Antimicrobial Resistance: Implications for the Food System Microorganisms have an inherent ability to evolve—to mutate and adapt to environmental stressors─allowing them to survive otherwise lethal conditions.

August 2, 2006


The safety of food worldwide remains challenged by the potential for emergence of new pathogens and re-emergence of known pathogens. Microorganisms have an inherent ability to evolve–to mutate and adapt to environmental stressors–allowing them to survive otherwise lethal conditions. The Institute of Food Technologists (IFT),1 the 22000-member nonprofit scientific and educational society, convened a panel of internationally renowned experts to address the concern that the use of antimicrobials in food production, manufacturing, and elsewhere may lead to the emergence of foodborne pathogens that are resistant to antimicrobials, thus compromising the ability to subsequently control them, whether in production agriculture, food processing, or human medicine. The outcome of the panel's deliberations is presented in this Expert Report. IFT's objective for this Expert Report is to increase the understanding–among IFT members, senior policy officials, and other interested groups–of the state of the science on the public health impact of the use of antimicrobials in the food system, and development and control of antimicrobial resistance. This report is the fourth Expert Report produced by IFT.

DIGITAL OBJECT IDENTIFIER (DOI) 10.1111/j.1541-4337.2006.00004.x


The availability of antibiotics to treat infectious diseases has radically improved human and animal well being, and to a minor degree, plant health. Paradoxically, this very success threatens the future utility of antibiotics. The discovery of penicillin in 1940 ushered in the era of "modern medicine." Numerous antimicrobials, including most structural classes of antibiotics were discovered during 1920 to 1970. Chemical modification of many of these compounds led to new entities with superior activities. Because of the great success in antibiotic discovery, by the late 1970s, many proclaimed that the war on infectious diseases had been won, leading ultimately to de-emphasis of antibiotic discovery during the 1980s and a decline in the 1990s. At the same time, however, widespread antibiotic resistance was emerging and resulting in impaired treatment of human diseases (Neu 1992). As the genomes of bacteria, especially pathogens, have become increasingly available, the prospect of using them to identify new targets for antibiotic discovery has renewed interest in such investigations between the public sector and large pharmaceutical and biotechnology companies. Many of the larger companies and much of the public sector, however, have redirected research efforts toward noninfectious disease targets.

All uses of antibiotics in human medicine and animal husbandry create selective pressure that favors emergence of antibiotic resistance among microorganisms, which could undermine the effectiveness of the antibiotics and potentially give rise to a "postantibiotic" era. The selection for antibiotic-resistant bacteria in agricultural production environments and the subsequent impact on animal and human health has become a major concern and is the subject of many reports (Table 1). This document focuses on the use of antimicrobial agents to control bacteria in the food system; other microorganisms are considered as well, however. This document builds upon the IFT Scientific Status Summary "Resistance and Adaptation to Food Antimicrobials, Sanitizers, and Other Process Controls" (IFT 2002a), to inform readers about the various types of antimicrobial agents, including antibiotics, food antimicrobial agents, and sanitizers that are used at various stages of the food system, and the mechanisms that microorganisms, particularly foodborne pathogens, have for surviving the stress of exposure to these substances in their environments. Trends in antimicrobial resistance, and the resultant human health, economic, and clinically relevant environmental impacts are also addressed.

Table 1–Reports of antimicrobial use, resistance, and human health impact

1969. English Parliament, United Kingdom. The Report to Parliament by the Joint Committee on Antibiotic Uses in Animal Husbandry and Veterinary Medicine ("Swann Report").

1980. National Research Council (NRC), United States. The Effects on Human Health of Subtherapeutic Use of Antimicrobials in Animal Feed. catalog/21.html

1981. Council for Agricultural Science & Technology, United States. Antibiotics in Animal Feeds, Report 88.

1981. Institute of Medicine (IOM), United States. Human Health Risks with the Subtherapeutic Use of Penicillin or Tetracyclines in Animal Feed.

1989. IOM Committee on Human Health Risk Assessment of Using Subtherapeutic Antibiotics in Animals, United States. Human Health Risks with the Subtherapeutic Use of Penicillin or Tetracyclines in Animal Feeds.

1997. World Health Organization (WHO), International. The Medical Impact of the Use of Antimicrobials in Food Animals.

1998. UK Ministry of Agriculture, Fisheries, and Food, United Kingdom. A Review of Antimicrobial Resistance in the Food Chain.

