Emerging Micro Expert Report on Emerging Microbiological Food Safety Issues Implications for Control

Microbiological food safety is a complex, fundamental issue

of continuing concern. Contributing to this complexity and

the emergence of food safety issues are ongoing changes in

demographics, geographic origin of food, food production

and processing, food consumption patterns, and microorgan-

isms themselves. These host, environmental, and pathogen

changes challenge our food safety policies and our ability to

manage food safety throughout the food system.

Recognizing this, the Institute of Food Technologists (IFT),

the 28,000-member nonprofit society for food science and tech-

nology, convened a panel of internationally renowned experts to

review the science related to emerging microbiological food safety

issues and implications for their control and to produce a com-

prehensive, scientific report. IFTs objective for this Expert Report

is to increase the understandingamong IFT members, senior

policy officials, and other interested groupsof the scientific in-formation on emerging foodborne pathogens (from a broad eco-logical perspective) relative to public policy issues and strategiesfor preventing foodborne illness.

This report is the second Expert Report produced by IFTsince the establishment of its Office of Science, Communica-tions, and Government Relations, which led the production ofthis report and the IFT Expert Report on Biotechnology andFoods. In the seven sections of this report, the expert panel fo-cuses on the complexity of emerging foodborne pathogens andfactors influencing emergence; manifestation of clinical food-borne disease; human susceptibility; ecology of pathogens inpre-harvest and post-harvest environments; microbial viru-lence, evolution, selection, adaptation, stress, and driving forces;risk analysis, the Hazard Analysis and Critical Control Pointsystem, Food Safety Objectives, microbiological performancecriteria, microbial testing, and surveillance; and steps for man-aging food safety in the future.

IFT Expert Report onEmerging Microbiological Food Safety IssuesImplications for Control in the 21st Century

Founded in 1939, the Institute of Food Technologists is a nonprofit scientific society with 28,000 membersworking in food science, technology, and related professions in the food industry, academia, and government.As the society for food science and technology, IFT brings sounds science to the public discussion of food issues.

2 INSTITUTE OF FOOD TECHNOLOGISTS

IFT Expert Report Panelists

IFT is deeply grateful to the expert report panelists for the time and effort that each of them expended on this project, bringingtheir expertise and insight into the state-of-the-science on the numerous topics addressed in the report. Panelists traveled to Chicagoto participate in full-day meetings and devoted considerable additional time to drafting the report, participating in conference calls todiscuss drafts, and reviewing the drafts. IFT sincerely appreciates these experts invaluable dedication to furthering the understandingof emerging microbiological food safety issues and food safety management.

Morris Potter, D.V.M., Panel ChairLead Scientist for EpidemiologyCenter for Food Safety and AppliedNutritionU.S. Food and Drug Administration,Atlanta, GA

Douglas Archer, Ph.D.Professor, Food Science and HumanNutritionUniversity of Florida, Gainesville

Andrew Benson, Ph.D.Assistant Professor, Food MicrobiologyUniversity of Nebraska, Lincoln

Frank Busta, Ph.D.Emeritus Professor, Food Scienceand NutritionUniversity of Minnesota, St. Paul

James S. Dickson, Ph.D.Dept. Chair and Associate Professor,Dept. of MicrobiologyIowa State University, Ames

Michael Doyle, Ph.D.Director, Center for Food SafetyUniversity of Georgia, Griffin

Jeffrey Farber, Ph.D.Director, Bureau of Microbial HazardsHealth CanadaOttawa, Ontario, Canada

B. Brett Finlay, Ph.D.Professor, Biotechnology LaboratoryUniversity of British Columbia,Vancouver

Michael Goldblatt, Ph.D.Director, Defense Advanced ResearchProjects AgencyDefense Sciences Office, Arlington, VA

Craig Hedberg, Ph.D.Associate Professor, Division of Environ-mental and Occupational HealthUniversity of Minnesota, Minneapolis

Dallas Hoover, Ph.D.Professor, Dept. of Animal andFood SciencesUniversity of Delaware, Newark

Michael Jahncke, Ph.D.Associate Professor and Director,Dept. of Food Science and TechnologyVirginia Seafood Agricultural Researchand Extension Center at HamptonVirginia Polytechnic Institute and StateUniversity, Hampton

Lee-Ann Jaykus, Ph.D.Associate Professor, Food MicrobiologyDept. of Food ScienceNorth Carolina State University, Raleigh

Charles Kaspar, Ph.D.Associate Professor, Food ResearchInstitute and Environmental ToxicologyCenterUniversity of Wisconsin, Madison

Arthur P. Liang, M.D., M.P.H.Director, Food Safety Initiative ActivityDivision of Bacterial and Mycotic DiseasesNational Center for Infectious DiseasesCenters for Disease Control and Preven-tion, Atlanta, GA

James Lindsay, Ph.D.National Program Leader, Food SafetyAgricultural Research ServiceU.S. Department of Agriculture,Beltsville, MD

James Pestka, Ph.D.Professor, Food Science and HumanNutritionMichigan State University, East Lansing

Merle Pierson, Ph.D.Professor, Dept. of Food Science andTechnologyVirginia Polytechnic Institute and StateUniversity, Blacksburg

Peter Slade, Ph.D.Director of Research & Technical ServicesNational Center for Food Safety andTechnology, Summit-Argo, IL

R. Bruce Tompkin, Ph.D.Vice President of Food SafetyConAgra Refrigerated Prepared Foods,Downers Grove, IL

Mary Lou Tortorello, Ph.D.Research MicrobiologistNational Center for Food Safetyand TechnologyU.S. Food and Drug Administration,Summit-Argo, IL

IFT Staff

Mary Helen Arthur, M.T.S.C.Lead Editor, Expert ReportDept. of Science and Communications,Chicago, IL

Rosetta Newsome, Ph.D.Director, Dept. of Science and Commu-nicationsChicago, IL

Fred Shank, Ph.D.Vice President, Office of Science, Com-munications, and Government RelationsWashington, D.C.

The participants on the expert panel were chosen based on theirscientific expertise. Their contributions represent their individualscientific perspective and do not represent the perspective of theiremployer.

3EXPERT REPORT

Introduction ...................................................................................... 4Trinity of Factors ..................................................................... 4Evolution of Controls ............................................................. 4Fig. 1a-Foodborne Illness ....................................................... 4Fig. 1b-Reducing One Factor .................................................. 4Fig. 1c-Reducing Multiple Factors .......................................... 4Table 1. Evolution of Food Processing .................................... 5Evolution of Food Safety Policies ........................................... 5Microbiology 101 .................................................................... 6Incidence and Prevalence of Foodborne Illness ..................... 8Emergence of Pathogens ......................................................... 8Fig. 2. Foodborne Illness Identification .................................. 8Table 2. Foodborne Disease in the United States ................... 9Complex Drivers of Change ................................................. 11Framework for Food Safety Management ............................ 12

Science of Pathogenicity ................................................................ 13Nomenclature ........................................................................ 13Table 3. Classic Microbial Nomenclature ............................. 13Nomenclature of Salmonella and Fig. 3 ................................ 14Virulence ............................................................................... 15Fig. 4. Virulence and Foodborne Illness ............................... 15Quorum Sensing ................................................................... 16Virulence of Salmonella ........................................................ 17Pathogens Are More Than Just Bacteria ............................... 18Evolution ............................................................................... 19Fig. 5. Contrasting Views of Pathogen Evolution ................. 20Fig. 6. Genetic Material in E. coli ........................................... 20Evolution of Salmonella ........................................................ 21Selection ................................................................................. 21Stress ...................................................................................... 22F38 Regulated Proteins and Table 4 ....................................... 24Driving Forces in Pathogenicity ............................................ 25Emergence of Viruses, Parasitic Protozoa and Marine Biotoxins as Foodborne Pathogens ................................... 25Pathogenicity of E. coli O157:H7 .......................................... 27

Humans as Hosts of Foodborne Disease ........................................ 28Manifestations of Clinical Disease ....................................... 28Table 5. Causes of Foodborne Illness ................................... 29Pfiesteria piscicida and Pfiesteria-like Microbes as Potential Foodborne Pathogens ........................................ 30Resistance to Microbial Foodborne Disease ........................ 31Susceptibility to Microbial Foodborne Disease ................... 34Table 6. Factors That Increase Host Susceptibility ............... 34Cryptosporidiosis .................................................................. 35Individual Choices that Affect Disease Risk ......................... 36Table 7. Factors That Increase Risk of Foodborne Disease .. 37Modification of Susceptibility ............................................... 39

Microbial Ecology and Foodborne Disease ..................................... 40PRE-HARVEST ENVIRONMENT ...................................... 40Overarching Issues ................................................................ 40Table 8. Sources of Imported Fresh and Frozen Produce .... 41Table 9. Percentage of Total U.S. Consumption Provided By Imports ......................................................................... 41Typical Pre-Harvest Environment for Foods of Plant Origin ... 42Production Practices and Mycotoxins .................................. 42Typical Pre-Harvest Environment for Foods of Animal Origin ...................................................................... 43

