Microbiological Data Program 

Progress Update and 2002 Data Summary 

United States 

Department of 

Agriculture 

Agricultural 

Marketing Service 

Science & 

Technology 

Programs 
March 2004 

To the Reader: 

I am pleased to present the Microbiological Data Program Progress Update and 2002 

Data Summary. In 2002, MDP tested five commodities: celery, leaf lettuce, romaine 

lettuce, tomatoes, and cantaloupes. Sample collection was performed using a 

statistical framework. These crops were selected for inclusion because they are high 

consumption commodities in the United States. The laboratory methods used in the 

program have been largely traditional cultural techniques. MDP is exploring the use 

of new and innovative technologies for the identification of microorganisms, which 

are also discussed in this publication. 

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

sample collection and analyses. Ten States participated in 2002: California, Colorado, 

Florida, Maryland, Michigan, New York, Ohio, Texas, Washington, and Wisconsin. 

Because these States together represent all regions of the country and over half the 

Nation’s population, these data can be used to make inferences about the national 

food supply. 

This document is intended to provide the reader with an update on the methods, 

modifications, and refinements made during program development, as well as provide 

an overview of the data obtained during the initial stages of the program. MDP data 

are important in developing baseline levels of targeted pathogens in the domestic food 

supply. MDP is a continuous data gathering program to identify microbial trends and 

to develop risk models. If you have comments or suggestions on how we can further 

improve this summary, please send electronic-mail to us at amsmpo.data@usda.gov 

or to our Web site http://www.ams.usda.gov/science/MPO/MDP.htm. 

Sincerely, 

A.J. Yates 

Administrator 

United States 

Department of 

Agriculture 

Marketing and 

Regulatory 

Programs 

Agricultural 

Marketing 

Service 

1400 Independence Ave. 

Washington, DC 

20090-6456 

AMS-Agricultural Marketing Service 

An Equal Opportunity Provider and Employer 
Microbiological Data Program — Annual Summary, Calendar Year 2002 

ii 
Contents

Page No.

Preface .......................................................................................................................................... vii 

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

 

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

 

Section II Sampling Operations ...................................................................................................... 2 

 

Section III Laboratory Operations ................................................................................................... 5 

 

Section IV Database Management .................................................................................................. 6 

 

Section V 2002 Data Summary ....................................................................................................... 8 

 

Microbiological Data Program — Annual Summary, Calendar Year 2002 

iii 
Microbiological Data Program — Annual Summary, Calendar Year 2002 

iv 
Figures and Tables

Figures Page No. 

 1 Participating States and Their Geographical Distribution ............................................ 2 

 2 Areas Overview of MDP Management and Operations ............................................... 3 

 3 Data Life Cycle ............................................................................................................. 7 

 

4 Commodity Origin and Distribution ............................................................................. 9 

 

Tables

 1 Samples Collected and Analyzed per Commodity by Participating States ................. 8 

 

 2 Summary of Sample Analysis for Salmonella ........................................................... 11 

 3 Virulence Attributes .................................................................................................. 11 

 4 Summary of Sample Analysis for E. coli .................................................................. 11 

 5 Virulence Factors by Commodity .............................................................................. 12 

Microbiological Data Program — Annual Summary, Calendar Year 2002 

v 
Acronyms

AMS Agricultural Marketing Service 

AOAC Association of Analytical Communities 

ARS Agricultural Research Service 

BAM Bacteriological Analytical Manual 

CDC Centers for Disease Control and Prevention 

CNF2 Cytotoxic Necrotizing Factor 2 

DNA Deoxyribonucleic acid 

ELISA Enzyme-Linked Immunosorbent Assay 

EPA Environmental Protection Agency 

ETEC Enterotoxigenic E. coli

FDA Food and Drug Administration 

FSIS Food Safety and Inspection Service 

GFP Green fluorescent plasmid 

GLPs Good Laboratory Practices 

MDP Microbiological Data Program 

MPO Monitoring Programs Office 

NARMS National Antimicrobial Resistance Monitoring System 

NASS National Agricultural Statistics Service 

NSL National Science Laboratory 

NTEC Necrotizing E. coli 

PCR Polymerase Chain Reaction 

PSU Pennsylvania State University 

QA/QC Quality Assurance/Quality Control 

QAU Quality Assurance Unit 

RDE Remote Data Entry 

SOP Standard Operating Procedure 

SRC Salmonella Reference Center 

SSL Secure Socket Layer 

STa Heat Stable Toxin a 

TAC Technical Advisory Committee 

UPenn University of Pennsylvania 

USDA United States Department of Agriculture 

Microbiological Data Program — Annual Summary, Calendar Year 2002 

vi 
Microbiological Data Program — Annual Summary, Calendar Year 2002 

vii 

In 2001, AMS received Congressional funding 

to implement a Microbiological Data Program 

(MDP). The purpose of the program is to 

provide statistically valid information about 

microbial organisms on fresh fruit and 

vegetables. It is a voluntary data gathering 

program, not a regulatory enforcement effort. 