1998. United States Food and Drug Administration (FDA) Center for Veterinary Medicine (CVM), United States. A proposed framework for evaluating and assuring the human safety of the microbial effects of antimicrobial new drugs intended for use in food-producing animals. VMAC/antimi18.html

1998. WHO, International. Use of Quinolones in Food Animals and Potential Impact on Human Health: Report and Proceedings of a WHO Meeting.

1999. The European Agency for the Evaluation of Medicinal products, European Union. Antibiotic Resistance in the European Union Associated with Therapeutic Use of Veterinary Medicines.

1999. EU Scientific Steering Committee, European Union. Opinion of the Scientific Steering Committee on Antimicrobial Resistance.

1999. FDA, United States. Risk Assessment on the Human Health Impact of Fluoroquinolone-resistant Campylobacter Associated with Consumption of Chicken. (revised as of Jan 5 2001).

1999. NRC National Academy of Sciences Committee on Drug Use in Food Animals and the Panel on Animal Health, Food Safety, and Public Health, United States. The Use of Drugs in Food Animals: Benefits and Risks. Benefits and Risks

1999. U.S. General Accounting Office (GAO), United States. Food Safety: The Agricultural Use of Antibiotics and Its Implications for Human Health. Antibiotics and Its Implications for Human Health

1999. Advisory Committee on the Microbiological Safety of Food, United Kingdom. Report on Microbial Antibiotic Resistance in Relation to Food Safety. (a synopsis)

1999. Joint Expert Advisory Committee on Antibiotic Resistance, Australia. The Use of Antibiotics in Food-Producing Animals: Antibiotic Resistant Bacteria in Animals and Humans.

1999. European Commission, European Union. Opinion of the Scientific Steering Committee on Antimicrobial Resistance, May 28, 1999.

1999. WHO, International. The Medical Impact of the Use of Antimicrobials in Food Animals.

2000. Centers for Disease Control and Prevention Interagency Task Force on Antimicrobial Resistance, United States. Disease Control and Prevention Interagency Task Force on Antimicrobial Resistance A Public Action Health Plan to Combat Antimicrobial Resistance.

2000. WHO, International. WHO Global Principles for the Containment of Antimicrobial Resistance in Animals Intended for Food.

2000. Food and Agriculture Organization of the United Nations (FAO)/WHO Codex Committee on Residues of Veterinary Drugs in Foods, International. Antimicrobial Resistance and the Use of Antimicrobials in Animal Production.

2001. Office International Des Epizooties (OIE), International. Antimicrobial Resistance: Reports prepared by the OIE Ad Hoc Group of Experts on Antimicrobial Resistance. prepared by the OIE Ad Hoc Group of Experts on Antimicrobial Resistance

2001. WHO, International. WHO Global Strategy for Containment of Antimicrobial Resistance. Antimicrobial Resistance

2001. WHO, International. Monitoring Antimicrobial Usage in Food Animals for the Protection of Human Health. AMRuseOslo.pdf

2002. Alliance for the Prudent Use of Antibiotics, United States. The Need to Improve Antimicrobial Use in Agriculture: Ecological and Human Health Consequences ("FAAIR Report").

2002. Veterinary Drugs Directorate, Health Canada Report of the Advisory Committee on Animal Uses of Antimicrobials and Impact on Resistance and Human Health, Canada. Uses of Antimicrobials in Food Animals in Canada: Impact on Resistance and Human Health.

2003. WHO Department of Communicable Diseases, Prevention and Eradication and Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens, International. Impacts of Antimicrobial Growth Promoter Termination in Denmark.

2004. FAO, OIE, and WHO, International. Joint FAO/OIE/WHO Workshop on Non-Human Antimicrobial Usage and Antimicrobial Resistance: Scientific Assessment.

2004. FAO, OIE, and WHO, International. Second Joint FAO/OIE/WHO Expert Workshop on Non-Human Antimicrobial Usage and Antimicrobial Resistance: Management Options.

2004. GAO, United States. Federal Agencies Need to Better Focus Efforts to Address Risk to Humans from Antibiotic Use in Animals.

Classification of antimicrobials

For the purposes of this report, "antimicrobial" is a general term used broadly to refer to any compound, including antibiotics, food antimicrobial agents, sanitizers, disinfectants, and other substances, that acts against microorganisms. The definitions and use of each of these terms differ among various groups. Legal definitions exist for use in a regulatory context.