Development and Dissemination of Resistant Organisms .. 44Wild-Caught Shellfish and Fish ............................................ 45The Role of Microbiological Indicators in Assuring Food Safety ........................................................................ 46Specific Production Methods ................................................ 47HARVEST ENVIRONMENT ............................................... 48Produce .................................................................................. 48Food Animals ........................................................................ 48Aquaculture and Wild-Caught Fish and Shellfish ............... 49POST-HARVEST ENVIRONMENT .................................... 49Food Animal Slaughter and Meat Processing ...................... 49Post-Harvest Processing of Other Commodities ................. 52Water ...................................................................................... 52Alternative Processing Technologies ..................................... 53Table 10. Limitations to Alternative Processing Technologies Currently Under Development ................... 54Validation of Treatment Effectiveness Using Microbiological Surrogates ............................................... 55Transportation and Storage .................................................. 60Retail and Food Service ......................................................... 61Outbreaks of Shigella sonnei Infection Associated with Fresh Parsley ...................................................................... 61Microbial Stress Responses to Processing ............................ 62Table 11. Conditions That Can Produce Sublethally Injured Cells ...................................................................... 64New Tools for Pathogen Research ......................................... 64Ability of Pathogens To Survive in the Environment ........... 66

Application of Science to Food Safety Management ...................... 67Risk Assessment .................................................................... 67Risk Management Using Food Safety Objectives ................. 69Fig. 7. Framework for Food Safety Management ................. 70Hazard Control and Monitoring .......................................... 71Table 12. FSOs in the Food Safety Management Framework ....72Fig. 8. Establishing Performance Criteria ............................. 74Fig. 9. Unequal Levels of Food Safety ................................... 75Table 13. Probability of Acceptance (P

a) of Defective

Product Using a 2-class Sampling Plan ............................ 76Table 14. USDA Monitoring Program for Salmonella ......... 76Value of Test Results and Fig. 10 ........................................... 77Testing for Mycotoxins .......................................................... 79Surveillance for Foodborne Hazards and Illness ................. 79Outbreak Investigations and New Foodborne Pathogens ... 80Animal Surveillance for E. coli O157:H7 .............................. 82

Next Steps in Food Safety Management ......................................... 85Strategic Prioritization to Reduce Foodborne Disease ........ 85Strategies for the Future ........................................................ 87A Cooperative Approach to the Safety of Sprouts ................ 89Anticipating the Future: Food Safety Issues on the Horizon.....92

Conclusions .................................................................................... 93

References ..................................................................................... 97

Table of Contents

On the CoverThe image on the cover is a scanning electron micrograph ofListeria monocytogenes, an emerging foodborne pathogen.

2000 S. Lowry/Univ. Ulster/Stone


The continued occurrence of

foodborne illness is not evidence of the

failure of our food safety system. In

fact, many of our prevention and

control efforts have beenand

continue to behighly effective. The

U.S. food supply is arguably among the

safest in the world, but significant

foodborne illness continues to occur.

Despite great strides in the area of

microbiological food safety, much

remains to be done.Foodborne illness is not a simple

problem in need of a solution; it is a com-plex combination of factors that must bemanaged on a continual basis. Aside fromthe inherent ability of pathogens them-selves to evolve, pathogens victims andthe microbial environment play a role inthe changing nature of foodborne illness,opening new niches and creating new vul-nerabilities. No matter how sophisticatedand complex a system is developed, foodsafety management is never finished orcomplete, because change is constant.

Recognizing that food safety is a fun-damental and continuing issue, the Insti-tute of Food Technologists commis-sioned an expert panel to review theavailable scientific literature related toemerging microbiological food safety is-sues. The experts were charged withidentifying the factors that make a mi-croorganism emerge as an importantfoodborne pathogen and identifyingmechanisms that use this knowledge toimprove the safety of our food supply.The objective of this report is to increaseunderstanding, among IFT membersand other interested parties, of the scien-

tific information on emerging foodbornepathogens relative to public policy issuesand strategies for preventing foodborneillness.

Trinity of Factors

At the simplest level, foodborne ill-ness can be reduced to three factors: thepathogen, the host, and the environmentin which they exist and interact (see Fig.1a). Complex relationships exist amongthese factors, and all three factors arenecessary for foodborne illness to occur.For example, a susceptible host may con-sume food that contains a significantamount of a microorganism, but if themicroorganism does not possess thetraits necessary to cause illness, food-borne disease does not occur. Similarly,adequately cooking a food to kill thepathogenic microbes can eliminate theexposure factor and render the food safe.

When one or more of the three fac-tors changes, new foodborne pathogensemerge. For example, host susceptibil-ity can increase so much that existingmicroorganisms that do not cause ill-ness in the general population achievepathogen status in the newly immuno-compromised individuals. The changealso can be increased virulence, e.g.,when a microorganism acquires charac-teristics that help it invade the humanbody. Or it can be new exposure, e.g.,when fruit from one region carries apathogenic microorganism to popula-tions in a different geographic regionthat have never before been exposed.

This trinity is also the key to reduc-ing foodborne illness. Prevention andcontrol efforts often focus on the contri-bution of one of these factors, such aswashing vegetables to remove surface

contamination (Fig. 1b). In many cases,however, the most effective approach ad-dresses more than one factor. Currenttechnologies and production methodscannot provide a food supply that iscompletely free of all pathogenic micro-organisms. Fortunately, even small re-ductions in several factors can have asubstantial combined effect (Fig. 1c).

Evolution of Controls

New technologies, production prac-tices and food manufacturing processesare developed to meet the needs of achanging society. Early food preservationmethodssuch as canning, cheese mak-ing, bread making, brewing, fermentation,pickling, salting, and dryingwere usedto provide sufficient year-round foodavailability. Later developments reflected anew focus on food safety, variety, conve-nience, and nutritive and sensory quality.

At the beginning of the 20th century,contaminated milk, meat, and otherfoods caused large outbreaks and manysporadic cases of foodborne disease, of-ten with fatal consequences. The revolu-tion in sanitation and hygiene related tofood and water and the almost universaladoption of thermal pasteurization formilk produced tremendous improve-ments in food safety. New technologieswith increasing sophistication have yield-ed continued improvements in microbi-ological food safety while delivering bet-ter quality foods with greater nutritionalvalue and superior sensory characteris-tics (see Table 1).

Innovations in packaging have beenintegral to the developments in food pro-cessing and product development. Pack-ages contain and protect their food con-tents and inform consumers; they also

Introduction

Fig. 1a- Foodborne Illness Fig. 1b-Reducing One Factor Fig. 1c-Reducing Multiple Factors

5EXPERT REPORT

preserve, perform, communicate, and sell(Downes, 1989). From the hermeticallysealed containers for shelf-stable foodsdeveloped in the early part of the 19th

century, to the metal cans for heat-pro-cessed foods, folding cartons, and milkbottles of the latter part of the 19th centu-ry, to the boil-in-bags, plastic tubs, highdensity polyethylene gallon milk jugs,aseptic cartons, and microwavable poly-mers of the 20th century, packaging hasplayed a key role in the development ofthe food industry in the Western worldin the 20th century (Downes, 1989).

However, changes in technology arenot without risk. Conventional wisdomof decades ago held that properly refrig-erated foods would remain safe becauseit was thought that pathogenic bacteriawould not grow at refrigeration tempera-tures, but this is not always the case(Marth, 1998). Innovations in food pro-cessing, such as modified atmospherepackaging, can offer the benefit of greatlyextending the shelf life of refrigeratedfoods but may present microbiological

safety challenges. For example, modifiedatmosphere packaging of fresh packed,sliced mushrooms may allow the growthof Clostridium botulinum and potentialtoxin production (Doyle, 1998). Alteringthe package, incorporating microscopicholes to allow oxygen to permeate the in-terior of the packaged product, was an-other factor critical to ensuring the safetyof modified atmosphere packaged freshpacked, sliced mushrooms. For extendedshelf life refrigerated foods, strict tem-perature control and acceptable productshelf life are critical factors to consider(Doyle, 1998). As new technologies areintroduced, they must be evaluated fortheir potential effect on microbiologicalfood safety.

Despite all of the significant advanc-es to date, our growing knowledge basecontinues to expose the role of variousfoods and technological innovations infoodborne hazards, and changes in thefood, the consuming public, and thepathogens themselves continue to makefoodborne disease an important and

ever-changing challenge both for the in-dustrialized and the developing world.

Evolution of Food Safety Policies

Current U.S. food safety policies arethe accretions of decades of relatively in-dependent efforts to address specificproblems. Most are rooted in the sani-tary revolution that occurred at the be-ginning of the 20th century, and theyhave characteristics that have served uswell during the transition from an agrar-ian to an industrialized society.

