Microbiological Data Program - Annual Summary, Calendar Year 2006 

United States 

Department of 

Agriculture 

Agricultural 

Marketing Service 

Science & 

Technology 

Programs 

Microbiological Data Program 

Progress Update and 2006 Data Summary 

Please Visit Our Website at http://www.ams.usda.gov/science/MPO/MDP.htm 
Microbiological Data Program - Annual Summary, Calendar Year 2006 

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 

January 2007 

To the Reader: 

I am pleased to present the USDA Microbiological Data Program 2006 Data 

Summary. In 2006, MDP tested six commodities (cantaloupe, leaf and romaine 

lettuce, tomatoes, green onions, and alfalfa sprouts). Leaf and romaine lettuce 

were combined as a single commodity with each variety being sampled at half the 

regular sampling rates. Alfalfa sprouts replaced cilantro and parsley. 

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

sample collection and analyses. In 2006, 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 2006 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 2006 

Contents

Page No.

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

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

 

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

 

Section II. Sampling........................................................................................................................ 4 

 

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

 

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

 

Section V. Summary of 2006 Data................................................................................................ 11 

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

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

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

 

iii 
Microbiological Data Program - Annual Summary, Calendar Year 2006 

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 and Serogroup ................................................................. 14 

v 
Microbiological Data Program - Annual Summary, Calendar Year 2006 

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 2006 

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 x117, 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 2006 

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 2006, 11 

States collected fruit and vegetable samples 

(California, Colorado, Florida, Maryland, 

Michigan, Minnesota, New York, Ohio, Texas, 

Washington, and Wisconsin). 

The program tested five commodities 

(cantaloupe, leaf and romaine lettuce, tomatoes, green onions, and alfalfa sprouts) for 

generic Escherichia coli (E. coli), E. coli with 

pathogenic potential, including E. coli

O157:H7, and Salmonella. 

In August 2006, MDP sampling operations 

were halted due to budget uncertainty for 

fiscal year (FY) 2007. Laboratory projects 

initiated earlier in the year were continued 

using remaining FY 2006 funds. Results 

presented in this summary cover program 

operations from January through August 31, 

2006. 

MDP analyzed a total of 7,646 samples. Sixtyone percent of the samples were from 

domestic sources, 34 percent were imported, 

and 5 percent were of unspecified origin. MDP 

identified 29 samples with potentially pathogenic E. coli; however, pathogenic E. coli

strains were isolated from only 6 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 three 

Salmonella isolates, one each from alfalfa 

sprouts, cantaloupe, and green onions. 

A number of important benefits are expected 

from MDP. Microbiological data obtained 

from this fresh produce screening effort will 

enhance the understanding of the microbial 

ecology of fresh fruit and vegetables in the 

food supply, permit the identification of longterm trends, and over time will contribute 

significantly to a national produce microbiological baseline. 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 2006 

1 

I. Introduction 

Fresh produce is recognized as an important 

component of a healthy diet. Because most 

produce is grown in a natural environment, it is 

vulnerable to contamination with pathogens. The 

fact that produce is often consumed raw without 

any type of intervention that would reduce, 

control, or eliminate pathogens prior to consumption contributes to its potential as a source of 

foodborne illness (1, 2). In 2001, Congress

authorized funding for a microbiological 

monitoring program to establish a microbial 

baseline for fresh produce. 

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 2006 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. MDP relies on the expertise 

of scientists from FDA and academia. 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) depicts MDP program testing 

operations. The participating State laboratories 

and AMS National Science Laboratory (NSL) 

analyze MDP samples collected by trained 

State sample collectors. FDA’s Center for 

Veterinary Medicine (CVM) and Pennsylvania 

State University (PSU) 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 foodborne 

outbreaks. Commodities tested in 2006 

included: cantaloupe, leaf and romaine lettuce, 

tomatoes, green onions, and alfalfa sprouts. 

Commodities were tested for generic 

Escherichia coli (E. 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). Also 

Microbiological Data Program (MDP) 

Annual Summary, Calendar Year 2006 

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

Operations, (IV.) Database Management, (V.) Summary of 2006 Data 
Microbiological Data Program - Annual Summary, Calendar Year 2006 

2 

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 

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. 
Microbiological Data Program - Annual Summary, Calendar Year 2006 

3 

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, Massachusetts, 

Nevada, New Jersey, New Mexico, Oklahoma, 

Vermont, Virginia, and Wyoming. 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. 

Microbiology laboratory services were provided 

by nine States (California, Colorado, Florida, 

Michigan, Minnesota, New York, Ohio, 

Washington, and Wisconsin) and AMS NSL. 

Due to internal State funding issues, the 

California laboratory voluntarily discontinued 

program participation in February 2006. 

Beginning in March 2006, samples collected 

by California were shipped to the Ohio and 

AMS NSL laboratories. 