This MDP Progress Update and 2002 Data 

Summary briefly describes program activities 

and results. 

MDP collects random produce samples from 

wholesale distribution centers on a year-round 

basis. The sampling protocol utilized provides 

a statistically-reliable method for collecting and 

analyzing samples close to consumers before 

other variables such as handling and treatment 

are introduced by distributors and retailers. 

Laboratories participating in MDP screen 

samples of fresh produce for the presence of 

Escherichia coli (E. coli) with pathogenic 

potential and Salmonella spp. Scheduled for 

introduction in 2004 are specific screening 

methods for targeting enterohemorrhagic, 

enterotoxigenic, and Shiga-toxin producing E. 

coli of importance to human health and 

screening methods for E. coli 0157:H7 and 

Shigella species. 

A number of important benefits are expected 

from the MDP program. Microbiological 

benchmark data obtained from this fresh 

produce screening effort will contribute 

significantly to a national produce microbiological baseline. Such baseline data, including 

the further characterization of bacterial 

pathogens as to virulence attributes, serotype, 

genomic fingerprints, and antimicrobial 

resistance, will provide rigorous benchmarks 

against which change can be measured. The 

data will enhance the understanding of the 

microbial ecology of fresh fruit and vegetables 

in the food supply and permit the identification 

of trends. MDP data also will allow better 

focus in the design of production and handling 

systems aimed at reducing potential 

microbiological pathogens on fresh fruit and 

vegetables. 

The MDP program was designed and is 

regularly reviewed in collaboration with the 

Centers for Disease Control and Prevention, the 

Food and Drug Administration, USDA’s 

Agricultural Research Service and National 

Agricultural Statistics Service, and the 

participating States. 

Preface 
Microbiological Data Program — Annual Summary, Calendar Year 2002 

viii 
Microbiological Data Program — Annual Summary, Calendar Year 2002 

ix 

In fiscal year 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. AMS coordinated its 

MDP planning and policy requirements with the 

Centers for Disease Control and Prevention 

(CDC), the Food and Drug Administration (FDA), 

the USDA Agricultural Research Service (ARS), 

and the USDA National Agricultural Statistics 

Service (NASS). Sampling and/or microbiology 

laboratory activities were conducted through 

cooperative agreements with 10 States (California, 

Colorado, Florida, Maryland, Michigan, New 

York, Ohio, Texas, Washington, and Wisconsin) 

and 1 Federal microbiology laboratory (AMS 

National Science Laboratory, Gastonia, NC). 

These State and Federal agencies continue to 

collaborate as the program advances. 

The purpose of MDP is to collect information 

regarding the incidence and identification of 

targeted foodborne pathogens and indicator 

organisms on fresh fruit and vegetables. MDP 

sampling is designed to obtain a statistical 

representation of the United States 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. 

In 2002, the program tested five commodities 

(cantaloupe, celery, leaf lettuce, romaine lettuce, 

and tomatoes) for Escherichia coli (E. coli) and 

Salmonella spp. 

For calendar year 2002, MDP analyzed a total of 

10,317 samples. Eighty-six percent of the samples 

came from domestic sources; 11 percent of the 

samples were imported; and no country of origin 

information was obtained on 3 percent of the 

samples. MDP identified E. coli isolates with 

virulence factors in 0.62 percent of the samples. 

The presence of virulence factors does not 

necessarily mean that these strains are pathogenic 

to humans, but may have pathogenic potential. 

MDP screening also resulted in three Salmonella

spp. isolates from domestic leaf lettuce samples. 

MDP is pursuing the use of new technologies to 

streamline laboratory procedures. DNA-based 

technologies were implemented for Salmonella

spp. screening in October 2003. Methods are 

being evaluated to enhance recovery of bacteria 

and to specifically capture targeted organisms 

such as E. coli O157:H7. AMS is seeking to 

improve data collection systems and to use 

improved microbial detection methods that are 

quicker, more reliable, and more sensitive. As the 

program expands, procedures and methods are 

being modified and refined to provide information 

necessary for making science-based food safety 

decisions. 