Generally, these regulatory policiesrespond in one of three ways to obvioushazards that pose clear risk to humanhealth. First, for hazards that havestraightforward technical fixes, regula-tions require the application of the ap-propriate technologies. Regulatory stan-dards frequently have been set at the per-formance limit of the technology or thedetection limit for the analytical test usedfor process verification. However, tech-nologies to mitigate hazards are not al-

Early times HeatingCooking food kills many foodborne pathogens

1770s-1800s Canning/Thermal ProcessingSignificant discoveries in response to industrialization forces and Napoleons armies need for less dependence on localprovisions

1890s PasteurizationThermal treatment of raw milk to prevent milk from transmitting pathogens

1920s - 1930s Safe Canning/Processing ParametersCalculation of product heat penetration curve and initial microbial contamination level to determine minimum time-temperaturecombination for commercial sterility

1940s FreezingMechanical quick-freezing methods to preserve while maintaining quality

1950s Controlled Atmosphere PackagingReduced oxygen levels, increased concentrations of carbon dioxide, or selective mixtures of atmospheric gases to limitrespiration and ethylene production, delay ripening and decay, and increase refrigerated product shelf life

1960s Freeze DryingRapid deep-freezing followed by sublimation of water by heating the frozen product in a vacuum chamber. Best known appliedto coffee, to preserve delicate aroma compounds and maintain flavor and odor

1940s-1980s Aseptic Processing and PackagingHigh-temperature, short-time sterilization of food product independent of the container, container sterilization, and filling ofproduct in sterile atmosphere, resulting in increased food quality and nutrient retention

IrradiationNon-thermal process to kill pathogens, insects, and larvae, inhibit sprouting, and delay ripening and food spoilage

1990s Carcass Spray Treatments (e.g., water, acid), Steam Vacuuming, Steam PasteurizationCarcass decontamination interventions to meet microbiological performance criteria

High Pressure ProcessingFoods subjected to specified pressures and temperatures to preserve food while maintaining quality

Table 1. Evolution of Food Processing (Goldblith, 1989; IFT, 2000a, 1989; Lund, 1989)

ways apparent. In these cases, the regula-tory response has been to either keep thehazardous food out of the marketplaceor to forgo regulatory action and rely onprudent people to protect themselves.

Numerous food safety concernshave been successfully addressed by thisregulatory paradigm. The promulgationof regulations for low acid canned foodvirtually ended the historic associationof botulism with commercially cannedfood. Under the regulations, commer-cially canned foods undergo a mini-mum calculated destruction of 12D for

C. botulinum. Another very successfulexample is the water quality standardsfor shellfish growing waters. Thesestandards protected consumers fromshellfish-associated typhoid fever at atime when typhoid was fairly commonin coastal communities and contami-nated shellfish was an important sourceof infection. Historically, the safety offoods without a pathogen eliminationstep earlier in the line has dependedupon proper cooking.

The extraordinary complexity ofcontemporary food safety issues presents

major challenges to food safety policyformulation. Factors like the globalsourcing of products and ingredients,changes in land use, and evolution ofscience and technology have radicallychanged hazards associated with a par-ticular food and the control optionsavailable.

These challenges present themselvesin many ways depending on the particu-lar hazard. For example, the indicator or-ganisms used to predict the presence ofSalmonella Typhi in shellfish growingwaters poorly predict the presence of

Microbiology 101

The characteristics of the variousmicroorganisms are part of whatmakes microbiological food safety is-sues so complex. One type of micro-organism may thrive under condi-tions that are fatal to a different mi-crobe. Some microbial pathogenscause disease by infecting the humanhost, while others produce toxins thatcause illness. Some pathogens canmultiply in food during storage whileothers cannot. Because most micro-organisms can reproduce within amatter of minutes, these pathogenscan evolve quickly when environ-mental stresses select for strains withunique survival characteristics.

Types of Microorganisms

Microorganisms are divided intothree distinct categories: prokaryotes,eukaryotes, and viruses. Bothprokaryotes and eukaryotes are highlyregulated cells that possess elaboratesensing systems, enabling them to beaware of and react to their environ-ment as it changes.

ProkaryotesBacteria

Prokaryotes are single-celled livingmicroorganisms that have no nuclearmembrane separating their geneticmaterial from the cytoplasm withinthe cell. They are microscopic, in thatthey cannot be seen with the unassist-ed human eye. Bacteria are generallyfree-living in the environment, al-though some have complex nutrientrequirements and can grow only inspecial niches.

Bacteria are arguably the worlds

most successful life form. Their diversityand complexity through simplicityhave and will continue to assure theirsurvival. Although the vast majority ofbacteria are harmless or helpful to hu-mans, some are pathogenic.

EukaryotesParasites and Fungi

Eukaryotes are multicellular livingorganisms that possess a nuclear mem-brane that separates their nucleic acidfrom the cytoplasm. They are larger thanbacteria and are sometimes able to beseen by the human eye. Eukaryotes aregenerally free-living in the environment.

Some protozoa can be foodbornepathogens (e.g., Cyclospora, Giardia).They usually exist in multiple forms,some of which are environmentally sta-ble, but they seldom multiply in or onhuman food. Fungi such as molds andyeasts can multiply in or on human foodand also can be pathogenic.

Viruses

Foodborne pathogenic viruses arecomprised of a single type of nucleicacid surrounded by a protein coat. Vi-ruses are not free-living. In fact, theyare not living beings at all, but are obli-gate intracellular parasites. They aresmaller than bacteria (10-350nm), andsome viruses prey on bacteria (bacte-riophages).

Types of Bacteria

Bacteria come in various shapes,such as rods, spheres (cocci), and spirals.As a response to certain adverse environ-mental conditions, some bacteria canform spores. The spores start as denseregions within the cell, but as the cell de-

teriorates, the spore is released into theenvironment. Spores are extremely im-pervious to physical and chemical harm,making them difficult to inactivate in thefood processing environment.

In general, the bacterial kingdom canbe divided into gram-positive and gram-negative cells. These designations aregiven based on the results of a stainingprocedure that separates the two divi-sions by color, which is reflective of thecomposition of their cell wall.

Growth and Life SpanBacteriaBacteria are the most

adaptable life form on Earth. Bacteriahave optimal (preferred) growth condi-tions, but some can grow and/or surviveat extremes of temperature, pH, osmoticpressure, and barometric pressure. Bacte-ria are genetically programmed for maxi-mum survival.

At optimal growth conditions, a bac-terial cell may divide every 10-20 min-utes. Assuming no death, a single cellcould thus give rise to a bacterial massequal to the Earths mass in one or twodays. Obviously death occurs, because offactors such as nutrient limitations orend product toxicity.

VirusesIn general, virusesreproduce more rapidly than bacteria,but they can only grow in an infectedhost cell, not in food. A single infectedhost cell may give rise to hundreds orthousands of new viruses within a fewhours, each of which may infect a newhost cell.

Roles of FoodborneMicroorganisms

Not all microorganisms in foods areharmful. In fact, only a small proportionof foodborne organisms have been asso-


7EXPERT REPORT

cooking will kill this parasite, the foodsassociated with human infectionrasp-berries, basil, and other fresh produceare generally not cooked before con-sumption.

When microorganisms such as Shigel-la or the hepatitis A virus are found onfresh produce, it can be difficult to deter-mine whether the contamination oc-curred during food preparation, duringdistribution, during processing and pack-ing, or in the growing fields. Under thesecircumstances, the appropriate point ofintervention is difficult to identify.

Modifications to thermal processinghave made a wide array of food typespossible, including a proliferation ofpasteurized food products distributedin flexible plastic packages that requirerefrigeration. Although thermal process-ing inactivates a large majority of thevegetative spoilage organisms, in con-trolled atmosphere packaging, it alsodrives off oxygen and fails to inactivatesporeformers like C. botulinum. If thecold chain is not properly maintained,botulinum toxin can be produced beforefood spoilage is detectable.

Vibrio, hepatitis A, or Norwalk-like vi-ruses. Typhoid fever is now extremelyuncommon in U.S. coastal waters, and itis now these other shellfish-associatedpathogens from which we need to protectourselves.

Pathogens on foods that are oftenconsumed without cooking present asignificant challenge. The pathogen Cy-clospora cayetanensis is very likely ofhuman origin, but our limited knowl-edge about its natural ecology does notenable us to assure its absence fromfresh produce. Although adequate

ciated with disease in normal, healthyanimals and humans.

Commensal Microbes

Virtually all raw food contains mi-croorganisms. The source of these is theproduction environment, where a widevariety of organisms are environmentallyubiquitous. Processing and handling offoods can also contribute to the typesand numbers of commensal organismson foods. Most of these commensal or-ganisms are harmless to animals and hu-mans; in fact, they may actually be bene-ficial in that they provide high levels ofcompetitive microflora that usuallygrow faster than contaminating patho-gens. Although the purpose of manycommon food processing methods suchas pasteurization and canning is the de-struction of pathogens, commensal mi-croorganisms are often destroyed in theprocess as well.