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 

Nevada 

Idaho 

Wyoming 

New 

Mexico 

Hawaii 

Alaska 

Virginia

Delaware 

Connecticut 

Massachusetts 

Michigan 

Vermont 

New Jersey 

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 

Figure 2. Program Participants. During 2006, 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. 

These two laboratories also analyzed California samples beginning March 2006. States that do not participate 

in MDP’s sampling program but are in the direct distribution networks of the participating States are also 

shown. 
Microbiological Data Program - Annual Summary, Calendar Year 2006 

4 

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 United States. as a whole, and between 

the wholesale and point-of-consumption 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. 

Cantaloupe, leaf and romaine lettuce, tomatoes, 

and green onions remained in the program at 

2005 levels. Based on consultations with FDA, 

alfalfa sprouts were introduced in 2006 

replacing cilantro and parsley, which were 

treated as a single commodity in 2005. These 

crops were selected because they are highconsumption 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 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 generate 

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 

Antimicrobial Resistance Monitoring System 

(NARMS) database. Additionally, CVM 

performs genomic fingerprinting on MDP 

isolates for inclusion in the PulseNet system. 

AMS implemented DNA-based screening for 

pathogenic E. coli, including E. coli O157:H7 

and Salmonella. MDP laboratories have been 

using an enzyme-based assay for detection of 

generic E. coli. Beginning in 2005, mPCR 

technology was used to screen all E. coli

positive samples for the presence of pathogenic 

E. coli that harbor shiga toxins (STEC) and 

enterotoxins (ETEC), two groups of E. coli that 

cause enteric diseases and are important to 

human health. 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 for better database management and to 

use quicker, more reliable, and more sensitive 

technologies for improved microbial detection. 

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 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 
Microbiological Data Program - Annual Summary, Calendar Year 2006 

5 

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 on a yearround 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. The 

monthly 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). 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 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 

2006, 7,646 samples were collected from over 

700 sites across the country and analyzed by 

the MDP participating State laboratories. Table 

2 provides a detailed breakdown of sample 

numbers collected by commodity. For lettuce, 

either leaf or romaine varieties were eligible for 

sampling. In May 2006, plum tomatoes, 

including roma tomatoes, were added to the list 

of tomato varieties for collection. 

All samples are selected and bagged 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. 

Commodity Country 

Number of 

Samples 

Cantaloupe Costa Rica 267 

 Guatemala 318 

 Honduras 246 

 Mexico 30 

 Nicaragua 3 

 Peru 3 

 TOTAL 981 

 

Green Onions Canada 18 

 Chile 3 

 Guatemala 24 

 Mexico 1,065 

 TOTAL 1,110 

 

Lettuce Canada 3 

 

Tomatoes Canada 87 

 Israel 3 

 Mexico 567 

 657 

Table 1. Distribution of Imported Samples. This 

table details the number of imported samples by 

country of origin and by commodity.
Microbiological Data Program - Annual Summary, Calendar Year 2006 

6 

Figure 3. Commodity Origin. The proportion of domestic, imported or unknown origin for 

each commodity is depicted for samples tested in 2006. 

Domestic 40.3% 

Unknown 3.1% 

Imported 56.6% 

Cantaloupe 

Domestic 23.8% 

Unknown 3.9% 

Imported 72.3% 

Green Onions 

Domestic 97.8% 

Unknown 2.0% 

Imported 0.2% 

Lettuce 

Domestic 91.3% 

Unknown 8.7% 

Sprouts (Alfalfa) 

Domestic 51.1% 

Unknown 6.1% 

Imported 42.8% 

Tomatoes 
Microbiological Data Program - Annual Summary, Calendar Year 2006 

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 foodgrade 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. 

7 

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 California, Maryland and 

Texas; these State samples are shipped to the 

Ohio laboratory and AMS NSL, Gastonia, NC, 

for analysis. 

Cantaloupe, leaf and romaine lettuce, tomatoes, 

green onions, and alfalfa sprouts were collected 

and tested as commodities for 2006. These 

commodities are harvested primarily by hand 

although some mechanical harvesting does 

occur. Alfalfa sprouts are most often grown in 

drums and packaged in controlled environments. The produce may be packaged in the 

field or taken to a packinghouse (e.g., tomatoes 

require classification for color and/or size). At 

State 

 

Total E. coli 

E. coli 

O157:H7 Salmonella 

California 336 336 336 336 330 1,674 1,674 1,674 1,674 

Colorado 48 48 48 48 48 240 240 240 240 

Florida 168 168 168 168 168 840 840 840 840 

Maryland 96 96 96 96 87 471 471 471 471 

Michigan 144 144 144 144 144 720 720 720 720 

Minnesota 48 48 48 48 48 240 240 240 240 

New York 216 216 216 216 216 1,080 1,080 1,080 1,080 

Ohio 144 144 141 143 138 710 710 710 710 

Texas 189 192 189 192 189 951 951 951 951 

Washington 96 96 96 96 96 480 480 480 480 

Wisconsin 48 48 48 48 48 240 240 240 240 

Totals 1,533 1,536 1,530 1,535 1,512 7,646 7,646 7,646 7,646 

Cantaloupe

Green Onions

Tomatoes

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)

