Microbiological Data Program - Annual Summary, Calendar Year 2005 

United States 

Department of 

Agriculture 

Agricultural 

Marketing Service 

Science & 

Technology 

Programs 

Microbiological Data Program 

Progress Update and 2005 Data Summary 

Please Visit Our Website at http://www.ams.usda.gov/science/MPO/MDP.htm 
Microbiological Data Program - Annual Summary, Calendar Year 2005 

United States 

Department of 

Agriculture 

Marketing and 

Regulatory 

Programs 

Agricultural 

Marketing 

Service 

1400 Independence Ave. 

Washington, DC 

20250 

AMS-Agricultural Marketing Service 

An Equal Opportunity Provider and Employer 

March 2006 

To the Reader: 

I am pleased to present the USDA Microbiological Data Program 2005 Data 

Summary. In 2005, MDP tested seven commodities (cantaloupe, leaf and 

romaine lettuce, tomatoes, green onions, cilantro, and parsley). Leaf and 

romaine lettuce were combined as a single commodity with each variety being 

sampled at half the regular sampling rates. Cilantro and parsley were each 

collected at half the regular sampling rates. Based on consultations with the 

U.S. Food and Drug Administration, alfalfa sprouts were introduced as a pilot 

project in October 2005. 

MDP is a partnership with cooperating State agencies that are responsible for 

sample collection and analyses. In 2005, eleven States participated in the 

program: California, Colorado, Florida, Maryland, Michigan, Minnesota, New 

York, Ohio, Texas, Washington, and Wisconsin. Because together these States 

represent all regions of the country and more than half the Nation’s population, 

MDP data can be used to develop inferences about the national food supply. 

This summary is intended to provide the reader with an overview of data 

collected in 2005 and summarizes program refinements made during that year. 

MDP data are important in developing baseline levels of targeted pathogens in 

the domestic food supply. As a continuous data-gathering program, MDP data 

can be used to identify microbial trends and to develop risk models. 

If you have comments or suggestions on how this summary can be improved, 

please send electronic-mail to amsmpo.data@usda.gov or visit our Web site at 

http://www.ams.usda.gov/science/MPO/MDP.htm. 

Sincerely, 

Lloyd C. Day 

Administrator 
Microbiological Data Program - Annual Summary, Calendar Year 2005 

Contents

Page No.

Acknowledgements ........................................................................................................................ vii 

Executive Summary ........................................................................................................................ ix

 

Section I. Introduction..................................................................................................................... 1 

 

Section II. Sampling........................................................................................................................ 3 

 

Section III. Laboratory Operations.................................................................................................. 8 

 

Section IV. Database Management ................................................................................................. 9 

 

Section V. Summary of 2004 Data.................................................................................................. 9 

References ..................................................................................................................................... 14 

Disclaimer ..................................................................................................................................... 14 

Definitions..................................................................................................................................... 14 

 

iii 
Microbiological Data Program - Annual Summary, Calendar Year 2005 

Figures and Tables

Figures Page No. 

 1 MDP Program Planning and Program Testing Operations........................................... 2 

 2 Program Participants .................................................................................................... 3 

 3 Commodity Origin ........................................................................................................ 6 

 

4 MDP Data Pathway .................................................................................................... 10 

 

Tables

 1 Distribution of Imported Samples ............................................................................... 5 

 

 2 Samples Collected and Analyzed by State .................................................................. 7 

 3 Summary of Sample Analysis for Pathogenic E. coli .............................................. 11 

 4 Characterization of Pathogenic E. coli Isolates Screened by mPCR......................... 12 

 5 Summary of Analysis for Salmonella........................................................................ 13 

 6 Salmonella Identification, Serogroup, and Genomic Fingerprinting ........................ 13 

v 
Microbiological Data Program - Annual Summary, Calendar Year 2005 

vii 

Data presented in this report were collected and 

processed through the efforts of the following 

organizations: 

State Agencies

California Department of Food and Agriculture 

California Department of Pesticide Regulation 

Colorado Department of Agriculture 

Florida Department of Agriculture and 

 Consumer Services 

Maryland Department of Agriculture 

Michigan Department of Agriculture 

Minnesota Department of Agriculture 

New York Department of Agriculture and 

 Markets 

Ohio Department of Agriculture 

Texas Department of Agriculture 

Washington State Department of Agriculture 

Wisconsin Department of Agriculture, Trade, 

 and Consumer Protection 

Laboratories

California Department of Food and Agriculture 

Division of Inspection Services 

CDFA Agricultural Microbiology Laboratory 

McClellan Park (McClellan AFB), Bldg. 929 

5431 Arnold Ave. 

Sacramento, CA 95652 

 

Colorado Department of Agriculture 

Inspection & Consumer Services Division 

Laboratory Section 

2331 West 31st Ave. 

Denver, CO 80211-3859 

Florida Department of Agriculture and 

 Consumer Services 

Bureau of Food Laboratories, Bldg. 9 

3125 Conner Blvd. 

Tallahassee, FL 32399-1650 

Michigan Department of Agriculture 

Laboratory Division 

1615 South Harrison Rd. 

East Lansing, MI 48823-5224 

 

Minnesota Department of Agriculture 

Laboratory Services Division 

601 Robert Street North 

St. Paul, MN 55155-2531 

New York Department of Agriculture and 

 Markets 

Food Laboratory 

1220 Washington Ave. 

State Office Campus, Bldg. 7 

Albany, NY 12235 

Ohio Department of Agriculture 

Consumer Analytical Laboratory Bldg. 3 

8995 East Main St. 

Reynoldsburg, OH 43068 

U.S. Department of Agriculture 

Agricultural Marketing Service 

National Science Laboratory 

801 Summit Crossing Pl. 

Gastonia, NC 28054 

 

Virginia Division of Consolidated 

 Laboratory Services 

600 North 5th Street 

Richmond, VA 23219 

Washington State Department of Agriculture 

3939 Cleveland Ave., SE. 

Olympia, WA 98501 

Wisconsin Department of Agriculture, Trade, 

 and Consumer Protection 

Bureau of Laboratory Services 

4702 University Ave. 

Madison, WI 53705 

Acknowledgements 
Microbiological Data Program - Annual Summary, Calendar Year 2005 

viii 

Program Administration

U.S. Department of Agriculture 

Agricultural Marketing Service 

Deputy Administrator, Science and Technology 

 Programs: 

