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United States Department of Agriculture

Agricultural Research Service

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National Program 108: Food Safety, (animal and plant products)
FY 2007
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Fiscal Year 2007 Annual Report for National Program 108

Food Safety


Food Safety falls under Goal 4 of the Agency Strategic Plan: Enhance Protection and Safety of the Nation’s Agriculture and Food Supply.  For the Nation to have affordable and safe food, the food system must be protected at each step from production through to consumption.  The production and distribution system for food in the United States is diverse, extensive, and potentially accessible.  The system is vulnerable to the introduction of pathogens, toxins and chemical contaminants through natural processes and global commerce, and by intentional means.  In response to these threats, crop and livestock production systems whether domestic or exotic in origin, must be protected.


Food safety research seeks ways to assess and control potentially harmful foodborne contaminants.  Research to ensure a secure agricultural production system refers to work that reduces or eliminates factors that threaten the ability of U.S. agriculture to produce enough food, year-to-year, to meet the needs of American consumers.  ARS conducts research designed to generate knowledge regarding new and improved management practices, pest management strategies, sustainable production systems, and control of potential contaminants for farms of all sizes.  These activities will ensure a secure production system able to provide a safe, plentiful, diverse, and affordable supply of food products.  ARS provides scientific information and technology to producers, manufacturers, regulatory agencies, and consumers to support their efforts in providing a secure, affordable, and safe food supply.


The Program’s Mission is to provide through scientific research, the means to ensure that the food supply is safe and secure for consumers and that food and feed meet foreign and domestic regulatory requirements.  Food safety research seeks ways to assess, control or eliminate potentially harmful food contaminants, including both introduced and naturally occurring pathogenic bacteria, viruses and parasites, toxins and non-biological-based chemical contaminants, mycotoxins and plant toxins.  Since food safety and food security are global issues, our research program involves both national and international collaborations through formal and informal partnerships.  Our accomplishments and outcomes are utilized in national and international strategies delivering research results to regulatory agencies, commodity organizations and consumers.


The Program’s Vision is to increase public health through the development of technologies which protect food from pathogens, toxins, and chemical contamination during production, processing, and preparation thus increasing the safety of the food supply.  The research components of the Program during 2007 were:


·        [Microbial] Pathogens, Toxins and [non-biological-based]; Chemical Contaminants: subdivided in Pre-harvest and Post-harvest.

·        Mycotoxins and Plant Toxins


During 2008, there will be several significant changes to the Program.

·        A new National Program Leader (NLP) will join National Program Staff.  The new NPL will fill the position in response to the retirement of Dr. Jane Robens.

·        The structure of the Program will be revised in light of the new Vision Statement outlined above, focusing on public health outcomes.  This requires reconsideration to a reverse food chain, which focuses on consumers first.

·        The Program Action Plan will be revised to refocus some research initiatives to address critical issues such as contamination of fresh produce.

·        The artificial research barrier of pre- and post-harvest research will also be eliminated.


Selected Research Highlights from 2007


Salmonella adapted to cattle.  Some multi-drug-resistant Salmonella have been purported to be more pathogenic than antibiotic-sensitive cohorts.  ARS scientists at Ames, Iowa, showed this phenomenon with Salmonella Dublin, a strain adapted to cattle, and exposure to protozoa from the first stomach of cattle.  Studies demonstrated that host-adapted strains, like S. dublin, are adept at causing disease.  Thus a more pathogenic strain can cause significant mortality in an infected herd.  The results provide the basis for ameliorating this problem by identifying an intervention point for cattle producers.  


Pathogens control in cattle feedlots.  Pathogen-contaminated manure accumulates at the feedlot pen surface and can serve as a source of pathogens for additional contamination in the cattle production environment.  ARS scientists at Clay Center, Nebraska evaluated if any essential oils and related compounds could control pathogens on cattle feedlot pen surfaces.  Field studies showed that the prevalence of E. coli O157:H7 prevalence in pen surface could be reduced by 99.9% with linalool containing thymol.  This indicates that pen feedlot surfaces can be treated to reduce the pathogen load in the cattle production environment, thereby removing pathogens for contamination of additional cattle, cattle hides, and runoff.  