Lettuce (Leaf or Romaine)
Microbiological Data Program - Annual Summary, Calendar Year 2006 

8 

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 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 chainof-custody 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 

handheld 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-of-custody. 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 

Participating microbiology laboratories tested 

samples of MDP commodities for generic 

Escherichia coli (E. coli), E. coli strains with 

human pathogenic potential including E. coli

O157:H7, and Salmonella. MDP laboratories also 

performed multiplex polymerase chain reaction 

(mPCR) screening for pathogenic E. coli on 

samples that tested positive for the presence of E. 

coli. Isolates of these organisms were sent to the 

Gastroenteric Disease Center at Pennsylvania 

State University (PSU) and FDA/CVM for 

further characterization. Tests performed by PSU 

and FDA CVM included serotyping, testing for 

antimicrobial resistance and virulence attributes, 

and genomic fingerprinting. In addition, the 

Commonwealth of Virginia Division of Consolidated Laboratory Services (DCLS) developed a 

realtime PCR based screening method for 

Shigella 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 Universal Preenrichment Broth (UPB) 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 DNAbased 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 
Microbiological Data Program - Annual Summary, Calendar Year 2006 

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 Quality Assurance/

Quality Control (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 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 the need for 

performing lengthy biochemical tests. All 

controls and blanks were taken along with the 

sample cultures from the preenrichment step to 

isolation and identification of target isolates 

using cultural, immunological and serological 

methods. MDP laboratories also used automated instrumentation for confirmation of 

isolates based on biochemical reactions. 

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 academia 

on technical issues. For day-to-day QA oversight, each participating facility was required 

9 

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 

on-site reviews by MDP staff to determine 

compliance with MDP SOPs. Corrective actions, 

if necessary, were performed as a result of onsite reviews. 

IV. Database Management

 

MDP maintains an electronic database that 

serves as a central data repository. The central 

database resides at MPO in Manassas, VA. 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 uses 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 
Microbiological Data Program - Annual Summary, Calendar Year 2006 

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 2006 

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 2006 Data 

MDP discontinued sampling operations on 

August 31, 2006 due to budget uncertainty for 

FY 2007. Consequently, results presented in 

this summary cover only eight months of 

11 

program operations. MDP collected a total of 

7,646 samples of cantaloupe (1,533), green 

onions (1,536), lettuce (1,539), tomatoes 

(1,535) and alfalfa sprouts (1,512). 

Table 1 specifies the distribution of imported 

samples by commodity and country of origin. 

Figure 3 illustrates the proportion of samples 

that were domestic, imported, and of unknown 

origin for each commodity. Sixty-one percent of 

the samples were from domestic sources, 34 

percent were imported, and 5 percent were of 

unspecified origin. Table 2 shows the distribution of samples among each commodity and 

collection State. 

In 2006, produce washes were preenriched in a 

single broth, Universal Preenrichment Broth 

(UPB), in an effort to streamline the screening 

process for all target bacteria. The BAX®

instrument, an automated PCR system, was 

used for screening samples for the presence of

Salmonella and enterohemorrhagic E. coli

O157:H7. Unlike in previous years, 2006 

samples were not pooled in order to test each 

sample individually. Genomic DNA was 

extracted from each of the 7,646 preenriched 

cultures. Appropriate aliquots of the genomic 

DNA samples were used for all BAX PCR 

testing of Salmonella and E. coli O157:H7. 

Similarly, appropriate aliquots of extracted 

DNA samples were used for screening for the 

Commodity 

Number of 

Samples 

Tested 

Number of 

Samples Screened 

by mPCR 

Number of 

Pathogenic E. coliPositive Samples 

Cantaloupe 1,533 225 3 

Green Onions 1,536 366 8 

Lettuce 1,530 294 8 

Sprouts (Alfalfa) 1,512 612 9 

Tomatoes 1,535 94 1 

Total 7,646 1,591 29 

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 2006 

12 

presence of pathogenic E. coli by mPCR (refer 

to Table 3). 

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 MDPapproved commercial biochemical kit or 

system. In addition to biochemical identification of an isolate, all MDP participating State 

laboratories were required to confirm the 

identification by serotyping. Isolates were then 

sent to FDA/CVM for expanded serotyping, 

antimicrobial resistance testing, and genomic 

fingerprinting. 