Robert L. Epstein 

1400 Independence Ave., SW., Room 1090-S 

Washington, DC 20250 

Director: 

Martha Lamont 

Monitoring Programs Office 

8609 Sudley Rd., Ste. 206 

Manassas, VA 20110 

(703) 330-2300 x17, Facsimile (703) 369-0678 

E-mail: amsmpo.data@usda.gov

Web site: http://www.ams.usda.gov/science/MPO/

MDP.htm
Microbiological Data Program - Annual Summary, Calendar Year 2005 

ix 

In 2001, the U.S. Department of Agriculture 

(USDA) Agricultural Marketing Service 

(AMS) was charged with implementing microbiological testing of fresh fruit and vegetables 

in the United States. The program’s mission is 

to provide statistically reliable information 

regarding targeted foodborne pathogens and 

indicator organisms on fresh fruit and vegetables. The Microbiological Data Program 

(MDP) is a voluntary data-gathering program, 

not a regulatory enforcement effort. 

AMS coordinates MDP planning and program 

requirements on a continual basis with the 

Centers for Disease Control and Prevention 

(CDC), the Food and Drug Administration 

(FDA), and the USDA National Agricultural 

Statistics Service (NASS). The USDA Agricultural Research Service (ARS) and Food Safety 

and Inspection Service (FSIS) provide consultation as independent research authorities on 

laboratory methods. The participating States 

are an important component of MDP program 

planning activities, particularly those involving 

technical and quality assurance (QA) issues. 

MDP collects produce samples from terminal 

markets and wholesale distribution centers on a 

year-round basis. The MDP sampling frame is 

designed to take into account population and 

consumption on a national scale. In 2005, 11 

States collected fruit and vegetable samples 

(California, Colorado, Florida, Maryland, 

Michigan, Minnesota, New York, Ohio, Texas, 

Washington, and Wisconsin). 

The program tested seven commodities 

(cantaloupe, leaf and romaine lettuce, tomatoes, green onions, cilantro, and parsley) for 

Escherichia coli (E. coli) with pathogenic 

potential and Salmonella. Alfalfa sprouts were 

implemented as a pilot project in October 

2005. Texas collected alfalfa sprouts in place 

of cilantro and parsley and shipped the samples to the USDA National Science Laboratory 

(NSL) for analysis. 

MDP analyzed a total of 11,513 samples. 

Sixty-three percent of the samples were from 

domestic sources, 32 percent were imported, 

and 5 percent were of unspecified origin. MDP 

identified 48 samples carrying pathogenic E. 

coli; however, pathogenic E. coli strains were 

isolated only from 9 samples. These isolates 

were sent to Pennsylvania State University for 

further characterization, including serotyping 

and testing for different virulence-specific 

genes associated with seven different categories of pathogenic E. coli. FDA’s Center for 

Veterinary Medicine (CVM) facility conducted tests on antimicrobial resistance and 

genomic fingerprinting on these isolates. 

MDP screening also resulted in six Salmonella

isolates: one each from cantaloupe and tomato 

and four from parsley. 

A number of important benefits are expected 

from MDP. Microbiological data obtained 

from this fresh produce screening effort will 

contribute significantly to a national produce 

microbiological baseline. The data will enhance the understanding of the microbial 

ecology of fresh fruit and vegetables in the 

food supply and permit the identification of 

long-term trends. Such baseline data, combined with virulence attributes, serotypes, 

antimicrobial resistance, and genomic fingerprints will help collaborators such as CDC and 

FDA in planning public health initiatives. 

Executive Summary 
Microbiological Data Program - Annual Summary, Calendar Year 2005 

1 

I. Introduction 

Many eminent national scientific organizations 

strongly advocate microbiological monitoring (1, 

2). In 2001, Congress authorized funding for a 

microbiological monitoring program to establish a 

microbial baseline for fresh produce. The 

Microbiological Data Program (MDP) was 

established as part of the broader 1997 Presidential 

Food Safety Initiative. 

MDP’s mission is to collect information regarding 

the incidence and identification of targeted foodborne pathogens and indicator organisms on fresh 

fruit and vegetables. This publication provides an 

overview of data collected in 2005 and summarizes program refinements made during that year. 

The Agricultural Marketing Service (AMS) Monitoring Programs Office (MPO) manages MDP and 

is responsible for administrative, sampling, technical, and database activities. This publication is 

available on the Internet at http://www.ams.usda. 

gov/science/MPO/MDP.htm. 

Figure 1 (a) illustrates MDP program planning 

activities. AMS coordinates its planning and program requirements with the Centers for Disease 

Control and Prevention (CDC) and the Food and 

Drug Administration (FDA). The USDA Agricultural Research Service (ARS) and Food Safety and 

Inspection Service (FSIS) provide consultation as 

independent research authorities on laboratory 

methods. Additionally, MDP consults with FDA 

scientists and a university-based eminent microbiologist on technical issues. AMS and USDA’s 

National Agricultural Statistics Service (NASS) 

statisticians designed sampling plans based on per 

capita consumption, marketplace availability, 

product origin, and time in transit and storage. The 

participating States are an important component of 

MDP program planning activities, particularly 

those involving technical and quality assurance 

(QA) issues. 

Figure 1 (b) also depicts MDP program testing 

operations. The participating State laboratories 

and the AMS National Science Laboratory 

(NSL) analyze the MDP samples collected by 

State samplers. FDA’s Center for Veterinary 

Medicine (CVM) and Pennsylvania State University provide additional testing services for isolate 

characterization. Information on MDP data and 

isolates is shared with USDA’s ARS and FSIS, 

CDC, and FDA. 

Commodities tested were selected in consultation 

with FDA and were chosen because they are 

high-consumption fruit and vegetables in the 

U.S. diet, are often consumed raw, and have been 

implicated in outbreaks. Commodities tested in 

2005 included: cantaloupe, leaf and romaine 

lettuce, tomatoes, green onions, cilantro, parsley, 

and alfalfa sprouts. Commodities were tested for 

Escherichia coli (E. coli) strains with human 

pathogenic potential including E. coli O157:H7 

and Salmonella. Isolates of these organisms were 

sent to specialized laboratories for further characterization including serotyping, testing for 

antimicrobial resistance and virulence attributes, 

and genomic fingerprinting. Each MDP laboratory also performed multiplex polymerase chain 

reaction (mPCR) screening for pathogenic E. coli

on samples that tested positive for the presence 

of E. coli. 