Data presented in this report were collected and 

processed through the efforts of the following 

organizations: 

U.S. Department of Agriculture 

Agricultural Marketing Service 

Science and Technology Programs 

1400 Independence Ave., SW. 

Mail Stop 0222 

Washington, DC 20250 

Deputy Administrator: Robert L. Epstein 

(202) 720-5231 

Monitoring Programs Office 

8609 Sudley Rd., Ste. 206 

Manassas, VA 20110 

Director: Martha Lamont 

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

E-mail: amsmpo.data@usda.gov 

Internet Home Page 

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

Executive Summary 
Microbiological Data Program — Annual Summary, Calendar Year 2002 

x 

Participating 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 

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 

Participating Laboratories

California Department of Food & Agriculture 

Division of Inspection Services 

Agriculture Microbiology Laboratory 

McClellan Park (McClellan AFB) 

5431 Arnold Ave., Bldg. 929 

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 & 

 Consumer Services 

Food Laboratory, 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 

90 West Plato Blvd. 

St. Paul, MN 55107 

New York Department of Agriculture and 

 Markets 

Food Laboratory 

1220 Washington Ave. 

State Office Campus, Bldg. 7, 3rd Floor 

Albany, NY 12235 

Ohio Department of Agriculture 

Consumer Analytical Laboratory 

8995 East Main St., Bldg. 3 

Reynoldsburg, OH 43068 

The Pennsylvania State University 

Gastroenteric Disease Center 

Wiley Laboratory 

Orchard Rd. 

University Park, PA 16802 

Washington State Department of Agriculture 

3939 Cleveland Ave., SE. 

Olympia, WA 98501 

Wisconsin Department of Agriculture, 

 Trade, and Consumer Protection 

Bureau of Lab Services 

4702 University Ave. 

Madison, WI 53707-7883 

United States Department of Agriculture 

Agricultural Marketing Service 

National Science Laboratory 

801 Summit Crossing Place, Ste. B 

Gastonia, NC 28054 

University of Pennsylvania 

The Salmonella Reference Center 

Myrin Building 

School of Veterinary Medicine 

382 West Street Rd. 

Kennette Square, PA 19348 
1 

I. Introduction 

In 2001, Congress authorized funding for a 

microbiological monitoring program to establish a 

microbial baseline in the domestic food supply. 

This publication summarizes progress made 

toward implementation of MDP and provides an 

overview of data collected in 2002. The AMS 

Monitoring Programs Office (MPO) manages the 

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. 

The purpose of MDP is to collect information 

regarding the incidence and identification of 

targeted foodborne pathogens and indicator 

organisms on fresh fruits and vegetables. MDP is 

a federal-state partnership between AMS and 10 

States (California, Colorado, Florida, Maryland, 

Michigan, New York, Ohio, Texas, Washington, 

and Wisconsin). MDP is a voluntary data 

gathering service, not a regulatory effort, and is 

part of the broader 1997 Presidential Food Safety 

Initiative. 

AMS coordinates its planning and policy 

requirements with the Centers for Disease Control 

and Prevention (CDC) and the Food and Drug 

Administration (FDA). The USDA Agricultural 

Research Service (ARS) provides consultation as 

an independent research authority on laboratory 

methods. AMS and the USDA National Agricultural Statistics Service (NASS) statisticians 

designed sampling plans based on per capita 

consumption, marketplace availability, product 

origin, and time in transit and storage. AMS used 

USDA consumption surveys to select commodities that are highly consumed in the United 

States and can be eaten raw: cantaloupe, celery, 

leaf lettuce, romaine lettuce, and tomatoes. 

Commodities were tested for E. coli strains with 

pathogenic potential and Salmonella spp. Isolates 

of these organisms were sent to specialized 

laboratories for further characterization including 

serotyping, antibiotic resistance, and virulence 

attributes. 

The three major MDP components are illustrated 

in Figure 2: sample collection, laboratory 

analysis, and database management. Samples are 

collected in the 10 participating States through 

cooperative agreements with their respective 

agencies (Figure 1). Also shown are the 12 

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, Vermont, Virginia, and Wyoming. 

Together these States represent approximately 50 

percent of the nation’s population and all 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 are provided by 

eight States (California, Colorado, Florida, 

Michigan, New York, Ohio, Washington, and 

Wisconsin) and one Federal laboratory [AMS 

National Science Laboratory (NSL), Gastonia, 

NC]. Laboratory operations are designed to 

minimize variability of results across laboratories. 

The data are submitted electronically via a Webbased Remote Data Entry (RDE) system and 

entered into a central database, managed by MPO 

in Manassas, VA. 

MDP data will be used to establish benchmarks 

for the incidence of target organisms at the 

wholesale level, understand trends, and improve 

risk communication. The information from MDP 

could help identify technology development 

priorities and risk modeling needs for fresh 

produce in the food chain. The MDP data also 

could supplement the FDA/USDA “Guidance for 

Industry—Guide to Minimize Microbial Food 

Safety Hazards for Fresh Fruits and Vegetables.” 