Salmonella antibiotic resistance factors.  Public health agencies are concerned that the agricultural use of antibiotics is contributing to the emergence of antibiotic-resistant bacterial populations in farm animals.  Studies are needed to assess the nature of antibiotic-resistant genetic factors (plasmids) that may occur in bacteria that colonize the gastrointestinal tracts of livestock.  ARS scientists at College Station, Texas, isolated Salmonella enterica from beef and dairy cattle from different areas of the U.S., and determined their antibiotic resistance characteristics.  Studies showed that the resistance factor "plasmid replicon IncA/C" was the predominant in all the isolates, and that this plasmid was not transmissible from animal-to-animal unless aided by a second plasmid which was absent in most of the serovars.  This suggests that antibiotic resistance elements are not likely to move easily from one bacteria to another rather, resistance spreads from animal-to-animal by movement of the bacteria themselves.  Implementation of manure management practices that minimize bacterial spread from animal-to-animal could help avoid the spread of antibiotic-resistant bacteria.  This would ensure microbiologically safer dairy and beef products for the American consumer. 


Salmonella transmission.  Salmonella has been isolated throughout all stages of the pork production cycle and has received considerable attention, not only from a food safety standpoint, but also because Salmonella can cause clinical infection in swine.  There needs to be increased understanding of the environmental factors that affect Salmonella colonization in farm animals, particularly as related to Salmonella transmission from animal-to-animal.  ARS scientists at College Station, Texas, showed that by varying the level of light exposure, the animal-to-animal transmission of Salmonella in weaned pigs could be significantly reduced.  This has important food safety and swine health implications since virtually all swine production in the U.S. occurs

indoors with controlled lighting regimes.  This work will allow producers to control lighting parameters to minimize the colonization and spread of Salmonella, resulting in less contamination of pork meat products reaching the consumer.

Commercial bird housing systems.  There is industry concern that specific bird housing systems may have a dramatic impact on the prevalence of bacterial foodborne pathogens.  ARS scientists at Ames, Iowa compared Campylobacter and Salmonella pathogen levels in hens raised under three different commercial systems.  When the three housing types were compared during the winter, the prevalence of Campylobacter was highest in the non-caged birds.  In contrast, for the summer sampling, there was no difference in either Campylobacter or Salmonella prevalence for the three housing types.  This indicates that commercial bird housing systems evaluations should consider animal welfare issues as well as microbial food safety impact.


Trichinella in horsemeat.  Trading partners require testing of pork, game, and horsemeat products for Trichinella infection prior to export, and the image of U.S. meat products with respect to Trichinella infection impacts accessibility to foreign markets as well as domestic consumption.  ARS scientists in Beltsville, Maryland developed a tissue digestion assay for the detection of Trichinella larvae in horsemeat using a double separatory funnel (DSF) procedure was validated for application in food safety programs and trade.  The assay, with defined critical control points, was conducted within a quality assurance system compliant with ISO 17025 guidelines, and was found reliable, efficient, and fit for its intended use in food safety and trade.  The DSF is the only validated digestion assay for trichinellosis demonstrating consistency and effectiveness at critical levels of sensitivity required by trading partners for exported pork, game, and horsemeat, and has been accepted by European Union trading partners for use in inspection of meat products destined for export. 


Bioenergy production.  Alternative energy products are needed to reduce our dependence on foreign petroleum; in addition, dairy cow manure must be treated to reduce pathogens which can cause human disease.  Dairy manure and food waste can both be used to generate methane, but neither is ideal.  Manure is a well buffered substrate that produces methane slowly, and food waste produces methane rapidly but is poorly buffered, which results in the inhibition of methane production.  In collaboration with scientists at the University of California at Davis , ARS scientists at Albany, California showed that a mixture of food waste and manure digests well, producing methane, reducing pathogens in the waste, and generating a compost suitable as a soil conditioner/fertilizer.  This research has the potential to produce biofuel while subsequently reducing pathogen levels in waste and wastewater.


Imported and domestic boneless beef trim for ground beef.  The U.S. imports lean boneless beef trim from Australia, New Zealand, and Uruguay to meet demand for ground beef production.  The reported incidence of; and the bacteria responsible for foodborne disease differs between these countries and the U.S.  ARS scientists from Clay Center, Nebraska, determined if current U.S. microbiological profiling adequately addresses the potential differences in the foreign and domestic beef trim, by comparing the hygienic status of imported and domestic beef trim.  The results showed that the current pathogen monitoring procedures in the U.S. do not need to be changed for imported material.