Samples were collected in the 11 participating 

States through cooperative agreements with their 

respective agencies (Figure 2). Together these 

States represent over 50 percent of the Nation’s 

population and all geographic regions of the 

country, with significant rural-to-urban variability. Therefore, MDP samples are a statistically 

defensible representation of the country as a 

whole. Also shown in Figure 2 are the 13 

neighboring States that are in the direct distribution networks for the MDP collection States: 

Alaska, Connecticut, Delaware, Hawaii, Idaho, 

Microbiological Data Program (MDP) 

Annual Summary, Calendar Year 2005 

This summary consists of the following sections: (I.) Introduction, (II.) Sampling, (III.) Laboratory 

Operations, (IV.) Database Management, (V.) Summary of 2005 Data 
Microbiological Data Program - Annual Summary, Calendar Year 2005 

2 

Figure 1. MDP Program Planning and Program Testing Operations. This figure illustrates (a) agencies/

groups that support MDP program policy and planning activities, and (b) agencies/groups that analyze 

MDP samples, isolates, or results. 

Food and Drug 

Administration Participating 

States 

(a) MDP Planning 

(b) MDP Program Operations 

Agricultural 

Research 

Service 

Food Safety 

and Inspection 

Service 

National 

Agricultural 

Statistics Service 

Centers for 

Disease Control 

and Prevention 

Agricultural 

Research 

Service 

Participating 

States 

National Science 

Laboratory 

Pennsylvania 

State University 

Food Safety 

and Inspection 

Service 

Centers for 

Disease Control 

and Prevention 

Food and Drug 

Administration / 

Center for Veterinary 

Medicine 
Microbiological Data Program - Annual Summary, Calendar Year 2005 

3 

Massachusetts, Nevada, New Jersey, New 

Mexico, Oklahoma, Vermont, Virginia, and 

Wyoming. 

Microbiology laboratory services were provided 

by nine States (California, Colorado, Florida, 

Michigan, Minnesota, New York, Ohio, Washington, and Wisconsin) and the AMS NSL. The 

Commonwealth of Virginia Division of Consolidated Services Laboratory (DCLS) provided 

method development services during 2005. 

USDA is a member of the interagency Task Force 

on Antimicrobial Resistance established in 1999 

to address antimicrobial resistance, which has 

been identified as a priority food safety and public 

health issue. As such, isolates from positive MDP 

samples were sent to FDA/CVM for antimicrobial resistance testing. These data will be 

added to the National Antimicrobial Resistance 

Monitoring System (NARMS) database. Additionally, CVM performs genomic fingerprinting 

on MDP isolates for inclusion in the PulseNet 

system. 

As the program evolves, procedures and methods 

will be modified and refined to provide information necessary for making science-based food 

safety decisions. AMS continues to improve data 

collection systems and to use improved microbial 

detection methods that are quicker, more reliable, 

and more sensitive. AMS implemented DNAbased testing of samples in October 2003 

following program-wide validation studies and 

introduced DNA-based screening for E. coli

O157:H7 in April 2004. In March 2004, MDP 

Nevada 

Idaho 

Wyoming 

New 

Mexico 

Hawaii 

Alaska 

Virginia

Delaware 

Connecticut 

Massachusetts 

Michigan 

Vermont 

New Jersey 

Figure 2. Program Participants. During 2005, AMS established cooperative agreements with 11 States to 

sample and/or test MDP commodities. Samples collected by Maryland are analyzed by the Ohio 

Laboratory. Samples collected by Texas are analyzed by the National Science Laboratory in Gastonia, 

North Carolina. States that do not participate in MDP’s sampling program but are in the direct 

distribution networks of the participating States are also shown. 

New 

York 

Texas 

California 

Oklahoma 

Washington 

Wisconsin 

Florida 

Participating State 

Minnesota 

States where produce is directly marketed from 

Participating States 

Location of Participating State Laboratories (white stars) 

Federal Laboratory (black star) 

Maryland 

Colorado 

Ohio 
Microbiological Data Program - Annual Summary, Calendar Year 2005 

4 

within a 2-day interval. Samples from a site 

consist of three individual units of produce generally collected from the same container. Inferences 

cannot reasonably be made from the sample units 

to the lots from which they originate because the 

units do not provide enough information to 

produce statistically reliable lot estimates. Nevertheless, statistical methods can be applied to make 

whole target-population inferences from the data 

and to compare these inferences over time. 

MDP benefited from the well-established sampling framework of the Pesticide Data Program 

(PDP), a program administered by MPO since 

1991. States that were already providing sampling 

services for PDP also began collecting samples 

for MDP in 2001 and continue, to date, through 

annual cooperative agreements with AMS. 

The sampling of commodities is conducted at 

distribution centers and terminal (wholesale) 

markets from which food commodities are 

released to supermarkets and grocery stores, 

including domestic and imported commodities 

(refer to Table 1 and Figure 3 for sample origin 

information). Samples are collected weekly on a 

year-round basis and typically over at least two 

growing seasons to accommodate differences in 

growing conditions. Sampling is apportioned 

according to population of the participating State. 

That is, the higher the population of the State, the 

greater the number of samples taken. These 

population-based collection numbers are as follows: California, 14; Colorado, 2; Florida, 7; 

Maryland, 4; Michigan, 6; Minnesota, 2; New 

York, 9; Ohio, 6; Texas, 8; Washington, 4; and 

Wisconsin, 2. This schedule results in a monthly 

target of 64 samples per commodity. Each site 

sample consists of three sub-samples taken from 

the same lot in each facility (each sub-sample is 

treated as a separate laboratory sample) and the 

total number of sub-samples collected every 

month for each commodity is 192. 

Distribution centers and terminal markets in each 

State are selected at random based on probability 

proportional to the site’s distribution volume (i.e., 

the amount of produce that moves through the 

site). Therefore, the larger the site, the greater the 

chance it will be sampled. If the commodity of 

laboratories moved from using the traditional gasproduction method for detection of E. coli to an 

enzyme-based assay. In 2005, mPCR technology 

was used to screen all E. coli positive samples for 

E. coli carrying toxins and therefore potentially 

pathogenic to humans. 