Microbiological Data Program (MDP) 

Annual Summary, Calendar Year 2002 

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

Laboratory Operations, (IV.) Database Management, (V.) 2002 Data Summary 

Microbiological Data Program — Annual Summary, Calendar Year 2002 
2 

Figure 1. Participating States and their Geographical Distribution Areas 

Nevada 

Idaho 

Wyoming 

New 

Hawaii 

Alaska 

Virginia 

Delaware 

Maryland 

Connecticut 

Massachusetts 

Michigan Vermont 

New Jersey Ohio 

Florida 

Wisconsin 

New 

York 

Texas 

Colorado 

Washington 

California 

Participating States 

States where produce is directly 

marketed from participating States 

The “Guide” developed in concert with industry, 

has fostered proactive leadership and broad 

adherence to good agricultural practices as well as 

a commitment to continually seeking practices 

based on the best available science that will 

minimize microbial contamination. 

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 are also being sent to ARS for testing and 

these data will be added to the National 

Antimicrobial Resistance Monitoring System 

(NARMS) database. 

As the program evolves, procedures and methods 

will be modified and refined to provide 

information necessary for making science-based 

food safety decisions. AMS is seeking to improve 

data collection systems and to use improved 

microbial detection methods that are quicker, 

more reliable, and more sensitive. AMS is 

pursuing the use of deoxyribonucleic acid (DNA)-

based detection technologies for the testing of 

fresh produce and is conducting validation studies 

at MDP laboratories. 

II. Sampling 

The goal of the MDP sampling program is to 

obtain a statistical representation of the United 

States 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 

Mexico 

Microbiological Data Program — Annual Summary, Calendar Year 2002 
Main Objectives

 Collect information at wholesale level regarding the incidence, number, and species of important foodborne 

pathogens and indicator organisms on frequently consumed domestic and imported fresh fruits and vegetables.

 Establish a microbial baseline on the U.S. food supply 

 Conduct planning in cooperation with FDA, CDC, ARS, and NASS 

 Provide data to CDC and FDA 

 Designed as a voluntary data gathering program and not a regulatory or enforcement effort 

 Data can be modeled to make national inferences 

Sample Collection

 Statistical sampling plan 

 Collected near consumer level 

 Represents about 50% of U.S. 

population 

 Country of origin retained 

 Reflects postharvest treatments 

Database Management

 Electronic transmission of 

data 

 Customized query capability

 Standardized data 

summaries 

 MDP summary available on 

Internet 

Participating States

 California 

 Colorado 

 Florida 

 Maryland 

 Michigan 

 New York 

 Ohio 

 Texas 

 Washington 

 Wisconsin 

Laboratory Analysis

 QA based on EPA Good Laboratory 

Practices 

 Standard Operating Procedures

 Implementing DNA-based technologies

 Technical direction is derived from 

consultation with MDP Technical Advisory 

Committee and Federal, State, & academic 

experts 

 Customized proficiency testing program is 

in development

Participating Laboratories

 AMS National Science Laboratory, Gastonia, NC 

 California Department of Food & Agriculture 

 Colorado Department of Agriculture 

 Florida Department of Agriculture & Consumer Services 

 Michigan Department of Agriculture 

 Minnesota Department of Agriculture 

 New York Department of Agriculture and Markets 

 Ohio Department of Agriculture 

 Washington State Department of Agriculture 

 Wisconsin Department of Agriculture, Trade, and 

 Consumer Protection 

 Pennsylvania State University, Gastroenteric Disease 

Center 

 University of Pennsylvania, The Salmonella Reference 

Center 

Microbiological Data Program — Annual Summary, Calendar Year 2002 

3 

Figure 2. Overview of MDP Management and Operations 
Microbiological Data Program — Annual Summary, Calendar Year 2002 

4 

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. 

MDP uses Sample Information Forms to document 

information required for chain-of-custody, which 

is captured in the MDP database files. Sample 

collectors use the forms to record information such 

as the (1) State of sample collection, (2) collection 

date, (3) commodity code, and (4) testing laboratory code. Information about the country of origin 

of the sample is collected, as well as any 

production claims, such as organic and any 

postharvest treatments. 

MDP samples are collected aseptically by trained 

collectors who safeguard sample integrity. Food 

samples are collected at terminal markets and large 

chain store distribution centers from which food 

commodities are released to supermarkets and 

grocery stores. If samples are not available at the 

designated site, an alternate site can be used. 

However, sampling at a retail grocery store is not 

permitted because commodity handling practices 

at this level in the distribution chain may vary. 

State population figures are used to assign the 

number of samples scheduled for collection each 

month. These population-based numbers are as 

follows: California, 14; Colorado, 2; Florida, 7; 

Maryland, 4; Michigan, 6; New York, 9; Ohio, 6; 

Texas, 8; Washington, 4; and Wisconsin, 2. This 

schedule results in a monthly target of 62 samples 

per commodity. Each site sample collected 

consists of three individual units, which are treated 

as three distinct laboratory samples. Samples are 

collected and transported using aseptic techniques 

(i.e., sterilized latex gloves and sample bags). To 

characterize conditions during shipping, samples 

are measured for surface temperature at the time of 

collection and on receipt at the laboratory. 

