive ceca samples regardless of isolate characterization progress 

and the “Isolates Characterized” columns reflect isolate numbers that have been completed and authorized and so do not include isolates where testing 

is still in progress. 

• The WGS and AST numbers are not the same due to delay in WGS which is an outcome of reagent delays (e.g., Campylobacter) 

• These numbers will change as WGS work continues and WGS-based Campylobacterspeciation is used. 

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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: 

• 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; 

• Foodborne illness and outbreak sampling in response to potential illness outbreaks; 

• Label verification sampling to identify mislabeling, economic fraud, and adulteration of meat, poultry, and egg products; 

• Species identification sampling to verify species claims 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 abnormal containers of thermally processed products. 

Results for these other sampling projects are not detailed in this report because the types of results for each project are unique to that project. 

Additionally, some of the results from these projects are used in ongoing investigations and cannot be publicly posted. The actual number of 

samples analyzed for each of these projects is included in the Annual Sampling Plan. 

Conclusion 

In FY 2019, 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. 

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