II. Sampling 

The goal of the MDP sampling program is to 

obtain a statistical representation of selected commodities in the U.S. food supply by randomly 

selecting samples from the national food distribution system. The MDP sampling frame is designed 

to take into account regional diversity, population, 

and consumption on a national scale. The sampling 

rationale was developed by MPO in consultation 

with the NASS (3), FDA, and CDC. 

Collecting data over time from a range of sources 

permits statistical statements to be made about the 

distribution of targeted pathogens within the target 

population. The target population is all units of a 

commodity available at the wholesale level in a 

participating State during a defined timeframe 

(e.g., 1 year). The extension of statistical statements to the distribution of microorganisms within 

the inferential population (the entire amount of the 

commodity actually consumed by the U.S. public 

during the same timeframe) requires that strong 

assumptions be made about the relationship 

between the participating States and the U.S. as a 

whole, and between the wholesale and point-ofconsumption levels. Nevertheless, because the 

States that participate in MDP fully represent the 

U.S. inferential population, and many microorganisms may enter the food supply at or before 

the wholesale level, the MDP is a useful and 

defensible baseline survey. 

Based on consultations with FDA, alfalfa sprouts 

were introduced as a pilot project in October 2005. 

Cantaloupe, leaf and romaine lettuce, tomatoes, 

green onions, cilantro, and parsley remained in the 

program at 2004 levels. These crops were selected 

because they are high-consumption fruit and 

vegetables in the U.S. diet, are often consumed 

raw, and have been implicated in outbreaks. All 

samples in a State are collected on the same day or 
Microbiological Data Program - Annual Summary, Calendar Year 2005 

5 

interest is not available at the designated 

primary site, an alternate site may be chosen. 

MDP does not allow samples to be taken from 

public markets or retail stores because of the 

potential for contamination by the consumer and 

because commodity handling practices at this 

level in the distribution chain may vary widely. 

In 2005, 11,513 samples were collected and 

analyzed from over 700 sites across the country. 

Table 2 provides a detailed breakdown of 

sample numbers collected by commodity. As a 

note, cilantro and parsley were treated as a 

single commodity in that each product was 

collected at a half sampling rate (to equal the 

total collected for one commodity). For lettuce, 

either leaf or romaine varieties were eligible for 

sampling. 

All samples are selected, bagged, and packed 

using aseptic techniques (i.e., sterile latex gloves 

and sterile sample bags). Once bagged, samples 

must be properly identified and tamper-proofed 

to ensure that chain-of-custody requirements are 

met. Sufficient frozen ice packs and the use of 

adequate packing materials for cushioning and 

insulation are required to maintain refrigerated 

temperatures during transport. Sample temperatures and the condition of each sample are 

observed and recorded upon receipt at each 

laboratory. If the integrity of a sample is in 

question, the laboratory will request that the 

particular commodity be sampled again. All 

samples are shipped on the same day as sample 

collection by overnight delivery so that 

laboratory analysis can begin the following day. 

Unlike PDP operations, where specific commodities are sent to laboratories specializing in 

the analysis of a particular commodity, MDP 

laboratory analyses are performed in the same 

State from which the sample was collected. 

Exceptions include Maryland and Texas; these 

State samples are shipped to the Ohio laboratory 

and the AMS NSL, Gastonia, North Carolina, 

respectively, for analysis. 

The commodities collected and tested in 2005 

were cantaloupe, leaf and romaine lettuce, 

tomatoes, green onions, cilantro, parsley, and 

alfalfa sprouts. These commodities are harvested 

Table 1. Distribution of Imported Samples. This 

table details the number of imported samples by 

country of origin and by commodity.

Commodity Country 

Number of 

Samples 

Cantaloupe Costa Rica 231 

 Dominican Republic 3 

 Guatemala 396 

 Honduras 273 

 Mexico 60 

 Nicaragua 12 

 Unknown 6 

 981 

 

Cilantro Mexico 165 

 

Green Onions Canada 21 

 Chile 18 

 Costa Rica 3 

 Guatemala 30 

Mexico 1,482 

 1,554 

 

Lettuce Canada 9 

 Mexico 9 

 18 

 

Parsley Canada 12 

 Mexico 165 

 177 

 

Tomatoes Belgium 3 

 Canada 180 

 Mexico 582 

 765 
Microbiological Data Program - Annual Summary, Calendar Year 2005 

6 

Figure 3. Commodity Origin. The proportion 

of domestic, imported or unknown origin for 

each commodity is depicted for samples tested 

in 2005. 

Domestic 55.5% 

Unknown 1.9% 

Imported 42.6% 

Cantaloupe 

Domestic 75.4% 

Unknown 9.9% 

Imported 14.7% 

Cilantro 

Domestic 28.7% 

Unknown 3.5% 

Imported 67.8% 

Green Onions 

Domestic 95.4% 

Unknown 3.8% 

Imported 0.8% 

Lettuce 

Domestic 77.5% 

Unknown 6.7% 

Imported 15.8% 

Parsley 

Domestic 91.7% 

Unknown 8.3% 

Sprouts (Alfalfa)* 

Domestic 58.2% 

Unknown 8.6% 

Imported 33.2% 

Tomatoes *Alfalfa sprouts were implemented as a pilot 

project in October 2005. Samples collected 

by Texas were shipped to the AMS National 

Science Laboratory for analysis. 
Microbiological Data Program - Annual Summary, Calendar Year 2005 

7 

primarily by hand although some mechanical 

harvesting does occur. The produce may be 

packaged in the field or taken to a packinghouse 

(e.g., tomatoes that require classification for color 

and/or size). At the packinghouse, the produce is 

cleaned, trimmed, sized, sorted, wrapped, and 

chilled for preservation until arrival at distribution centers and terminal markets. Cleaning is 

typically accomplished with chlorinated water, 

although other disinfecting agents, such as ozone, 

may be used. Some commodities may have a 

food-grade wax applied to replace natural waxes 

removed during washing to help prevent water 

loss. Fungicides may be added to the wax or 

applied separately to retard spoilage. Chilling 

may be accomplished by various means such as 

vacuum cooling, hydrovac cooling, room chilling, 

or forced air cooling. After initial chilling, the 

produce is stored under chilled conditions 

(avoiding freezing) and, depending on the 

commodity, under low-oxygen atmospheric 

conditions (primarily carbon dioxide). To 

minimize spoilage and bruising, the produce is 

often harvested before reaching full ripeness. 