MDP is collecting data on cantaloupes, celery, leaf 

lettuce, romaine lettuce, and tomatoes. These 

commodities are primarily harvested by hand 

although some mechanical harvesting does occur. 

rationale was developed by AMS Science and 

Technology Programs in consultation with the 

FDA, CDC, and NASS (1). 

The sampling of commodities in commerce is 

conducted at wholesale markets and/or distribution 

centers, on a year-round basis and over at least two 

growing seasons to accommodate differences in 

growing conditions. The data will therefore reflect 

differences in microbial concentrations on produce 

samples across varying conditions of production, 

transport, and storage. Sampling is apportioned 

according to population of the participating State, 

i.e., the higher the population in the State, the 

greater the number of samples taken. 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). In this manner, sites located near large 

populations have higher volumes and therefore are 

more likely to be selected than sites with smaller 

volume. 

Collecting data over time from a range of sources 

permits statistical statements to be made about the 

distribution of microorganisms within the target 

population. The target population is all units of a 

commodity available in a participating State 

during a defined time frame (e.g., one year). The 

extension of statistical statements to the distribution of microorganisms within the inferential 

population requires an assumption to be made 

about the relationship between the participating 

States and the United States as a whole. The 

inferential population is the entire amount of the 

commodity actually consumed by the U.S. public 

during the same time frame. Because the States 

that participate in MDP fully represent the 

inferential population, MDP is a comprehensive 

and defensible baseline survey. 

MDP sampling is 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 
Microbiological Data Program — Annual Summary, Calendar Year 2002 

5 

The produce may be packaged in the field (except 

tomatoes, which require classification for color 

and size) or taken to a packinghouse. 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. Tomatoes and 

cantaloupes often 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 atmospheres 

(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, tomatoes 

are often artificially ripened using techniques such 

as ethylene oxide gas. Therefore, the data will 

reflect any handling practice or post-harvest 

treatments up to that point in the food distribution 

chain. 

III. Laboratory Operations

Nine microbiology laboratories (eight State and 

one Federal) perform analyses for MDP. 

Specialized laboratories are used to perform 

additional identification and antimicrobial 

resistance testing: The Salmonella Reference 

Center (SRC), University of Pennsylvania 

(UPenn), and The Gastroenteric Disease Center, 

Pennsylvania State University (PSU). 

The initial laboratory methods adopted were 

predominantly traditional microbiological techniques; these initial methods, used in obtaining the 

2002 data, are described in Section V. As the data 

have been obtained and reviewed, modifications 

are being introduced to refine and improve the 

techniques used to produce these data. 

MDP has been evaluating the use of DNA-based 

polymerase chain reaction (PCR) and instruments 

associated with this technology. This technology 

has been shown to adequately address concerns 

such as sample matrix interferences, low cell 

counts, and reaction inhibition due to enrichment 

media. In addition, other Federal agencies such as

FDA and the USDA Food Safety and Inspection 

Service (FSIS) have approved and are currently 

using these instruments and methodologies for 

microbial screening programs. MDP has 

successfully completed validation studies and 

began using DNA-based automated instruments 

for the detection of Salmonella spp. in October 

2003. Validation studies will also be conducted to 

determine the use of the instrument for screening 

of E. coli O157:H7 and other targeted pathogens. 

Currently, samples are washed in a buffed saline 

solution and all analyses are conducted from this 

surface wash diluent. MDP is also investigating 

the use of newly developed wash buffers and 

growth media. Trial studies are being conducted 

by the Minnesota Department of Agriculture to 

evaluate the various options and the potential for 

introduction into MDP methodologies. 

MDP is conducting method comparison studies to 

validate and implement a more rapid and effective 

screening method for E. coli. This new method, 

which has been tested by FDA, will be evaluated 

by MDP laboratories for recovery of E. coli strains 

of interest to MDP. 

MDP methods will be reviewed and modified as 

necessary to enhance productivity and to provide 

data that will be useful for risk model development. As new microbial technologies are 

developed and become commercially available, 

they will be evaluated for use in the program. As 

with all methods modifications, all programmatic 

quality assurance/quality control (QA/QC) criteria 

must be met prior to implementation by MDP 

laboratories. 