Spoilage Microbes

Spoilage may be defined as a condi-tion in which food becomes inedible be-cause of undesirable changes in color,flavor, odor, appearance, and texture.This condition occurs primarily be-cause the organisms grow to high levels,producing enzymes that break downfood components such as fats, proteins,and sugars. In most instances, spoilageis caused by commensal organisms thathave been allowed to reach populationsin the range of 105 to 107 CFU/g offood. Different classifications of foods(such as red meats, vegetables, fish, etc.)have different spoilage profiles becausethe food environment will dictate whichorganisms will grow, dominate, and

cause spoilage. For instance, spoilage ofraw meats is almost always associatedwith gram-negative psychrotrophs, theso-called cold-thriving organisms, be-cause they grow at refrigeration temper-atures. Fresh fruits are frequentlyspoiled by yeasts and molds that areable to thrive in acidic conditions. Mostspoiled foods do not cause foodbornedisease; in reality, the high levels ofspoilage organisms have frequentlyout-competed the pathogens, keepingpathogen growth in check.

Beneficial Microbes

Perhaps the most widely recognizedgroup of beneficial foodborne microor-ganisms are the members of the lactic acidbacteria (LAB) group. This is a functionalname used to classify fermentative organ-isms that produce lactic acid as the prima-ry by-product of metabolic activity, al-though other products, such as alcoholand carbon dioxide may be produced aswell. These metabolic products are re-sponsible for the characteristic flavor,odor and texture of fermented food prod-ucts. The lactic acid bacteria are com-monly used in dairy, vegetable and meatfermentations. Notable members of thisgroup belong to the Lactococcus, Lactoba-cillus, Pediococcus, and Leuconostoc genera.Some species of yeasts and molds can alsobe used in the commercial production offermented foods, including Saccharomycescerevisiae, used frequently for producingbread, beer and wines, and Aspergillusoryzae, used in the fermentation of orien-tal foods such as soy sauce.

Foodborne Pathogens

Foodborne pathogens encompass arelatively small group of foodborne micro-

organisms that are associated with dis-ease in humans and/or animals. Patho-genic microbes are capable of causing ill-ness, either by infecting the host or byproducing toxins that cause the host tobecome ill. Some microorganisms arepathogenic in one host species but not inanother. For example, Escherichia coliO157:H7 causes illness in humans butnot in cattle, its primary host.

Microbiological Indicators

An index or indicator refers to asingle or group of microorganisms, oralternatively, a metabolic product,whose presence in a food or the envi-ronment at a given level is indicativeof a potential quality or safety prob-lem. Microbiological indicators areused in place of direct testing for apathogen, largely because they areeasier to work with. Indicators maybe a specific microorganism (e.g., E.coli), a metabolite (e.g., lactic acid ti-tration), or some other indirect mea-sure (e.g., ATP bioluminescence as ameasure of sanitation efficacy). Usinga specific microorganism as an indi-cator is difficult, because appropriateindicator organisms are difficult toidentify. An ideal indicator organ-ism: (1) has a history of presence infoods at any time that the targetpathogen or toxin might be present;(2) is present at concentrations di-rectly related to that of the targetpathogen or toxin; (3) is absent fromfood when the target is not present;(4) has growth rates equivalent to, orslightly greater than, the pathogen;(5) has rapid, simple, and inexpensivequantitative assays available; (6) hassimilar resistance profiles to the tar-get; and (7) is nonpathogenic.


Non-thermal processes also havebeen modified over time. Consumerswant foods with fewer preservatives, lesssalt, fewer calories, and better texture; thefood industry has responded with manynew formulations. However, substitut-ing ingredients with gums or other fat re-placers and reducing salt or sugar can re-quire a reevaluation of food safety con-trol measures. For example, the replace-ment of sugar with an alternative sweet-ener in hazelnut yogurt and failure toevaluate the impact of this change onfood safety resulted in an outbreak ofbotulism (OMahony et al., 1990).

In addition to the impact of changesin processing, scientists have discoveredthat some foodborne pathogens survivetraditional processes better than expect-ed. For example, Salmonella have beenfound in 60-day aged cheese and on rawalmonds, and newly recognized patho-gens such as E. coli O157:H7 are moretolerant of conditions of low pH andother traditional barriers than antici-pated. The resistance of pathogens totraditional treatments affects the safetyof our drinking and processing water aswell. We have relied on chlorination torid drinking water of pathogens for de-cades, but recent waterborne outbreakshave been caused by parasites, such asGiardia and Cryptosporidium, that arenot controlled by chlorine.

Handling during preparation in thehome or foodservice establishment mayaffect the pathogens present in the food.For foods in which preparation shouldkill the pathogens, recurring outbreaks offoodborne illness highlight our limitedability to tightly control food preparationbehaviors and practices. Certainly the in-cidence of foodborne disease would besignificantly reduced if we could eliminatepathogens earlier in the food chain. How-ever, the initial number of the pathogen inthe food is only one factor in the risk offoodborne illness. At some point, im-provements in sanitation will produceonly small incremental gains. As the levelof contamination becomes increasinglysmall, other food safety approaches willneed to be adopted.

Incidence and Prevalence ofFoodborne Illness

Food safety is a complex issue that de-pends on a number of interrelated envi-ronmental, cultural, and socioeconomicfactors. More than 200 known diseasesare transmitted through food, and more

than half of all recognized foodborne dis-ease outbreaks have unknown causes, in-dicating the real number of disease-caus-ing agents is likely much larger than 200.The recognized causes of foodborne ill-ness include viruses, bacteria, parasites,manmade chemicals, biotoxins, heavymetals, and prions. The symptoms offoodborne illnesses range from mild gas-troenteritis to life threatening neurologic,hepatic, and renal syndromes.

In the United States, foodborne dis-eases have been estimated to cause ap-proximately 76 million illnesses,325,000 hospitalizations, and 5,000deaths each year (Mead et al., 1999). Apathogens ability to cause illness can bevery different from the severity of theillness it causes. Some pathogens suchas Norwalk-like viruses cause a greatnumber of illnesses (9.2 million peryear) but the fatality rate is very small(0.001%) (see Table 2). Others such asVibrio vulnificus cause few illnesses (47per year), but many of those illnessesare fatal (38.3%). Salmonella, Listeriamonocytogenes, and Toxoplasma gondiiare responsible for more that 78% ofthe deaths but only approximately 11%of total cases of foodborne disease. Theissue is further complicated by patho-gens, such as L. monocytogenes, thatcause little or no illness in healthy indi-viduals but cause severe illness anddeath in sensitive populations, includ-ing the immunosuppressed, the elderlyand the developing fetus. Prioritizingfood safety resources can be difficult.

Scientists gather data about the inci-dence and severity of foodborne illnessthrough surveillance, both passive andactive. Mild cases of illness often are notcaptured by surveil-lance programs becausemedical intervention isnot required for recov-ery. Many steps are re-quired for a foodbornepathogen to be identi-fied as the cause of ill-ness and for data to begathered through sur-veillance programs (seeFig. 2). Furthermore,because many patho-gens transmittedthrough food also maybe spread by contami-nated water and per-son-to-person contact,the role of food can bedifficult to assess. Fi-

nally, some proportion of foodborne ill-ness is caused by pathogens that have notyet been identified and thus cannot bediagnosed. In fact, many of the patho-gens of concern today were not recog-nized as causes of foodborne illness just20 years ago (Mead et al., 1999).

New scientific advances make it pos-sible to approach foodborne illness froma different, broader perspective. Morepowerful diagnostic procedures and bet-ter communication technology allow im-proved tracking and surveillance forfoodborne illness. Genetic identificationmethods allow scientists to link geo-graphically distinct outbreaks of food-borne illness to a single source. Patho-gens can appear to emerge simply be-cause scientists develop methods to iden-tify the presence of certain microorgan-isms and link them to foodborne disease.

New technologies based on recentadvances in genomics also give scientistsgreater insight into pathogen virulenceand evolution, opening the door to bettercontrols and therapeutics. Future scien-tific advances will continue to enhanceefforts to identify and understand food-borne pathogens, and these insights willcontribute the data necessary for science-based risk assessment and food safetymanagement.

Emergence of Pathogens

The terminology newly emergingpathogen has become somewhat over-used, or perhaps it is merely ill defined.True pathogen emergence could be di-rectly linked to evolution, whether thatevolution occurs gradually or rapidly.

In a broader context, emergence can

Sick individual seeks medical attention.

Clinician considers cause to be foodborne,requests proper tests and collects appropriate specimen.

Proper test is performed correctly.

Results are reported to the health departmentand ultimately the CDC.

Regulatory agency investigates.

Identification of the source of the illnessprompts product recall or other action.

Fig. 2. Foodborne Illness Identification

9EXPERT REPORT

Microorganism

Bacteria

Bacillus cereus

Brucella spp.