Prior to shipment to distribution centers and 

terminal markets, some commodities are often 

artificially ripened using techniques such as 

ethylene oxide gassing. Some shipping companies 

transport produce in refrigerated trucks or rail 

cars; others use ice; still others use no method of 

cooling, depending on the commodity. Therefore, 

MDP data reflect not only agricultural practices, 

State 

 

Total E. coli 

E. coli 

O157:H7 Salmonella 

California 507 258 504 504 258 — 507 2,538 2,538 2,538 2,538 

Colorado 72 36 72 72 36 - 72 360 360 360 360 

Florida 252 129 252 252 126 - 252 1,263 1,263 1,263 1,263 

Maryland 144 72 141 141 69 - 144 711 708 711 711 

Michigan 216 108 216 216 108 - 216 1,080 1,080 1,080 1,080 

Minnesota 72 36 72 72 36 - 72 360 360 360 360 

New York 324 162 324 324 162 - 324 1,620 1,620 1,620 1,620 

Ohio 213 102 209 216 108 - 213 1,061 1,059 1,061 1,061 

Texas 288 108 288 285 108 72 288 1,437 1,437 1,435 1,436 

Washington 144 75 144 147 72 - 144 726 726 726 726 

Wisconsin 72 36 72 69 36 - 72 357 357 357 357 

Totals 2,304 1,112 2,294 2,298 1,119 72 2,304 11,513 11,508 11,511 11,512 

Cantaloupe

Cilantro

Green Onions

Lettuce (Leaf or Romaine)

Parsley 

Tomatoes

Note: There were 5 samples that were analyzed for E. coli O157:H7 and Salmonella, but not for E. coli. There 

was 1 sample that was analyzed for E. coli and Salmonella, but not for O157:H7. There was 1 sample that was 

analyzed for E. coli, but not for O157:H7 or Salmonella. This explains the difference between the sample total 

(11,513) and the totals per test. 

Note: Alfalfa sprouts were collected by Texas and analyzed by the National Science Laboratory in place of 

Cilantro and Parsley during October-December 2005. 

Table 2. Samples Collected and Analyzed by State. This table shows the number of samples collected 

by each State by commodity and the total number of collected samples tested for each organism. 

Sprouts (Alfalfa)
Microbiological Data Program - Annual Summary, Calendar Year 2005 

8 

but also handling practices occurring during harvesting, storage (including postharvest treatment), 

and shipping operations. 

MDP uses Sample Information Forms (SIFs) to 

document information required for chain-ofcustody and to capture other information needed to 

characterize the sample. Sample collectors use the 

forms to record information such as: (1) State of 

sample collection; (2) collection date; (3) commodity code; (4) testing laboratory code; and (5) 

sample collector name. Other information collected includes the country of origin of the sample, 

any production claims (such as organic), and any 

postharvest treatments. 

An electronic SIF (e-SIF) capturing system was 

implemented in 2003 and continues to be used to 

record relevant sample information. A customized 

software application allows States to capture SIFs 

electronically using laptop or hand-held computers. Sample information is captured in the 

MDP database files on the same day as sample 

collection. 

MDP sampling operations are conducted with the 

use of Standard Operating Procedures (SOPs) designed to provide consistency across the program 

and ensure the integrity of the analytical data. 

SOPs also contain specific instructions for sample 

selection, shipping and handling, and chain-ofcustody. SOPs are updated as needed and serve as 

a technical reference for conducting program sampling reviews to ensure that program goals and 

objectives are met. All program SOPs are available on the Internet at http://www. ams.usda.gov/

science/MPO/SOPs.htm. 

III. Laboratory Operations 

Ten microbiology laboratories performed analyses 

for MDP in 2005, including multiplex polymerase 

chain reaction (mPCR) screening for the presence 

of pathogenic E. coli in samples that tested positive for E. coli. The laboratories also performed 

cultural analyses to isolate the pathogens from the 

positive samples. Further analyses on the isolates 

were performed by the Gastroenteric Disease Center at Pennsylvania State University and FDA/

CVM. These additional tests included serotyping, 

testing for antimicrobial resistance and virulence 

attributes, and genomic fingerprinting. In 

addition, the Commonwealth of Virginia Division 

of Consolidated Laboratory Services (DCLS) 

performed method development studies for MDP. 

Upon arrival at the testing facility, samples were 

logged, visually examined for acceptability, and 

discarded if determined to be damaged (decayed, 

extensively bruised, or spoiled). Samples were refrigerated until analysis commenced. Laboratories 

were permitted to refrigerate commodities for up 

to 24 hours to allow for different sample arrival 

times from the various collection sites. Only 

excess soil was removed prior to testing. 

Samples were washed in buffered peptone water 

and all analyses were conducted from this surface 

wash eluent. For E. coli assays, an AOAC®-

approved enzyme-based method specific for 

detecting E. coli was used. Enumeration was accomplished using the standard Most Probable 

Number (MPN) method. The presumptive E. coli

positive cultures were screened by each laboratory 

via multiplex DNA-based PCR procedures for 

shiga-toxin-producing E. coli (STEC) and enterotoxigenic E. coli (ETEC). MDP used DNA-based 

PCR assays and automated instruments for the 

detection of Salmonella and enterohemorrhagic E. 

coli O157:H7 in produce samples. Cultural and 

Immunomagnetic Separation (IMS) technology 

were employed for isolation of target bacteria. 

Automated biochemical tests and cultural methods 

were used in the verification of any preliminary 

findings. 

The main objectives of the QA/QC program were 

to ensure the reliability of MDP data and to ensure 

performance equivalency of participating 

laboratories. Direction for the MDP QA program 

was provided through written SOPs based on 

FDA’s 2001 Bacterial Analytical Methods 

(BAM), AOAC® methods, the FSIS Microbiological Laboratory Guide, and the Environmental Protection Agency’s Good Laboratory 

Practices. MDP analytical methods are published 

at http://www.ams.usda.gov/science/MPO/SOPs. 

htm. SOPs provide uniform administrative, 

sampling, and laboratory procedures. 

Positive and negative controls and a sterile media 

blank were required for each sample set. MDP 
Microbiological Data Program - Annual Summary, Calendar Year 2005 

laboratories use positive control strains of E. coli

O157:H7 and Salmonella typhimurium that carry a 

gene coding for Green Fluorescent Protein (GFP). 