The main objectives of the QA/QC program are to 

ensure the reliability of MDP data and to ensure 

performance equivalency of participating 
Microbiological Data Program — Annual Summary, Calendar Year 2002 

6 

laboratories. Direction for the MDP QA program 

is provided through written SOPs based on FDA’s 

Bacteriological Analytical Manual (BAM) 

methods, Association of Analytical Communities 

(AOAC)-certified methods, and the Environmental 

Protection Agency’s (EPA) Good Laboratory 

Practices (GLPs). SOPs provide uniform administrative, sampling, and laboratory procedures. 

Positive and negative controls and a sterile media 

blank are required for each sample set. MDP 

laboratories use positive control strains of E. coli

and Salmonella spp. that carry a gene for Green 

Fluorescent Protein (GFP) encoded in a stable 

plasmid. 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 are taken through the entire analytical 

procedure. MDP laboratories use automated 

instrumentation for confirmation of isolates. 

A Technical Advisory Committee (TAC), comprised of microbiologists from each participating 

laboratory, is responsible for revising program 

SOPs and addressing technical and QA issues. 

For day-to-day quality assurance over-sight, each 

participating facility is required to have a Quality 

Assurance Unit (QAU) that operates independently from the laboratory staff. Preliminary QA/

QC review procedures are performed on-site by 

each laboratory’s QAU. Final review procedures 

are performed by MDP staff who are responsible 

for collating and reviewing data for conformance 

with SOPs. 

Laboratory performance is also monitored through 

on-site reviews by MDP staff to determine 

compliance with MDP SOPs. Corrective actions, 

if necessary, are performed as a result of on-site 

reviews. Performance equivalency of the participating laboratories is monitored by a programwide proficiency testing program. MDP 

laboratories have participated in a check sample 

program administered through AOAC. MPO is 

working to develop a customized proficiency 

testing program. 

IV. Database Management 

 

MDP maintains an electronic database that serves 

as a central data repository. The central database 

resides at the Monitoring Programs Office 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 life-cycle is depicted in Figure 3. 

 

MDP utilizes a Web-based 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. At MDP headquarters, the RDE 

system allows the staff scientists to review and 

approve the data for inclusion in the central 

database. 

The RDE data entry screens have extensive edits 

and cross-checks built in to ensure that valid 

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 ad-hoc queries (data 

searches) 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. The central MDP 

database is maintained using Microsoft Access in 

a Windows 2000 operating environment. MDP 

headquarters plans to migrate to the Microsoft 

SQL Server 2000 environment for more secure 

and robust database management. 
Sample Collection

- Collection in 10 States

- Samples taken close to consumer

- Standardized Sample Information Form

- Data entry on handheld/laptop computers

- 8 State labs + 1 USDA lab

- Standardized sample preparation

- Test for specific foodborne pathogens

Laboratory Analysis

Lab Remote Data Entry (RDE)

Data Review at HQ

- Scientists review data on-screen

- Upload data to central database

- Web-based data entry software

- Import data from other systems

- Access controlled by user login

- Extensive data cross-checks

Internet

Year-end

Review

Data Reporting

- Centralized data storage

- Encrypted data transmissions

Internet

- Data reconciliation

- Standard & ad-hoc reporting

Microbiological Data Program — Annual Summary, Calendar Year 2002 

7 

Figure 3. Data Life Cycle 
Microbiological Data Program — Annual Summary, Calendar Year 2002 

8 

Access to the central MDP database is limited to 

MDP headquarters personnel and is controlled 

through password protection and user access 

rights. System back-ups are done each night and 

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

week. 

V. 2002 Data Summary 

In 2002, the first full year of testing, MDP 

screened commodities for the presence of E. coli

and Salmonella spp. Both organisms are of public 

health significance. E. coli has historically been 

used as an indicator of fecal contamination in food 

and water. Salmonella spp. are most often 

implicated in foodborne outbreaks involving 

produce (2). The 2002 data set represents 1 year 

of data and is insufficient to draw any inferences. 

Baseline studies require data generated over more 

than one growing season and representing several 

years. 

Table 1 shows the number of samples collected by 

each State and tested for E. coli and Salmonella 

spp. Commodities in the program for 2002 

included celery, leaf lettuce, romaine lettuce, and 

tomatoes; in July 2002, cantaloupe was added. 

These crops were selected for inclusion in the 

program because they are high consumption 

items in the U.S. diet and can be consumed raw. 

Figure 4 shows the proportion of domestic and 

imported samples for all of the 10,317 samples 

analyzed. This figure also shows the portion of 

domestic and imported samples for each of the 

five commodities in the program: cantaloupe, 

celery, leaf lettuce, romaine lettuce, and 

tomatoes. No other information regarding the 

source of the samples is collected, as 

congressional language required the sampling to 

occur in a blind fashion. 

Samples from a site consist of three individual 

units generally collected from the same 

container. All samples in a State are collected on 

the same day or within a two-day interval. 