Campylobacter spp. C. jejuni

Clostridium botulinum

Clostridium perfringens

Escherichia coli

Enterotoxigenic

Enteropathogenic

E. coli O157:H7

Enteroinvasive

Listeria monocytogenes

Salmonella spp.

S. Typhi and S. Paratyphi

Other Salmonella spp.

Shigella spp.

Staphylococcus aureus

Streptococcus spp.

Group A (S. pyogenes)

Principal Symptomsa

DiarrhealWatery diarrhea, abdominal cramps and painEmeticNausea and vomiting

Sweating, headache, lack of appetite, fatigue, feverc

Watery diarrhea, fever, abdominal pain, nausea, headache,muscle pain

Weariness, weakness, vertigo, double vision, difficultyswallowing and speaking

Intense abdominal cramps, diarrhea

Watery diarrhea, abdominal cramps, fever, nausea, malaise

Watery or bloody diarrhea

Severe abdominal cramps, watery or bloody diarrhea,hemolytic uremic syndrome

Abdominal cramps, vomiting, fever, chills, generalizedmalaise, hemolytic uremic syndrome

Nausea, vomiting, diarrhea; influenza-like symptoms;meningitis, encephalitis; septicemia in pregnant women,their fetuses or newborns; intrauterine or cervical infectionthat may result in spontaneous abortion or stillbirth

Typhoid-like fever, malaise, headache, abdominal pain, bodyaches, diarrhea or constipation

Nausea, vomiting, abdominal cramps, fever, headache;chronic symptoms (e.g., arthritis)

Abdominal pain and cramps; diarrhea; fever; vomiting;blood, pus or mucus in stools; tenesmus

Nausea, vomiting, retching, abdominal cramps, prostration

Sore, red throat; pain on swallowing; tonsillitis; high fever;headache; nausea; vomiting; malaise; rhinorrhea

Onseta

6-15 hr0.5-6 hr

Days to weeksc

2-5 days

18-36 hr

8-22 hr

24 hr

n/a

1-2 days

12-72 hr

Few days-3 weeks

7-28 daysc

6-48 hr3-4 weeks

12-50 hr

1-7 hr

1-3 days

Potential Food Contaminationa

Meats, milk, vegetables and fishRice products, starchy foods (e.g., potato, pasta, and cheese products

Raw or unheated processed foods of animal origin (e.g., milk, milkproducts, cream, cheese, butter)c

Raw chicken, beef, pork, shellfish; raw milk

Improperly canned or fermented goods

Meat, meat products, gravies

Foods contaminated by human sewage or infected food handlers

Raw beef and chicken; food contaminated by feces or contami-nated water

Undercooked or raw hamburger, alfalfa sprouts, unpasteurized juices,dry-cured salami, lettuce, game meat, cheese curds, raw milk

Food contaminated by human feces or contaminated water,hamburger meat, unpasteurized milk

Raw milk, cheeses (particularly soft-ripened varieties), rawvegetables, raw meats, raw and smoked fish, fermented sausages

Raw meats, poultry, eggs, milk and dairy products, fish, shrimp,frog legs, yeast, coconut, sauces and salad dressings

Salads (potato, tuna, chicken, macaroni), raw vegetables, bakeryproducts (e.g., cream-filled pastries), sandwich fillings, milk anddairy products, poultry

Meat and meat products, poultry, egg products, salads (egg, tuna,chicken, potato, macaroni), cream-filled bakery products, milk anddairy products

Temperature-abused milk, ice cream, eggs, steamed lobster, groundham, potato salad, egg salad, custard, rice pudding, shrimp salad

Illnessesb

27,360n/an/a

777

1,963,141n/a

58

248,520

55,594

n/a

62,458

n/a

2,493

n/a

659

1,341,873

89,648

185,060

50,920

n/a

Deathsb

0n/an/a

6

99n/a

4

7

0

n/a

52

n/a

499

n/a

3

553

14

2

0

n/a

Table 2. Foodborne Disease in the United States, Including Estimated Annual Prevalence (FDA/CFSAN, 2002; Mead et al., 1999)

a n/a indicates FDA/CFSAN (2002) did not provide information.b n/a indicates Mead et al. (1999) did not provide an estimate for this pathogen.c As described by ICMSF (1996).

10INSTITUTE OF FOOD TECHNOLOGISTS

Principal Symptomsa

Diarrhea, abdominal cramps, nausea, vomiting, fever, chills, dizziness

Mild watery diarrhea, acute diarrhea, rice-water stools

Diarrhea, abdominal cramps, fever, vomiting, nausea; blood or mucus-containing stools

Diarrhea, abdominal cramps, nausea, vomiting, headache, fever, chills

Fever, chills, nausea, septicemia in individuals with some underlyingdiseases or taking immunosuppressive drugs or steroids

n/a

Fever, abdominal pain, diarrhea and/or vomiting

Tingling or tickling in the throat, vomiting or coughing up worm(s),abdominal pain, nausea

Exiting of roundworm, vague digestive tract discomfort, pneumonitis

Severe watery diarrhea (intestinal illness); coughing, fever and intestinaldistress (pulmonary and tracheal illness)

Watery diarrhea, explosive stools, loss of appetite, bloating, stomachcramps, vomiting, aching muscles

Diarrhea, abdominal cramps, bloating, weight loss, malabsorption

Discharge of proglottids, anal itching, abdominal pain, nausea, weakness,weight loss, intestinal disorder

Flu-like symptoms, swollen lymph glands, muscle aches and painsd

Severe gastrointestinal distress, nausea, vomiting, headaches, weakness,muscle pain, chills, difficulty breathing, body swelling, visual deficiencies,fever, night sweatingc

Fever, anorexia, malaise, nausea, abdominal discomfort; jaundice mayfollow

Nausea, vomiting, low-grade fever, diarrhea, abdominal pain

Vomiting, watery diarrhea, low-grade fever; severe in infants and youngchildren

Microorganism

Group D (other Streptococcusspp.)

Vibrio cholerae

V. cholerae serogroup O1

V. cholerae serogroup non-O1

Vibrio parahaemolyticus

Vibrio vulnificus

Vibrio, other

Yersinia enterocolitica

Parasites and Protozoa

Anisakis simplex

Ascaris lumbricoides

Cryptosporidium parvum

Cyclospora cayetanensis

Giardia lamblia

Taenia spp.

Toxoplasma gondii

Trichinella spiralis

Viruses

Hepatitis A

Norwalk-like viruses

Rotavirus

Onseta

2-36 hr

6hr-5 days

48 hr

4-96 hr

16 hr

n/a

24-48 hr

1hr-2 weeks

n/a

1-12 days

1 week

1 week

n/a

10-23 daysd

3-14 days

10-50 days

24-48 hr

1-3 days

Potential Food Contaminationa

Underprocessed or improperly prepared sausage, evaporatedmilk, cheese, meat croquettes, meat pie, pudding, raw milk,pasteurized milk

Raw, improperly cooked, or recontaminated shellfish

Raw, improperly cooked, or recontaminated shellfish

Raw, improperly cooked, or recontaminated shellfish and fish

Raw or recontaminated oysters, clams, crabs

n/a

Meats, oysters, fish, raw milk

Raw or undercooked seafood

Raw produce grown in soil contaminated by insufficientlytreated sewage

Foods contaminated via food handlers and manure

Water or food contaminated with infected stool

Food contaminated via infected food handlers

Raw or undercooked beef, pork

Raw or undercooked meats, especially pork, lamb,venisond

Raw or undercooked pork or wild game

Shellfish, salads, other foods contaminated via infectedfood handlers or water

Shellfish and salad ingredients contaminated by infectedfood handlers or fecally contaminated water

Foods contaminated via fecal contaminated food handlers

Illnessesb

n/a

49

n/a

n/a

n/a

47

5,122

86,731

n/a

n/a

30,000

14,638

200,000

n/a

112,500

52

4,170

9,200,000

39,000

Deathsb

n/a

0

n/a

n/a

n/a

18

13

2

n/a

n/a

7

0

1

n/a

375

0

4

124

0

Table 2. Foodborne Disease in the United States, Including Estimated Annual Prevalence, continued

a n/a indicates FDA/CFSAN (2002) did not provide information.b n/a indicates Mead et al. (1999) did not provide an estimate for this pathogen.c As described by ICMSF (1996).d From CDC (2002).

11EXPERT REPORT

be used to describe a recent significantchange. Using this interpretation, apathogen could be described as emergingwhen it is first linked to disease, when theillness it causes suddenly increases infrequency or severity, or even when apathogen recognized for a significantamount of time suddenly reappears. Interms of public perception, all these sce-narios may be considered emerging mi-crobiological food safety issues.

Public Perception of Emergence

C. cayetanensis, a recent arrival inthe United States, is an example of thekinds of surprises that can occur as aresult of increasing world trade inready-to-eat foodstuffs. As foodstuffsare transported ever greater distances,pathogens can be transported to newareas as well. The United States also hasexperienced illness outbreaks caused bySalmonella serotypes either rarely ornever before isolated here, apparentlyfor the same reason(s) that Cyclosporaemerged.