Expression of the GFP, detected by exposing the 

cultures to ultraviolet light, indicates the presence of 

the control cultures without having to perform 

lengthy biochemical tests. All controls and blanks 

were taken through the entire analytical procedure. 

MDP laboratories used automated instrumentation 

for confirmation of isolates. 

A Technical Advisory Group, comprised of 

microbiologists from each participating laboratory, 

provided technical feedback on program SOP 

revisions and addressed technical and QA issues. 

Additionally, MDP consulted with scientists from 

other Federal agencies (FDA, ARS and FSIS) and a 

university-based eminent microbiologist on technical issues. For day-to-day QA oversight, each 

participating facility was required to have a Quality 

Assurance Unit (QAU) that operated independently 

from the laboratory staff. Preliminary QA/QC 

review procedures were performed on-site by each 

laboratory’s QAU. Final review procedures are 

performed by MDP staff responsible for collating 

and reviewing data for conformance with SOPs. 

Laboratory performance was monitored through onsite reviews by MDP staff to determine compliance 

with MDP SOPs. Corrective actions, if necessary, 

were performed as a result of on-site reviews. 

IV. Database Management

 

MDP maintains an electronic database that serves as 

a central data repository. The central database 

resides at MPO in Manassas, Virginia. The data 

captured and stored in the MDP database include 

product information and analytical findings for each 

sample collected along with QA/QC results for each 

set of samples. The MDP data pathway is depicted 

in Figure 4. 

MDP utilizes a Web-based Remote Data Entry 

(RDE) system to capture and report MDP data. The 

RDE system is centralized, with all user interface 

software and database files residing in Washington, 

DC. The laboratory users need only a Web browser 

to interface with the RDE system. Access to the 

RDE system is controlled through separate user 

login/password accounts and user access rights 

for the various system functions based on 

position requirements. The RDE system utilizes 

Secure Socket Layer (SSL) technology to encrypt 

all data passed between users’ computers and the 

central Web server. 

A separate Windows-based system allows 

sample collectors to electronically capture the 

standardized Sample Information Form (SIF) on 

handheld or laptop computers. The e-SIF system 

generates formatted text files containing sample 

information that are e-mailed to MDP headquarters and then imported into the Web-based 

RDE system. 

The RDE data entry screens have extensive edits 

and cross-checks built in to ensure that 

acceptable values are entered for all critical data 

elements. This task is made easier by the practice 

of capturing and storing standardized codes for 

all critical alphanumeric data elements rather 

than their complete names, meanings, or 

descriptions. This coding scheme allows for 

faster and more accurate data entry, saves disk 

storage space, and makes it easy to perform 

queries on the database. The data entry screens 

also perform edits on numeric fields, dates, and 

other character fields to ensure that entries are 

within prescribed boundaries. 

At MDP headquarters, the RDE system allows 

scientists to review and approve the data for 

inclusion in the central database. The central 

MDP database is maintained using Microsoft® 

Access in a Windows® operating environment. 

Access to the central MDP database is limited to 

MDP headquarters personnel and is controlled 

through password protection and user access 

rights. The system is backed up each night and 

back-up tapes are sent to off-site storage once a 

week. 

V. Summary of 2005 Data 

Table 1 specifies the distribution of imported 

samples by commodity and country of origin. 

Figure 3 illustrates the proportion of samples that 

9 
Microbiological Data Program - Annual Summary, Calendar Year 2005 

10 

Figure 4. MDP Data Pathway. An illustration of MDP data path from sample collection, through 

laboratory analysis and reporting. 

- 9 State labs + 1 Federal lab for sample testing 

- Standardized sample preparation 

- Test for specific foodborne pathogens

Laboratory Analysis 

Sample Collection

- Collection in 11 States 

- Samples taken close to consumer 

- Standardized Sample Information Form 

- Data entry on handheld/laptop computers

- Web-based data entry software 

- Import data from other systems 

- Access controlled by user login 

- Extensive data cross-checks 

Laboratory Remote Data Entry (RDE) 

Data Review at HQ 

- Scientists review data on-screen 

- Upload data to central database

Year-end Review 

- Data reconciliation

Internet

Internet 

- Standard & adhoc reporting 

- Annual Summary 

Data Reporting 
Microbiological Data Program - Annual Summary, Calendar Year 2005 

were domestic, imported, and of unknown origin 

for each commodity. Sixty-three percent of the 

samples were from domestic sources, 32 percent 

were imported, and 5 percent were of unspecified 

origin. Table 2 shows the distribution of samples 

among each commodity and collection State. 

In 2005, the fourth full year of testing, MDP 

collected 11,513 samples. Of these, 11,508 samples 

were screened for the presence of E. coli; 11,512 

samples were screened for Salmonella; and 11,511 

samples were screened for enterohemorrhagic E. 

coli O157:H7. Table 2 shows the number of 

samples collected and analyzed by each State. E. 

coli has been used as an indicator of fecal 

contamination in food and water; pathogenic E. coli

and Salmonella are frequently implicated in 

foodborne outbreaks where produce was involved 

(1). Consequently, these organisms are of public 

health significance. Baseline data-gathering efforts 

designed to identify relevant trends ideally require 

data generated over multiple growing seasons that 

span several years. Although 2005 provided a 

fourth year of data for MDP, continued data 

collection is needed before multi-year inferences 

can be made. 

The 11,508 samples were initially screened for E. 

coli using an AOAC-official method for detection 

and enumeration. Presumptive E. coli-positive samples were further screened for pathogenic E. coli

that harbor shiga-toxins (STEC) and 

enterotoxins (ETEC) (refer to Table 3) using a 

multiplex polymerase chain reaction (mPCR) 

assay developed by FDA. Toxin genes 

associated with pathogenic E. coli were found in 

48 samples. Successful isolation of pathogenic 

E. coli strains was attained for nine of these samples. In addition to the technological differences 

between the detection by PCR and isolation by 

cultural means, several other factors influence 

the rate of successful isolation including: an 

overwhelming amount of background microflora in comparison to a small number of target 

bacterial cells; differential growth rates of 

various bacteria; and additional growth 

requirements. 