The term antibiotic is used in this report to refer to drugs used to treat infectious disease in humans, animals, or plants, by inhibiting the growth of or destroying microorganisms; such substances may be naturally occurring, semisynthetic, or synthetic. Antibiotics are also used in food animals to prevent infectious disease and improve the efficiency of feed utilization. Within the antibiotic classification are synthetic antimicrobials such as quinolones, that differ from other substances such as streptomycin, which are natural products or fermentation derived antibiotics. Antibiotics are legally classified as such only when used in humans. They are classified as "veterinary antimicrobial drugs" when used in animals and as "pesticides" when used in plants.

"Biocide" is a general term that refers to chemical agents, such as disinfectants and sanitizers, which are usually broad spectrum. Because biocides vary in antimicrobial activity, other terms may be used to more specifically describe the nature of the antimicrobial activity. For example, terms ending in the suffix "-static," such as "bacteriostatic," are used for agents that inhibit microbial growth without killing the microbes, and terms with the suffix "-cidal," such as "fungicidal," refer to agents that kill the target microbe (McDonnell and Russell 1999). "Disinfectants" destroy or irreversibly inactivate infectious fungi and vegetative bacteria (growing or nonsporeforming), and are used in hospitals, food processing facilities, restaurants, and elsewhere for general purposes (EPA 2005). In the legal connotation, disinfectants include "any oxidant, including but not limited to chlorine, chlorine dioxide, chloramines, and ozone, added to water in any part of the treatment or distribution process, that is intended to kill or inactivate pathogenic microorganisms" (40 CFR §141.2). "Sanitizers," comprised of 2 categories–no-rinse food contact surface sanitizers and nonfood contact surface sanitizers–refer to substances that reduce microbial contamination and destroy vegetative pathogens of public health significance on treated inanimate surfaces. "Sterilants," such as peroxyacetic acid, refer to substances that eliminate all forms of microbial life, including bacterial spores, fungi, and viruses. IFT uses the legal connotation "food antimicrobial agent" to refer to antimicrobial substances, such as nisin and other bacteriocins, including mold inhibitors, which are used to preserve food by preventing microbial growth and subsequent spoilage. Antibiotics cannot legally be used as food additives; thus, they are specifically excluded from this classification.

Classification of resistance

Discussion of antimicrobial resistance, by necessity, must include defining what is meant by resistance. While it would seem that defining resistance would be a simple matter, many definitions exist (Davison and others 2000). Resistance to most traditional, regulatory-approved, or naturally occurring food antimicrobial agents is difficult to characterize because of the lack of a precise definition for such resistance. From a functional perspective, resistance correlates with failure of a given antimicrobial treatment, whereas from a laboratory perspective, resistance is denoted through a "Minimal Inhibitory Concentration" (MIC)2 value that exceeds a threshold value, which may or may not be associated with a clinical outcome. Chapman (1998) stated that a microorganism is resistant if it exhibits "significantly reduced susceptibility" when compared with that of the "original isolate" or a group of sensitive strains. In this report, resistance means "temporary or permanent ability of a microorganism and its progeny to remain viable and/or multiply under conditions that would destroy or inhibit other members of the strain" (Cloete 2003). These terms and the different types of resistance are described below.

As Courvalin (2005) describes, resistance can result from mutations in housekeeping structural or regulatory genes, or alternatively, horizontal acquisition of foreign genetic information. In some cases, resistance may manifest through multiple mechanisms. For example, three different strategies are thought to be involved in resistance to tetracycline (Schnappinger and Hillen 1996). Resistance can also be intrinsic, that is microorganisms without known exposure to antimicrobial agents may be resistant to some agents (see below).

If a resistant strain is isolated from an environment containing an antimicrobial or prepared in the laboratory by exposure to increasing concentrations of an antimicrobial, resistance may be due to a genetic alteration or a temporary adaptation. It may be that temporary adaptation to an antimicrobial through some type of homeostatic mechanism plays a much larger role than true genetic mutation among food-related antimicrobials. To date, research on resistance to food antimicrobials has focused almost exclusively on innate or intrinsic mechanisms of the target microorganisms.