Campylobacter jejuni and L. monocy-togenes were well accepted as foodbornepathogens in the 1970s and 1980s, re-spectively, and, as such, they are hardlynew. Prior to 1972, C. jejuni could not becultured from feces, so it was not recog-nized as a common human pathogen, norwas the frequency of its presence in food,particularly raw poultry, realized. Withimprovements in both the sensitivity andrapidity of the available methodology, C.jejuni may appear to be an emergingpathogen. However, scientists cannot de-termine if the frequency of C. jejuni isola-tion from human stool or food is truly in-creasing, or if laboratory-induced biasgives the appearance of an increase. Simi-larly, methods for isolation of L. monocy-togenes from foods and the environmenthave improved since its emergence as afoodborne pathogen in the mid-1980s. Asa result, it appears that the frequency of L.monocytogenes in foods and the environ-ment is increasing, but the influence oflaboratory-induced bias is difficult toweigh. For both of these pathogens, in-creased awareness of analytical laboratorypersonnel and physicians have affected thefrequency of isolation from foods and di-agnosis of human illness.

Changes in foods serving as vectorshave brought new attention to a long-recognized pathogen, C. botulinum, thecausative agent of botulism. Botulismfrom commercially canned foods has

been essentially eliminated; however, cas-es of botulism in the late 1980s and early1990s led scientists to discover that C.botulinum could grow and produce tox-ins in foods such as twice-baked pota-toes, grilled onions, and garlic-in-oil.When these new food associations werediscovered, even C. botulinum was de-scribed by some as an emerging patho-gen. Large outbreaksalthough recur-rences of situations that have happenedin the pastcan propel a pathogen toemerging status whether truly deservedor not. In many cases, it is the new foodvehicle that is the surprise, and not somuch the pathogen itself.

Emergence as a Function of Evolution

Evolution can produce pathogensthat are truly emerging, in that the mi-croorganisms have new characteristicsthat enable them to cause disease. Bacte-ria have evolved highly sophisticated sig-nal transduction systems that allow themicroorganisms to respond at a geneticlevel to environmental conditions in acoordinated manner. The many envi-ronmental stimuli that trigger such activ-ity are collectively referred to as stresses.

The genetic response to stress(es) canactivate certain virulence determinants, amicrobes contingency plan for surviv-ing in hostile environments. Beyond ac-tivating virulence determinants, externalstresses also accelerate the bacterias rateof evolution, meaning new pathogenscould emerge relatively quickly. Suchevents probably contributed substantial-ly to the evolution of the highly virulentO157:H7 strain of E. coli.

Bacteria are constantly mutating, andenvironmental forces may select a muta-tion that confers an advantage in the faceof the environmental challenge. Themany and varied environmental stressescommonly include starvation, high orlow pH, oxidation, heat, cold, and os-motic imbalance. The genetic responseto one stress may protect the microbefrom a different stress, a phenomenonknown as cross protection.

Bacteria possess specific genetic loci,particularly in contingency genes, thatare highly mutable when compared withhousekeeping genes that are relativelystable. Contingency genes help a mi-crobe successfully interface with envi-ronmental change, while housekeepinggenes run the routine cellular machinery.Genetic variation can occur in manyways, including increased mutation.

Stresses can create microorganisms withgreatly enhanced mutation frequencies(1000-fold or more). The large numberof different mutations increases thechance of a mutation that will enablesurvival in the stressful environment.These hypermutable microorganismsalso may more readily share DNA withother microorganisms, even remotely re-lated species. Horizontal transmissionof genetic material from one microor-ganism to another can result in quantumjumps in evolution. Gene transfer be-tween separate lineages of a bacterialpathogen can lead to the emergence ofaltogether new pathogens. Recently se-quenced bacterial genomes reveal moreextensive exchange of genetic materialbetween species than had been expected.

Complex Drivers of Change

No matter how emergence is defined,it becomes clear that the interrelation-ship of pathogen, host and environmentplays a key role in microbiological foodsafety. A number of factors will drive theemergence of new food safety concerns,including changes in the characteristicsof the consuming public, changes in thefoods we manufacture and sell, changesin the hazards themselves, and changesin the ability of public health officials toidentify illnesses as foodborne and totrace the illnesses to their food source.

Host Factors

Changing demographic characteris-tics of consumers affect the number ofcases of foodborne illness. As theworlds population continues to grow,constant rates of disease will increase thetotal number of cases. In addition, theproportion of the population that is athigh risk of foodborne infections, illness,and death is rising. Factors that increasethe impact of foodborne diseases includeage, chronic diseases, immunosuppres-sive conditions, and pregnancy. The im-mune system functions less effectively inthe elderly, putting them at greater risk. Agrowing proportion of our population isimmunocompromised due to HIV infec-tion, cancer chemotherapy, and drugsused to combat rejection of transplantedorgans. Larger numbers of people withchronic diseases, like diabetes, now livelonger and also are at increased risk offoodborne diseases.

Other consumers are at elevated riskof foodborne illness because of the in-


creased likelihood of exposure. This ele-vated risk is sometimes due to food pref-erences based on ethnicity, age, or gender.Young adult males, for example, aremore likely to eat inadequately cookedground beef.

Environmental Factors

Food industry economics and tech-nical factors continue to drive consolida-tion in primary agricultural productionand food processing. Although thishelps reduce costs and assure uniformquality, when a large lot of a contaminat-ed food enters distribution, the scope ofthe resulting outbreak is increased.

Global sourcing also carries the po-tential to move pathogens and toxinsfrom areas in which the pathogen is in-digenous to areas in which it has not pre-viously existed. Unfamiliarity compli-cates diagnosis and containment and canresult in outbreaks that become quitelarge before they are recognized. Haz-ards are truly mobile, and our food safe-ty programs must be very agile to reduceour risk.

Even slight increases in environmen-tal temperatures can significantly affectthe risk of foodborne illness. The growthof algae in surface waters, estuaries, andcoastal waters is sensitive to temperature.About 40 of the approximately 5,000known species of marine phytoplankton(algae) can produce biotoxins, whichmay reach human consumers throughshellfish. Warmer sea temperatures canencourage a shift in species compositionof algae toward the more toxic di-noflagellates. Upsurges of toxic phy-toplankton blooms in Asia are stronglycorrelated with El Nio, and in the Unit-ed States, paralytic shellfish poisoningand other marine biotoxin-induced dis-eases have been associated with shellstock harvested from beds traditionallyconsidered safe.

Consumer desires drive food prod-uct development. Food manufacturersrespond to desires for fresher food,low fat products, or ready-to-eat foodsby developing new processes or refor-mulating existing products. Changes inthe food processing environment orproduct formulations can create a newniche for pathogenic microorganisms.Producing familiar foods in nontradi-tional sites also may lead to introduc-tion of new food hazards; such was thecase with the first outbreaks of cy-closporiasis associated with raspberries

imported into the United States andCanada from Guatemala.

Pathogen Factors

Stable and accurate transfer of genet-ic information from parent to offspringis essential for the preservation of a spe-cies. However, keeping pace with anever-changing environment also requiresvariability. When naturally occurringbacteria, for example, divide, most of theoffspring look and act just like their par-ents, but a small proportion of the off-spring mutate, increasing the chance thatsome might survive in a new, hostile en-vironment. If the environment has notchanged, these new strains may not sur-vive, but this natural occurrence makes italmost certain that traditional food pro-cesses will fail to deliver their predictedlevel of safety at some point. This is partof nature and happens without humanintervention.

In addition to this unstimulated hy-permutability, the food production andprocessing environment can increase therate of change in foodborne pathogens.Bacterial stress responses may increasepathogen virulence, and other actionscan affect which microorganisms surviveand dominate in a particular environ-ment. For example, use of antimicrobialagents during livestock production mayselect resistant strains from a back-ground of susceptible microorganisms,increasing the likelihood that the micro-organisms in a food are resistant to thoseand related antimicrobials. Even if thesemicroorganisms are not pathogenic, theycan share the genetic material that en-ables them to resist antimicrobials withpathogenic microorganisms in the hu-man gut, producing pathogens that causeinfections that may be difficult to treat.

Through improved laboratory tech-niques, scientists are identifying adversehealth effects associated with ever-small-er levels of exposure to natural and an-thropogenic substances. New ELISA andradioimmunoassays for various myc-otoxins are pushing tolerances for com-mon mycotoxins down and are findingmore poorly characterized mycotoxinsin a broad array of commodities. Ourunderstanding of biology, however, isnot keeping up with our laboratoryskills, and judging the public health sig-nificance of positive laboratory resultsis becoming more difficult. Unlockingthe human genome and the genomes ofpathogenic microorganisms, however, is

beginning to clarify the very basis of theinteraction between humans and the mi-croorganisms that can make us sick.