The 9 isolates were sent to Pennsylvania State 

University for serotyping and further characterization, including 13 virulence-specific genes 

associated with different categories of pathogenic E. coli. FDA/CVM conducted tests on 

antimicrobial resistance and genomic fingerprinting on these isolates. The results of testing 

conducted by Pennsylvania State University and 

FDA/CVM are shown in Table 4. The ETEC 

isolate from cilantro was found resistant to 

multiple antimicrobial agents including tetracycline, sulfasoxazole, ampicillin, streptomycin 

and trimethoprim/sulfamethoxazole. The STEC 

isolate from cilantro was found resistant to 

11 

Commodity 

Number of 

Samples Tested 

Number of Pathogenic E. coliPositive Samples 

Cantaloupe 2,304 8 

Cilantro 1,122 8 

Green Onions 2,294 9 

Lettuce 2,298 8 

Parsley 1,119 10 

Sprouts (Alfalfa) 72 2 

Tomatoes 2,299 3 

Total 11,508 48 

Number of Samples 

Screened by mPCR 

748 

721 

655 

1,005 

788 

27 

206 

4,150 

Table 3. Summary of Sample Analysis for Pathogenic E. coli. This table summarizes the 

number of samples initially screened for E. coli and further tested for pathogenic E. coli 

and the number of samples that tested positive for pathogenic E. coli. 
Microbiological Data Program - Annual Summary, Calendar Year 2005 

tetracycline. The two ETEC isolates from parsley 

carried resistance to kanamycin. For an isolate to 

be characterized as a human pathogen and cause 

disease, there must be an interplay of several 

proteins including toxins, encoded by respective 

genes. MDP only identified toxin genes; 

additional testing is required to determine the 

actual pathogenicity of these isolates and is not 

within the scope of MDP. 

In 2005 the BAX® instrument, an automated PCR 

system, was used for screening samples for the 

presence of Salmonella and enterohemorrhagic E. 

coli O157:H7. For all BAX determinations, 

pooled samples were initially screened. If a 

positive result was obtained, the three individual 

samples were tested. Positive individual samples 

were cultured for isolation and identification of 

the organism. Identification of isolates was confirmed using a conventional biochemical testing 

system, an AOAC® performance-tested kit, or a 

MDP-approved commercial biochemical kit or 

system. Isolates were then sent to FDA’s CVM 

for serotyping, antimicrobial resistance testing, 

and genomic fingerprinting. 

12 

As depicted in Table 5, a total of 11,512 samples 

were screened for Salmonella by BAX-PCR. 

Forty-seven of these samples were positive and 

six Salmonella isolates were obtained: one each 

from cantaloupe and tomato and four from 

parsley. These six isolates were sent to FDA’s 

CVM for identification by serotyping, antimicrobial resistance, and genomic fingerprinting. The 

results are shown in Table 6. One isolate, S. 

tucson, belonging to serogroup H, was resistant 

to multiple antimicrobial agents (ampicillin, 

amoxicillin/clavulanic acid, and cefoxitin). Other 

isolates, S. florida and S. gaminara, belonging to 

serogroups H and I, respectively, were found 

sensitive to antimicrobial agents tested. 

No enterohemorrhagic E. coli O157:H7 strain 

was isolated from the 11,511 samples screened, 

although 12 samples tested positive by BAXPCR. In this case, as with pathogenic E. coli

analysis, a number of factors can be involved in 

the rate of isolation, including the level of 

background microflora versus the number of 

target bacterial cells, differential bacterial growth 

rates, and additional growth requirements. 

Commodity 

Pathogenic 

Class 

Toxic Genes 

Identified O Antigen H Antigen 

Cilantro ETEC LT 159 34 

Cilantro STEC Stx neg 31 

Green Onion ETEC ST 170w pos 

Green Onion ETEC LT, ST 126 9 

Lettuce ETEC ST 25 51 

Lettuce STEC Stx 174 36 

Parsley ETEC ST neg 56 

Parsley ETEC ST 70w 56 

Parsley STEC Stx neg 38 

Pulsed-Field Gel Electrophoresis 

Serotyping 

Table 4. Characterization of Pathogenic E. coli Isolates Screened by mPCR. This table provides data obtained 

from additional testing of pathogenic E. coli isolates initially screened by MDP laboratories. Information 

includes: pathogenic class, identified toxin genes, and serotyping results. 

LT - heat-labile toxin 

STx - shigatoxin 

ST - heat-stable toxin 

pos - novel positive reaction that did not fall into any known standards 

neg - no serological reaction; did not react with standard antisera 
Microbiological Data Program - Annual Summary, Calendar Year 2005 

Commodity 

Number of Samples 

Tested 

Number of Positive 

Isolates 

Cantaloupe 2,304 1 

Cilantro 1,122 0 

Green Onions 2,294 0 

Lettuce 2,298 0 

Parsley 1,118 4 

Sprouts (Alfalfa) 72 0 

Tomatoes 2,304 1 

TOTALS 11,512 6 

Number of Positive 

Individual Samples 

8 

0 

9 

22 

3 

0 

5 

47 

Table 5. Summary of Analysis for Salmonella. This table shows the number of 

samples screened for Salmonella, the number of positive individual samples, and the 

number of isolates obtained. 

13 

Commodity Genus Species Serogroup 

Cantaloupe Salmonella carrau H 

Parsley Salmonella tucson H 

Parsley Salmonella florida H 

Parsley Salmonella florida H 

Parsley Salmonella florida H 

Tomato Salmonella gaminara I 

Pulsed-Field Gel Electrophoresis 

Serotype/Identification 

Table 6. Salmonella Identification and Serogroup. This table summarizes the genus, species, and 

serogroup for each of the six Salmonella isolates obtained in 2005. 
Microbiological Data Program - Annual Summary, Calendar Year 2005 

Commodity 

Number of Samples 

Tested 

Number of Positive 

Isolates 

Cantaloupe 2,304 1 

Cilantro 1,122 0 

Green Onions 2,294 0 

Lettuce 2,298 0 

Parsley 1,118 4 

Sprouts (Alfalfa) 72 0 

Tomatoes 2,304 1 

TOTALS 11,512 6 

Number of Positive 

Individual Samples 

8 

0 

9 

22 

3 

0 

5 

47 

Table 5. Summary of Analysis for Salmonella. This table shows the number of 

samples screened for Salmonella, the number of positive individual samples, and the 

number of isolates obtained. 