Innate (Intrinsic) resistance. As is the case for a natural property of a microorganism, innate resistance is chromosomally controlled (Russell 1991). Innate resistance is related to the general physiology or anatomy of a microorganism and stems from pre-existing mechanisms or properties. This type of resistance is most likely responsible for differences in resistance observed among different types, genera, species, and strains of microorganisms in identical environmental conditions and concentrations. Innate resistance may stem from the complexity of the cell wall, efflux mechanisms (means by which microbes pump antimicrobials out of the cell [Gilbert and McBain 2003]), or enzymatic inactivation of the antimicrobial (Russell 2001). For example, because of the complexity of their cell walls, Gram-negative bacteria generally have a higher level of resistance to antibacterial agents than typical Gram-positive bacteria (Russell and Chopra 1996). More specifically, Gram-negative bacteria are innately resistant to penicillin G by virtue of their double membrane structure, which prevents the antibiotic from accessing the cell wall target. Similarly, Mycobacterium species are more resistant than other nonsporeforming bacteria due to high lipid content in their cell walls and comparatively high hydrophobicity. Other bacteria–Bacillus, Pseudomonas, Corynebacterium, Micrococcus, and the fungus Aspergillus have innate resistance to benzoate because they are capable of metabolizing the compound to succinic acid and acetyl coenzyme A (Chipley 1993). Innate resistance is not considered an important clinical problem because antibiotics were never intended for use against intrinsically resistant bacteria.

There are certain circumstances in which antimicrobial agents do not adversely affect bacteria that are generally susceptible to the particular agent. Because the efficacy of most food antimicrobials and sanitizers is dependent upon and influenced by the conditions of the application, some situations may permit bacterial resistance that would not have occurred otherwise (IFT 2002a). Exposure conditions, such as the environmental conditions (temperature, pH, and food composition) of the antimicrobial application, or interaction of the antimicrobial with components of the suspension medium or food product can influence the efficacy of the antimicrobial agent (Davidson 2001). For example, organic matter can quench the hypochlorite ion and therefore eliminate its efficacy at killing generally susceptible bacterial populations (Kotula and others 1997). However, microorganisms that are generally susceptible to antibiotics can themselves also become temporarily resistant to an antimicrobial through activation of silent, resident gene(s) that confer this resistance. A good example of this occurring is observed with the survivability of biofilm-associated cells versus planktonic (free floating/living) cells (Frank and Koffi 1990; Mosteller and Bishop 1993; Mustapha and Liewen 1989). Microbial cells in biofilms exhibit resistance primarily through the protection provided by extracellular materials such as exopolysaccharides. Also, nongrowing bacterial cells are resistant to many antibiotics that target cell wall synthesis. Once conditions again become favorable for growth, these bacterial cells become susceptible again to these cell wall inhibitors. Also, the few reports of resistance to food antimicrobial preservatives and sanitizers are attributed to microbial stress responses to sublethal stressors, such as low or high temperatures, acidity, osmolarity, low moisture, high atmospheric pressure, low oxygen or anaerobic conditions, gas atmospheres, competing bacteria, and low nutrient environments that trigger physiological changes and subsequently confer resistance to these compounds (Abee and Wouters 1999; Archer 1996; Samelis and Sofos 2003a; Sheridan and McDowell 1998; Sofos 2002a).

Acquired (Extrinsic) resistance. Acquired resistance results from genetic changes that occur through mutation of the antimicrobial's target site within the bacterium or acquisition of genetic material encoding resistance via plasmids3 or transposons4 containing integron sequences5 (Roe and Pillai 2003; Russell 1991, 1996; Russell and Chopra 1996). Acquired resistance, the most common type of antibiotic resistance, has been well studied for antibiotics, but has not been well studied for food antimicrobial agents and sanitizers. Acquisition of genes for β-lactamase (an enzyme capable of breaking down and inactivating β-lactam antibiotics [penicillins and cephalosporins]) and mutation of one of the subunits of DNA gyrase (the target of fluoroquinolones) are examples of this type of resistance. Another example includes resistance of some microorganisms to sanitizing compounds, such as quaternary ammonium compounds (QACs), as a result of the presence of plasmid-encoded efflux pumps that remove the QACs (Russell 1997).

Although acquired resistance is of concern in the use of food antimicrobial agents and sanitizers, occurrence of such resistance appears to be rare. Unlike antibiotics, which generally have specific target sites, biocides (that is, disinfectants, sanitizers, antimicrobials) typically act nondiscriminately against multiple nonspecific targets (Bower and Daeschel 1999); thus, single mutations or biochemical alterations of cellular targets seldom confer resistance to biocides.