Industrialized and developing nationshave improved their ability to conductsurveillance and investigate outbreaks ofdisease in humans during the last two de-cades of the 20th century, and this progressis continuing. In addition, the combina-tion of molecular biology and electronicinformation technology in centers aroundthe globe is refining the quality of the datathat links cases together around commonexposures. National and multinationalnetworks of collaborators are beingpulled together with help and guidancefrom the World Health Organization andthe Food and Agriculture Organizationof the United Nations, to facilitate therapid sharing of data.

The process of ensuring the safety offood is dynamic as well as complex.Changes in the types of food that are con-sumed, the geographic origins of foodproducts, and the ways in which differentfoods are processed affect both the risk forcontamination and the adequacy of safetymeasures. The processes used to controlfoodborne hazards to limit the potentialfor foodborne disease must be continu-ously reviewed and judged against newinformation and new hazards. Advancesin risk assessment methodologies andavailability of additional data make it pos-sible to integrate information from thevarious stages in the food productionprocess for those foodborne hazards weknow about. This capability can be usedto identify particular steps in the foodsupply system for targeted intervention tocontrol hazards and prevent disease. It ismore difficult to provide specific adviceon how to prevent foodborne hazards thathave not yet been identified.

Framework for Food SafetyManagement

Our existing approach to food safetymanagement has given the United Statesan extremely safe food supply. However,estimates of the incidence of foodborneillness clearly show that, in some cases,the existing approach to control is inade-quate. The complex, ever-changing na-ture of microbiological food safety guar-antees that new challenges will continueto emerge.

Microbiological food safety is not anissue only for microbiologists. Just as thefarm-to-table approach to food safetyhas provided an overall picture of food

13EXPERT REPORT

safety management, many scientific dis-ciplines contribute to our knowledgeabout food safety. The scientific commu-nity must pull together multidisciplinaryteams that combine microbiology, epide-miology, genetics, evolutionary biology,immunology and other areas of expertiseto enhance our understanding of the in-terrelated factors that drive emergingfood safety issues.

Just as the issues change over time, so

too must our management strategies andour regulatory framework. Regulatoryprograms must be flexible to address is-sues as they arise and to benefit from sci-entific advances. Continued research willimprove our understanding of the com-plex factors that cause foodborne illness,and surveillance programs will gatherdata to document the effectiveness of ourcontrols and identify new problems asthey emerge. A science-based food safety

management framework should use foodsafety objectives to translate data aboutrisk into achievable public policy goals.

Microbiological food safety issueswill continue to emerge. Although wecannot expect to accurately predict thedetails of complex changes such aspathogen evolution, scientific knowledgecan be used to identify the areas of great-est concern, so that we may be ready torespond as issues arise.

Science of PathogenicityPathogenicity is the ability to cause

illness. Because pathogens are living

organisms that rapidly adapt and

evolve, the methods they use to cause

illness are never static. Pathogen

evolution is continuous and is driven

by a variety of forces, only some of

which relate to human activities. The

continual evolution of foodborne

pathogens forces us to change food

production processes and products to

maintain and improve microbiological

food safety. Control strategies that

were once effective may not remain so

if the pathogens become tolerant.Fortunately, genomic and improved

molecular and imaging techniques havevastly expanded scientific understandingof the organisms that cause foodbornedisease. These tools also have enabledscientists to attribute foodborne diseaseto microorganisms that had not previ-ously been identified as pathogenic or asfoodborne.

However, researchers still have manyquestions to answer: What makes onestrain of a microbe pathogenic whenother microorganisms within the samespecies are not? How do microorganismsbecome pathogenic? Understandingpathogenicity is not just necessary fordeveloping methods to treat illness but isalso needed for pathogen control.

Pathogen control includes preven-tion of food contamination, eliminationfrom the food, reduction to an acceptablelevel, or prevention of multiplication andtoxin formation. In addition, when sci-

entists understand how a particularpathogen is able to cause illness, thenthey can look for ways to disrupt thisprocess and render the microorganismharmless or find treatments that mitigateillness. The very factors that createpathogenicity are opportunities for con-trol. Just as the pathogens adapt andevolve, so can our understanding andour response.

Nomenclature

Traditionally, the first step in under-standing foodborne pathogens has beento develop a system of nomenclature anddescriptions of microorganisms withinthis system. For the purposes of study,scientists try to classify microorganismsbased on a set of common characteristicsthat sometimes include presumed patho-genic attributes. However, as our scientif-ic understanding has improved, theinitial classifications often no longerpresent a full and accurate picture. Whennomenclature becomes outdated, ques-tions are raised about the scientific valid-ity of regulatory policies based on classi-fication schemes that predict pathogenic-

ity poorly or that cluster pathogenic andnonpathogenic microbes together underone name.

The names used to describe variousmicrobiological foodborne pathogensare based on systematic nomenclature. Itis common practice to identify an organ-ism based on its genus and species. Toprovide additional detail, classificationssuch as subspecies, strain, serotype,pathovar, and toxin type may be used(see Table 3).

In the past, the classification of mi-croorganisms has relied primarily onstructural (morphological) and func-tional (physiological) characteristics.For example, shape is a morphologicalcharacteristic, and the pattern of en-zymes produced is a physiological char-acteristic. The commonly used morpho-logical distinctions of gram-positive andgram-negative are based on differencesin cell wall composition. Morphologicalfeatures remain the primary means ofclassification for molds. Although mor-phological characteristics can classifybacteria into broad categories (e.g.,spherical, rod-shaped, or curved), bacte-ria generally have few morphological fea-

Nomenclature

Family

Genera/genus

Species

Subspecies

Serovar

Table 3. Classic Microbial Nomenclature

Example 1

Enterobacteriaceae

Escherichia

coli

O157:H7

Example 2

Enterobacteriaceae

Salmonella

enterica

enterica

Typhimurium

Example 3

Mycobacteriaceae

Mycobacterium

avium

paratuberculosis


Nomenclature ofSalmonella

Bacteria in the genus Salmonellaare important contaminants in foodand water. Recently, efforts have beenmade to simplify the nomenclatureof Salmonella. Instead of using sero-type designations (of which there aremore than 2,000) incorrectly as spe-cies designations, most Salmonellaspecies are now classified as Salmo-nella enterica and then further iden-tified by serovar (e.g., Salmonella ty-phimurium becomes S. enteri-ca serovar Typhimurium, seeFig. 3). For convenience, thespecies (enterica) designationis frequently eliminated, leav-ing Salmonella Typhimurium.

The diverse population oforganisms sharing the samename has complicated effortsto study Salmonella, but re-cent advances illustrate thatmost Salmonella are actuallyquite similar to each other, es-pecially at the virulence factorlevel.

Salmonella typically causethree diseases in humans:

gastroenteritis (caused by S. Typhimu-riuim, S. Enteritidis, and others); enter-ic fever (S. Typhi and S. Paratyphi); andan invasive systemic disease (S. Choler-aesuis). In the United States, nonty-phoidal Salmonella account for an esti-mated 1.3 million illnesses annually,with several hundred deaths (Mead etal., 1999). The U.S. incidence of typhoidfever is relatively lowapproximately700 cases annually, mainly as a result ofinternational travel. Worldwide, the in-

cidence of typhoid fever is declining(due, in part, to better distribution ofsafe water and successful vaccines),while the incidence of nontyphoidalsalmonellosis is increasing rapidly.A portion of this increase correlatesto changes in the food productionenvironment that may have givenSalmonella the opportunity to spreadand to contaminate foods that aredistributed through large complexnetworks.

tures that are readily discernible by lightmicroscopy or that are stable under abroad range of environmental conditions.To create a system with more precision,taxonomists were forced to base classifica-tion schemes on both morphologicalcharacteristics and physiological charac-teristics that generally reflect the biochem-ical diversity among bacterial species.

As the available techniques and tech-nology advanced, scientists found newways to classify microorganisms. The ad-vent of ribosomal RNA (ribonucleicacid) sequencing began a new era of tax-onomy (Woese et al., 1990). rRNA ispresent in organisms in all kingdomsand performs the same essential func-tions in all organisms. rRNA evolvesslowly so it serves as the ideal evolution-ary clock. Scientists soon developed largedatabases of rRNA sequences used toclassify new species (Olsen et al., 1992).This era also produced many of the cur-rent DNA (deoxyribonucleic acid) hy-bridization strategies used to detect andidentify pathogenic microorganisms in

food and clinical samples (King et al.,1989). Although the use of rRNA se-quences as a chronometer to measure re-lationships among species has disruptedtraditional groupings based on pheno-typic characteristics, many of the taxa ofimportance to food microbiology remainintact, with some modifications amonggroupings of certain species. For exam-ple, Campylobacter pylori, initiallynamed pyloric campylobacter for itssimilarity to Campylobacter jejuni, wassubsequently renamed Helicobacter py-lori (Dubois, 1995).