Generic E. coli and Pathogenic E. coli

The 7,646 samples were initially screened for 

generic E. coli using an AOAC-official method 

for detection and enumeration which resulted 

in 1,591 samples that tested positive for E. 

coli. These 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 29 

samples. Successful isolation of pathogenic E. 

coli strains was attained for six 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 the small 

number of target bacterial cells, differential 

growth rates of various bacteria, and additional 

growth requirements. 

 

The six isolates were sent to PSU for serotyping 

and further characterization and to FDA/CVM 

for antimicrobial resistance testing. PSU 

conducted tests that included 13 virulencespecific genes associated with different classes 

of pathogenic E. coli. FDA/CVM conducted 

tests on antimicrobial resistance and genomic 

fingerprinting on these isolates. The results of 

PSU and FDA/CVM testing are shown in Table 

4. Five of the pathogenic E. coli isolates were 

from lettuce and one from alfalfa sprouts. Five 

out of six isolates carried more than one toxin 

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 - shiga toxin 

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 

HlyA - hemolysin 

Commodity 

Pathogenic 

Class 

Toxic Genes 

Identified O Antigen H Antigen Pulsed-Field Gel Electrophoresis 

Alfalfa Sprouts STEC STa, Stx-2, HlyA 36 14 

Lettuce STEC Stx-2 Neg 2 or 35 

Lettuce ETEC LT, STb N 14 

Lettuce STEC Stx-2, HlyA 8 28 

Lettuce STEC Stx-2, HlyA 8 28 

Lettuce STEC Stx-1, Stx-2, HlyA 141 38 
Microbiological Data Program - Annual Summary, Calendar Year 2006 

13 

Commodity 

Number of Samples 

Tested 

Number of Positive 

Individual Samples 

Number of Positive 

Isolates 

Cantaloupe 1,533 5 1 

Green Onions 1,536 4 1 

Lettuce 1,530 5 0 

Sprouts (Alfalfa) 1,512 7 1 

Tomatoes 1,535 1 0 

TOTALS 7,646 22 3 

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. 

gene. One ETEC isolate, carrying both the heatlabile and heat-stable enterotoxins, was resistant 

to antimicrobial agent, sulfasoxazole. One of the 

STEC isolates, that carried a single toxin gene, 

was found to be resistant to antimicrobial agents, 

tetracycline and sulfasoxazole. To characterize 

an isolate as a human pathogen capable of 

causing disease, there must be an interplay of 

several proteins including toxins, encoded by 

respective genes. MDP only identified toxin 

genes; the additional testing, required to 

determine the actual pathogenicity of these 

isolates, is not within the scope of MDP. 

Salmonella

As depicted in Table 5, a total of 7,646 samples 

were screened for Salmonella by BAX PCR. 

Twenty-two of these samples were positive and 

three Salmonella isolates were obtained: one 

each from cantaloupe, green onion, and alfalfa

sprouts. These three isolates were sent to FDA/

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

Table 6 identifies each isolate and the associated 

serogroup. The isolate from green onions, S. 

agona, belonging to serogroup B, was resistant 

to antimicrobial agent, tetracycline. The isolate 

found in alfalfa sprouts, S. havana, belonging to 

serogroup G and the isolate from cantaloupe, S. 

sandiego, belonging to serogroup B, were found 

sensitive to antimicrobial agents tested.

E. coli O157:H7

No enterohemorrhagic E. coli O157:H7 strain 

was isolated from the 7,646 samples screened, 

although 3 samples tested positive by BAX PCR. 

In this case, as with pathogenic E. coli analysis, 

several factors contribute to successful isolation, 

including the level of background microflora 

versus the number of target bacterial cells, 

differential bacterial growth rates, and additional 

growth requirements. 
Microbiological Data Program - Annual Summary, Calendar Year 2006 

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: 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. 

14 

References: 

1. Produce Safety from Production to Consumption: 2004 Action Plan to Minimize Foodborne Illness 

Associated with Fresh Produce Consumption (October 2004). U.S. Food and Drug Administration, Center 

for Food Safety and Applied Nutrition, Office of Plant and Dairy Foods, http://www.cfsan.fda.gov/~dms/

prodpla2.html

2. E. coli O157:H7 Outbreaks (September 2006, December 2006). U.S. Food and Drug Administration, Center 

for Food Safety and Applied Nutrition, Office of Plant and Dairy Foods, http://www.cfsan.fda.gov/list.html

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 2006 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. 

Commodity Genus Species Serogroup Pulsed-Field Gel Electrophoresis 

Cantaloupe Salmonella sandiego B 

Green Onions Salmonella agona B 

Alfalfa Sprouts Salmonella havana G 

Serotype/Identification 

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

serogroup for each of the three Salmonella isolates obtained in 2006. 
Microbiological Data Program - Annual Summary, Calendar Year 2006 

15 

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. 

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

condition 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 (e.g. 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 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. 
Microbiological Data Program - Annual Summary, Calendar Year 2006 

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

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