Inferences cannot reasonably be made from the 

sample units to the lots from which they 

originate, because the units do not provide 

Collection 

State Cantaloupe Celery 

Leaf 

Lettuce 

Romaine 

Lettuce Tomatoes Total E. coli Salmonella 

California 249 504 492 492 624 2,361 2,361 2,361 

Colorado 36 72 72 72 90 342 342 342 

Florida 126 250 249 254 291 1,170 1,134 1,170 

Maryland 68 141 140 144 179 672 672 672 

Michigan 107 216 213 213 268 1,017 1,015 1,017 

New York 162 311 324 322 387 1,506 1,505 1,505 

Ohio 96 202 212 213 252 975 975 975 

Texas 129 273 273 261 349 1,285 1,285 1,285 

Washington 72 138 139 141 179 669 667 668 

Wisconsin 33 69 66 65 87 320 320 320 

TOTAL 1,078 2,176 2,180 2,177 2,706 10,317 10,276 10,315 

Samples Analyzed for 

Table 1. Number of Samples Collected and Analyzed by State 
Domestic 86% 

Unknown 3% 

Import 11% 

Origin Commodity Distribution 

Celery 21% 

Cantaloupe 11% 

Leaf Lettuce 21% 

Romaine Lettuce 21% 

Tomato 26% 

Commodity Origin 

No. of 

samples 

Percent of 

Total 

Cantaloupe Domestic 961 89.1 

Import 72 6.7 

Unknown 45 4.2 

 1,078 

 

Celery Domestic 2,083 95.7 

Import 54 2.5 

Unknown 39 1.8 

 2,176 

 

Lettuce, Leaf Domestic 2,117 97.1 

Import 18 0.8 

Unknown 45 2.1 

 2,180 

 

Lettuce, Romaine Domestic 2,108 96.8 

Import 33 1.5 

Unknown 36 1.7 

 2,177 

 

Tomatoes Domestic 1,647 60.9 

Import 930 34.4 

Unknown 129 4.7 

 2,706 

TOTAL 10,317 

Microbiological Data Program — Annual Summary, Calendar Year 2002 

9 

Figure 4. Commodity Origin and Distribution 
Microbiological Data Program — Annual Summary, Calendar Year 2002 

10 

enough information to produce statistically 

reliable lot estimates. However, over time, 

statistical methods can be applied to make 

national inferences from the data. 

Upon arrival at the testing facility, samples are 

visually examined for acceptability and 

discarded if determined to be damaged (decayed, 

extensively bruised, or spoiled). Samples are 

refrigerated until analysis begins. Laboratories 

are permitted to refrigerate commodities for up 

to 24 hours to allow for different sample arrival 

times from the various collection sites. Only 

excess soil is removed prior to testing. 

With the inception of MDP in 2001, experts 

from State and Federal governments, industry, 

and academia were consulted in program 

development and implementation of methodologies. The samples were screened for E. coli

using an FDA BAM method. If E. coli isolates 

were detected, additional screening for 

potentially pathogenic strains of E. coli was 

conducted. E. coli isolates were sent to PSU for 

further identification and characterization, 

including serotyping, antimicrobial resistance 

testing, and testing for virulence attributes. 

Salmonella spp. isolates were identified using a 

fully automated enzyme-linked immunosorbent 

assay (ELISA) system. Isolates were then sent 

to the SRC at UPenn for further identification 

(serotyping) and to PSU for antimicrobial 

resistance testing. In addition, selected isolates 

of E. coli and Salmonella spp. were sent to ARS 

for antimicrobial resistance testing and inclusion 

into the NARMS database. 

Identification of isolates was confirmed using 

either a conventional biochemical testing system 

or an AOAC-certified or MDP-accepted 

commercial biochemical kit or system. MDP 

analytical methods are published at http://www.

ams.usda.gov/science/MPO/SOPs.htm 

MDP utilized the legacy RDE system, which was 

a customized software application developed at 

MDP headquarters, to capture and report MDP 

data. The legacy RDE system provided 

interactive data entry screens to participating 

laboratories in a distributed, Windows-based 

application. The MDP results were electronically 

transmitted to MDP headquarters through an email system. 

In 2002, three domestic leaf lettuce samples were 

found to be positive for Salmonella spp. The 

numbers of each commodity analyzed for 

Salmonella spp. with subsequent characterization 

is shown in Table 2. Confirmed cultures were 

sent to the SRC at UPenn for serotyping; all three 

isolates were further identified as Salmonella 

typhimurium group B strains. 

The data show increased E. coli detections in the 

spring and the fall. To determine pathogenic 

potential, PSU tested the isolates for the presence 

of 13 different virulence-related genes associated 

with 7 different categories of virulent E. coli 

(Table 3). The predominant virulence factors 

were Cytotoxic Necrotizing Factor 2 (CNF2) and 

Heat Stable Toxin a (STa), which are associated 

with cytotoxic necrotizing E. coli (NTEC) and 

enterotoxigenic E. coli (ETEC), respectively. 