The era of microbial genomicsreached full swing in the 1990s. Usingseveral available microbial genome se-quences, scientists have been able to com-pare the evolutionary histories of differentbacterial races (phylogenies) to the uni-versal phylogenetic tree predicted fromrRNA sequences. These efforts resulted inthe disappointing discovery that the ge-nome-based phylogenies were frequentlydiscordant with rRNA predictions (Brownand Doolittle, 1997).

Mining the sequences for the relativetime that specific segments appearedwithin the genome revealed the reasonsfor the discordance: significant portionsof microbial genomes have been ac-quired through gene transfer from othermicroorganisms (Lawrence andOchman, 1998). Examining large sets ofvirulence genes on contiguous segmentsof DNA (known as pathogenicity is-lands) also demonstrated that genesconferring virulence characteristics areoften some of the most recent acquisi-tions among the genomes of pathogenicspecies (Hacker and Kaper, 2000). Asidefrom the impact on nomenclature, thisnew information has profoundlychanged scientific thinking about theevolution of virulence. The ability of apathogen to suddenly obtain a criticalvirulence factor through genetic ex-change is at odds with the idea of slow,gradual evolution of virulence.

Now that scientists know that micro-bial genomes change more rapidly thanpreviously believed, the concept of bac-

Genus Salmonella

enterica

entericasalamai arizonidiarizoni houtenae indica bongori

Enteritidis Typhi Paratyphi CholeraesuisTyphimurium

Species

Subspecies

Serovar

Fig. 3. Nomenclature of Salmonella

15EXPERT REPORT

terial species is in flux. In terms of di-versity, genome size may vary by 20%among subpopulations of a single spe-cies (for example, see Bergthorsen andOchman, 1998). This variability cancover as many as 1-2 megabases of DNAthat code for thousands of genes, whichcan confer unique characteristicssuchas virulenceon specific subpopula-tions. Still, a subset of genes that definesignature characteristics of the speciesmust be shared among all members ofthat species.

These contrasting views of what con-stitutes a bacterial species challenge theconcepts that underlie microbiologicalcriteria and testing for the control ofpathogens in food manufacturing. Insome cases, the potential to cause food-borne disease can be characteristic of anentire species, such as S. enterica, but inother cases it may be a consequence ofrecently evolved virulence characteristicsamong specific subpopulations of a spe-cies, such as Escherichia coli O157:H7.The sensitivity of genome-based finger-printing methods has even called intoquestion the equality of virulence in ge-netically distinct subpopulations of E.coli O157:H7 (Kim et al., 1999). As an-other example, it is questionable whetherall microorganisms in the Listeria mono-cytogenes species are capable of causingdisease in humans. Even though eachdistinct genetic lineage of the species ap-pears to harbor the known virulencegenes, mounting phylogenetic evidenceindicates that virulence characteristicsdiffer (Rasmussen et al., 1995; Wied-mann et al., 1997).

New scientific information providesthe opportunity to better target thepathogenic subpopulations within a spe-cies. Present day approaches to controlmust be modified to be consistent withthe information presently available. Asimproved detection and identificationmethods enable scientists to differentiatebetween virulent and avirulent organ-isms, we should be able to allocate ourrisk management resources more effi-ciently, focusing only on pathogenic or-ganisms in our food supply.

Virulence

If pathogenicity is a microorganismsability to cause disease, then virulencecan be considered the degree of pathoge-nicity. Some pathogens are particularlyefficient at causing clinically significantdisease (highly virulent), while others

may cause only minor effects in a smallnumber of cases (less virulent). Viru-lence is related to the severity of diseaseand the number of ingested pathogens(infectious dose) required to cause ill-ness (see Fig. 4). Within the Escherichiacoli species, for example, there is greatcontrast in virulence. Enterohemorrhag-ic E. coli (e.g., O157:H7) can cause sig-nificant and severe illness even if verysmall numbers of cells (10 or less) areingested, whereas enterotoxigenic E. colirequire an estimated 100 million to 10billion cells to cause a relatively mild setof symptoms (FDA/CFSAN, 2002). Theunderlying reasons for observed differ-ences in virulence among various patho-gens, and even within a single species ofpathogen is difficult to state with abso-lute certainty, as at least two dynamicsare operative, the microorganism and thehost. Even less virulent pathogens cancause serious illness in debilitated hosts.Likewise, it is probable that fewer patho-gens need to be ingested by a debilitatedhost than a healthy host to cause infec-tion if all else is equal.

The infectious dose is different foreach pathogen. As stated above, E. coliO157:H7 is infectious in very low num-bers. There may be several possibleexplanations for this, including:(1) O157:H7 is more acid tolerant andtherefore fewer cells are killed by gastricacidity, (2) O157:H7s virulence may beinfluenced by intestinal flora via quorumsensing (see sidebar, p. 16), (3) its com-bined virulence factors simply make itmore adaptable to the intestinal lumen,or (4) its virulence factors are more po-tent.

The situation among Salmonella ismore complex. Prior to the 1980s, con-ventional wisdom held that large num-bers of Salmonella were necessary for in-fection. Human feeding trials of volun-teers from penal institutions with several

different Salmonella sub-types certainly suggestedthat numbers >100,000cells were required for ill-ness (DAoust, 1985).However, outbreaks in-volving cheddar cheeseand chocolate were ap-parently caused by veryfew cells (


ized testing might be prudent beforefoods are rejected for the presence of L.monocytogenes that may not be patho-genic.

The inherent ability to cause diseaseis the result of virulence factors encodedat the genetic level (Finlay and Cossart,1997; Finlay and Falkow, 1997). Manydiverse characteristics are considered vir-ulence factors. If these factors are miss-ing, the microorganism would be expect-ed to be less virulent or avirulent. Someexamples of virulence factors include: toxins (molecules secreted by thebacteria that affect host cell processes),such as cholera toxin; adhesins (molecules that enablepathogens to adhere to host surfaces),such as fimbriae; and, invasins (molecules that enablepathogens to actively enter into a hostcell (invasion) where they can exist as anintracellular pathogen), such as thoseused by Shigella and Salmonella.

Most pathogens have a variety of vir-ulence factors that assist in host coloni-zation and disease. The repertoire of

Quorum SensingNot long ago, bacteria were

thought to lead a solitary existenceand either live or die as a single cell. Ithas been established that intercellularcommunication is fairly commonamong bacteria, and that this intercel-lular communication can lead to co-ordinated activities once thought tobe the exclusive domain of multi-cel-lular organisms. It was not surprisingthen that researchers asked whetherintercellular communication was in-volved in virulence, and it was alsonot surprising that genetically wellcharacterized foodborne pathogenssuch as Salmonella and Escherichiacoli would be investigated.

Intercellular communicationamong bacteria is carried out bysmall molecules called autoinducers.The theory is that at very low popu-lation densities, there is insufficientautoinducer in the environment tobe detected by those bacteria present,but that when some thresholdnumber of bacteria is reached, auto-inducer is present in sufficient con-centration to trigger some activity inbacteria capable of detecting the au-

toinducer. The terminology to describethese events is quorum sensing.

Quorum sensing has been demon-strated in E. coli and Salmonella Typh-imurium (Surette and Bassler, 1998),and more recently, the role of quorumsensing in the virulence of enterohem-orrhagic (EHEC) and enteropathogen-ic (EPEC) E. coli has been elucidated(Sperandio et al., 1999). The hallmarkintestinal lesion caused by EHEC andEPEC is called attaching and effacing,and is coded by the Locus of Entero-cyte Effacement (LEE). This pathoge-nicity island codes for a type III secre-tion system, as well as other virulencefactors such as the intimin intestinalcolonization factor and the translocat-ed intimin receptor protein. It is possi-ble that the low infectious dose of E.coli O157:H7 is in part because thepathogen is induced to colonize the in-testine by quorum sensing of signalsfrom resident, nonpathogenic E. coli inthe intestine of the host.

Quorum sensing appears to regu-late the virulence factors of a wide vari-ety of plant and animal pathogens(Day and Maurelli, 2001). Unlike oth-er enteric pathogens, the signalling sys-

tem in Shigella flexneri does not reg-ulate virulence. There may besound ecologic reasons why someenteric pathogens regulate virulencewith quorum sensing systems andothers do not. Quorum sensing sys-tems are not limited to the gram-negative bacteria, and notable gram-positive bacteria, such as the patho-gen Staphylococcus aureus and itsnumerous virulence factors are un-der the control of intercellular sig-nals (de Kievit and Iglewski, 2000).

Obviously it is important thatwe gain a better understanding ofthe regulation of virulence via quo-rum sensing systems. One obviousquestion is: Does quorum sensingoccur in or on foodstuffs, and if so,is it a factor in the virulence of food-borne pathogens? Many pathogenicbacteria have evolved a chemicallanguage, and it would behoove usto learn and understand that lan-guage. It may be possible to exploitthese intercellular communicationpathways to reduce virulence, or usethem as targets of novel antimicro-bial substances (de Kievet and Ig-lewski, 2000).

functional virulence factors will dictatewhic

Emerging Micro Expert Report on Emerging Microbiological Food Safety Issues Implications for Control

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