Adaptation. For certain types of antimicrobials, adaptation may be demonstrated by exposing a microorganism to a stepwise increase in concentration of the substance. This type of resistance, however, is often unstable; the microorganism may revert back to the sensitive phenotype when grown in an antimicrobial-free medium, termed "back-mutation" (Russell 1991). In the absence of selection pressure, the mutations associated with resistance may actually reduce fitness of the bacterial strain compared to the wild type, parental strain. Stabilizing, secondary, compensatory mutations are sometimes needed to maintain resistance and reduce fitness cost associated with the original "resistance" mutation.

Antimicrobial Applications

During food production and manufacturing, a variety of antimicrobials, including antibiotics, antifungals, sanitizers, and food preservatives, are applied to improve the efficiency of the system, and increase the safety and quality of the product. The multiple points throughout the ecosystem where antimicrobials may be used and subsequently impact the epidemiology of resistance are shown in Figures 1 and 2. Microorganisms encounter and are subjected to a variety of antimicrobial stressors as they move throughout the food system, from the environment to the plant, through food processing, shipping, distribution, storage, and into kitchen food preparation areas. The variety of antimicrobial uses at each of the various stages of the food system may create selective pressure that promotes resistance.

Epidemiology of antimicrobial resistance (adapted and modified from Linton [1977] by Rebecca Irwin, Health Canada [Prescott 2000] and IFT, with permission).
Figure 1–Epidemiology of antimicrobial resistance (adapted and modified from Linton [1977] by Rebecca Irwin, Health Canada [Prescott 2000] and IFT, with permission).
Application of antimicrobials from farm to table
Figure 2–Application of antimicrobials from farm to table

The major classes of antibiotics and their various uses in animals, plants, and humans are listed in Table 2. Detailed information on the mechanism of action of specific classes of antimicrobials can be found elsewhere (Prescott and others 2000; Walsh and others 2003). Some of the antibiotics and fungicides used in agriculture have identical chemical counterparts in human medicine. The majority of antibiotics used in food animals belong to classes of antibiotics that are also used to treat human illness; these include tetracyclines, sulfonamides, penicillins, macrolides, fluoroquinolones, cephalosporins, aminoglycosides (gentamicin and kanamycin), chloramphenicols, and streptogramins (NARMS 2006).

Table 2–Examples of antimicrobial drugs and antibiotics, by major class, approved in the United States for animal, plant, or human use

Antimicrobial, drug class (selected examples) Mode of action/spectrum Food animal use Plant use Human use

Animal Species Disease treatment Disease prevention Growth promotion
Aminoglycosides (gentamycin, neomycin, streptomycin) Inhibit protein synthesis/broad spectrum Beef cattle, goats, poultry, sheep, swine
• (Certain plants)
Beta-lactams penicillins (amoxicillin, ampicillin) Inhibit cell wall synthesis Beef cattle, dairy cows, fowl, poultry sheep, swine
cephalosporins 1st generation (cefadroxil) Broad spectrum
cephalosporins 2nd generation (cefuroxime)

cephalosporins 3rd generation (ceftiofur) Beef cattle, dairy cows, poultry, sheep swine

Chloramphenicol Inhibit protein synthesis/
(Florfenicol) broad spectrum

Inhibit protein synthesis/broad spectrum Beef cattle
Cycloserines (cycloserine) Inhibit cell wall synthesis/narrow spectrum
Glycopeptides (vancomycin) Inhibit cell wall synthesis/narrow spectrum
Ionophores (monensin, salinomycin, semduramicin, lasalocid) Disrupts osmotic balance/narrow spectrum Beef cattle, fowl, goats, poultry, rabbits, sheep
Lincosamides (lincomycin) Inhibit protein synthesis/narrow spectrum Poultry, swine
Macrolides (tylosin, tilmicosin erythromycin) Inhibit protein synthesis/narrow spectrum Beef cattle, poultry, swine
Monobactrams (aztreonam) Inhibit cell wall synthesis broad spectrum
Polypeptides Inhibit cell Fowl, poultry,
(bacitracin) wall synthesis narrow spectrum swine

Fluoroquinolones Inhibit DNA Beef cattle
(enrofloxacin, danofloxacin) synthesis/broad spectrum
Streptogramins (virginiamycin) Inhibit protein synthesis/narrow spectrum