13 

Commodity Genus Species Serogroup 

Cantaloupe Salmonella carrau H 

Parsley Salmonella tucson H 

Parsley Salmonella florida H 

Parsley Salmonella florida H 

Parsley Salmonella florida H 

Tomato Salmonella gaminara I 

Pulsed-Field Gel Electrophoresis 

Serotype/Identification 

Table 6. Salmonella Identification and Serogroup. This table summarizes the genus, species, and 

serogroup for each of the six Salmonella isolates obtained in 2005. 
Microbiological Data Program - Annual Summary, Calendar Year 2005 

Definitions: 

Antimicrobial resistance: The result of microbes changing in ways that reduce or eliminate the 

effectiveness of drugs, chemicals, or other agents to cure or prevent infections. 

AOAC® INTERNATIONAL: An internationally recognized organization that validates and approves 

analytical methods for foods and agriculture. 

Aseptic: Refers to free of microbial contamination. 

Cultural Methods: Use of rich or selective media for the growth and identification of target bacteria. 

Deoxyribonucleic acid (DNA): The molecule that encodes genetic information required to constitute a 

living and reproducing organism. DNA-based technologies exploit the uniqueness in the DNA sequences of 

a given organism in detection and identification methods. 

Enterohemorrhagic E. coli (EHEC): Strains of E. coli that are the primary cause of hemorrhagic colitis or 

bloody diarrhea, which can progress to the potentially fatal hemolytic uremic syndrome. EHEC are typified 

by the production of verotoxin or Shiga toxins (Stx). E. coli O157:H7 is the prototypic EHEC. 

Enterotoxigenic E. coli (ETEC): Strains of E. coli that are the causative agent of travelers’ diarrhea and 

illness characterized by watery diarrhea with little or no fever. Pathogenesis of ETEC is due to the 

production of any of several enterotoxins, including heat-labile enterotoxin and heat-stable toxin. 

Genomic fingerprinting: Techniques used in the identification and/or classification of organisms exploiting 

the differences in the DNA sequence. 

Green Fluorescent Protein (GFP): Expression of the gene encoding this protein is used as a marker in 

control cultures. 

14 

References: 

1. Scientific Criteria to Ensure Safe Food (2003). Institute of Medicine, National Research Council of the 

National Academies. The National Academies Press, Washington, DC. 

2. Isaacson, R.E., Torrence, M., and Buckley, M.R. Preharvest Food Safety and Security. American Society 

for Microbiology. 2004. 

3. USDA, Agricultural Marketing Service, Science and Technology Programs, AMS Microbiological Data 

Program Sampling Rationale and Principles, February 2002 (rev. 2), http://www.ams.usda.gov/

science/MPO/SamplingOverview.pdf

4. Bacteriological Analytical Manual (BAM) (2001). US Food and Drug Administration, http://

www.cfsan.fda.gov/~ebam/bam-toc.html 

Disclaimer: 

The use of trade, firm, or corporation names, references to published work, and analytical methodology 

referred to in this 2004 Microbiological Data Program Summary is for the information and convenience of 

the reader. Such use does not constitute an official endorsement or approval by the U.S. Department of 

Agriculture of any product, service, or analytical method to the exclusion of others that may be suitable. 
Microbiological Data Program - Annual Summary, Calendar Year 2005 

15 

Indicator organism: A microorganism or group of microorganisms whose presence indicates insanitation or 

fecal contamination. 

Isolate: Target bacterial strain isolated as a pure culture and identified. 

National Antimicrobial Resistance Monitoring System (NARMS): A collaborative effort among the 

Centers for Disease Control and Prevention, the Food and Drug Administration, and the U.S. Department 

of Agriculture to monitor antimicrobial resistance of human enteric bacteria, including Campylobacter, 

Salmonella, Escherichia coli O157:H7, and Shigella. 

Pathogen: Specific causative agent (as a bacterium or virus) of disease. 

Polymerase Chain Reaction (PCR): A technique used to amplify a specific region of DNA into a large 

number of copies in order to produce enough DNA to be adequately tested. PCR can be used to identify, 

with a very high probability, disease-causing viruses and/or bacteria. Multiplex PCR (mPCR) involves 

simultaneous amplification of more than one specific region of DNA or specific genes for various analytes. 

Proficiency test sample: Any matrix sample prepared for the purpose of determining biases, accuracy, and/

or precision among analysts and/or laboratories or of a single analyst or laboratory. 

PulseNet: A national network of local, State, and Federal public health and food laboratories coordinated 

by the Centers for Disease Control and Prevention (CDC) to detect foodborne disease case clusters and 

outbreaks and facilitate identification of the source by standardized genomic fingerprinting (molecular 

subtyping) of various pathogenic bacteria using pulsed-field gel electrophoresis (PFGE) technology. 

Serotyping: An antigen and antibody reaction technique that is used to differentiate strains of 

microorganisms based on differences in the antigenic composition of a certain structure such as the cell 

wall components or flagella. 

Shiga toxin: A family of toxins produced by Shigella dysenteriae type I and Shiga toxin-producing E. coli. 

These toxins have a cytotoxic effect on intestinal epithelial cells that causes the characteristic bloody 

diarrhea. 

Virulence attributes/factors: A bacterial product, usually a protein or carbohydrate (polysaccharide) that 

contributes to virulence or pathogenicity. 

Virulence: The degree or intensity of pathogenicity of an organism as indicated by case fatality rates and/

or ability to invade host tissues and cause disease.

The U.S. Department of Agriculture (USDA) prohibits discrimination in all its programs and activities on the basis of race, 

color, national origin, age, disability, and where applicable, sex, marital status, familial status, parental status, religion,

sexual orientation, genetic information, political beliefs, reprisal, or because all or part of an individual’s income is derived 

from any public assistance program (Not all prohibited bases apply to all programs.) Persons with disabilities who require 

alternative means for communication of program information (Braille, large print, audiotape, etc.) should contact USDA’s 

TARGET Center at (202) 720-2600 (voice and TDD). To file a complaint of discrimination, write to USDA, Director, Office of 

Civil Rights, 1400 Independence Avenue, S.W., Washington, D.C. 20250-9410, or call (800) 795-3272 (voice) or (202) 720-

6382 (TDD). USDA is an equal opportunity provider and employer. 

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