The numbers of each commodity analyzed for E. 

coli with subsequent characterization are shown 

in Table 4. The virulence factors identified by 

commodity are shown in Table 5. Virulence 

attributes were identified in 64 E. coli isolates. 

These isolates may have pathogenic potential but 

cannot be characterized as pathogenic to humans. 

The ability of a bacterial pathogen to cause a 

disease in humans requires a complex interplay 

of proteins encoded by numerous genes including 

a few genes from the host. PSU also classified 

the E. coli strains based on the somatic “O” type 

antigens using the ELISA method designed 

specifically for their identification. 

The traditional microbiological methods used by 

MDP laboratories in 2002 were resourceintensive and less sensitive. DNA-based 

technologies offer rapid detection with greater 

sensitivity and specificity. Therefore, MDP is 

pursuing the use of new technologies to improve 

sensitivities and refine laboratory procedures. 
Number of Number of Percent of 

Samples Tested Positive Samples Testing 

Commodity for Salmonella Isolates Positive 

Cantaloupe 1,077 0 0.00 

Celery 2,175 0 0.00 

Leaf Lettuce 2,180 3 0.14 

Romaine Lettuce 2,177 0 0.00 

Tomato 2,706 0 0.00 

TOTAL 10,315 3 0.03 

Table 2. Summary of Sample Analysis for Salmonella 

Microbiological Data Program — Annual Summary, Calendar Year 2002 

11 

E. coli Attributes 

EHEC Enterohemorrhagic Shiga-toxins SLT-1 and SLT-2 

-- Hemolysin HlyA 

-- Invasive trait (Intimin-eae) 

ETEC Enterotoxigenic Toxins (Heat stable –STa, STb; Heat Labile-LT 

EPEC Enteropathogenic Invasive character (Intimin eae-α) 

EAEC Enteroaggregative Gene associated with the virulent plasmid 

NTEC Necrotizing cytotoxic Cytotoxic Necrotizing Factor (CNF-1 and 2) 

EIEC Enteroinvasive IpaH gene known to be associated with EIEC 

Others K1 capsular antigen 

Table 3. Virulence Attributes 

Number of Number of Isolates Percent of Isolates 

Samples Tested Testing Positive for Testing Positive for 

Commodity for E. coli Virulence Attributes* Virulence Attributes 

Cantaloupe 1,077 2 0.19 

Celery 2,174 3 0.14 

Leaf Lettuce 2,161 27 1.25 

Romaine Lettuce 2,158 29 1.34 

Tomato 2,706 3 0.11 

TOTAL 10,276 64 0.62 

Table 4. Summary of Sample Analysis for E. coli 

* The presence of virulence factors does not necessarily mean that these 

strains are pathogenic to humans, but may have pathogenic potential. 
Microbiological Data Program — Annual Summary, Calendar Year 2002 

12 

Table 5. Virulence Factors by Commodity 

Leaf Romaine 

Virotype Celery Cantaloupe Lettuce Lettuce Tomato Virulent Attributes Attribute Description 

EHEC - 1 8 7 1 SLT-1, SLT-2, HIyA, Intimin eae-gamma Shiga-toxins 

ETEC - - 6 2 1 Heat stable (Sta, STb), Heat Labile (LT) Toxins 

EPEC 1 - 2 3 - EAggEC Invasive Character 

NTEC 1 1 9 12 - CNF-1, CNF-2 Cytotoxic Necrotizing Factor 

EIEC - - 1 - - IpaH 

Other 1 - 2 5 1 K1 Capsular antigen 

3 2 28 29 3 

References 

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

Program Sampling Overview, Feb. 2002 (rev. 2), http://www.ams.usda.gov/science/MPO/

SamplingOverview.pdf. 

2. Scientific Criteria to Ensure Safe Food (2003). A report by the Committee on the review of the 

use of scientific criteria and performance standards for safe food, Food and Nutrition Board, and 

Board on Agriculture and Natural Resources. By Institute of Medicine and National Research 

Council of the National Academies. The National Academies Press, Washington, DC. 

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

color, national origin, sex, religion, age, disability, political beliefs, sexual orientation, or marital or family status. (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 USDA, Director, Office of Civil Rights, Room 326-W, Whitten Building, 1400 

Independence Avenue, SW, Washington, DC 20250-9410 or call (202) 720-5964 (voice and TDD). USDA is an equal 

opportunity provider and employer. 

●●●●●

Note: One isolate from leaf lettuce had more than 1 virulence attribute (EHEC and NTEC), resulting in 65 virulence factors from 64 isolates.