Bone detection.  Bones in boneless poultry filets are still one of the largest food safety issues affecting the poultry industry.  ARS scientists in Athens, Georgia, developed an on-line imaging system to detect bones in breast filets.  The technology requires images of both sides of the filets and for the filet to be compressed to a uniform thickness, which can be accomplished with a forming machine.  This technology, which can be readily implemented, has a critical impact for processors providing filets for the USDA school lunch program.


Dry air and immersion chilling.  Broilers are traditionally chilled using chlorinated ice-water. This is a significant trade issue especially with countries in the European Union who do not allow importation of chicken meat processed in this manner.  Air chilled meats are, however, allowed to be imported.  ARS scientists at Athens, Georgia, conducted comparative studies to determine the efficacy of dry air versus traditional immersion chilling of broiler carcasses.  Studies indicated that the numbers of bacteria found on dry air and immersion chilled chickens were the same, reducing pathogen levels by over 90%.  Chilling method did not affect prevalence, the number of Campylobacter or Salmonella positive carcasses.  Implementation of air chilling by industry would provide increased opportunity for trade with equivalent control of pathogen levels to immersion chilling.      


Simultaneous detection of Salmonella, Escherichia coli O157:H7 and Listeria monocytogenes.  A prerequisite to the use of microbial biosensors is the development of a microbiological medium that enhances and allows selective growth of each targeted pathogen.  ARS scientists at the Eastern Regional Research Center, Wyndmoor, Pennsylvania, in collaboration with Purdue University developed a selective broth for the simultaneous enrichment of Salmonella spp., E. coli O157:H7 and L. monocytogenes (SEL).  SEL was evaluated for its suitability to recover pathogens from inoculated ready-to-eat (RTE) meats (deli turkey and salami).  When the performance of SEL was compared with the Universal Pre-enrichment Broth (UPB, a commercial multiplex medium), SEL performance was comparable.  Moreover, SEL was able to inhibit the growth of food associated spoilage or natural contaminants while UPB failed to do so.  These results indicate that SEL can be used as a single selective enrichment medium for the growth of multiple target pathogens critical to industry and regulatory agencies.


Controlling Listeria monocytogenes in ready-to-eat meats.  The presence of L. monocytogenes in food products is strictly regulated by Federal agencies.  ARS scientists at Wyndmoor,  Pennsylvania, have evaluated the effectiveness of the Sprayed Lethality in Container method in combination with the antimicrobial lauric arginate (LAE) to lower the levels of L. monocytogenes on the surface of frankfurters, roast beef, and turkey breast logs.  The results showed the intervention significantly reduced L. monocytogenes levels on the surfaces of vacuum-packaged roast beef, turkey breast, and frankfurters within 24 h at 4°C.  The application of LAE as a post-process intervention should assist ready-to-eat food manufacturers in achieving the USDA/FSIS alternative 2 status.


Subtyping of Listeria monocytogenes.  The CDC PulseNet Task Force requested the development and validation of DNA sequence-based methods for subtyping L. monocytogenes for use in outbreak detection and epidemiological investigations.  In addition, the recent L. monocytogenes risk assessment completed by the FDA, FSIS, and CDC identified significant gaps in knowledge regarding subtype prevalence and cited as critical the need for methods to determine the virulence potential of individual strains as FSIS transitions to a risk-based monitoring program.  In response, ARS scientists at Peoria, Illinois, developed and validated the first single-nucleotide-polymorphism-based subtyping assay for the group of L. monocytogenes strains most commonly associated with human illness. Studies demonstrated that the multi-locus genotyping (MLGT) assay provided high discriminatory power and differentiated groups relevant to epidemiological investigations.  In addition, the technology provided for the identification of specific virulence-attenuated subtypes, and was used to document the frequency of epidemic and virulence-attenuated subtypes in ready-to-eat meat products.  Implementation of this technology by regulatory agencies will have significant impact on monitoring public health and development of threat-based risk assessment programs. 


Food security.  Breaches to the security of our Nation’s food supply may arise due to the addition of threat agents such as Bacillus anthracis (BA) to higher risk foods such as milk ARS scientists at Wyndmoor, Pennsylvania, developed an intervention strategies using microfiltation technology to eliminate BA spores in bulk, fluid milk.  The research established that microfiltration of milk prior to pasteurization had the ability to remove greater than 99.9999% of BA spores while maintaining the quality of milk.  The addition of a microfiltration step by industry, in conjunction with an ultrapasteurization step for the retentate, will lessen the likelihood that pathogenic bacteria and/or their spores will contaminate the milk supply.


Immunoassays for biothreat toxins.  There is a need for rapid, sensitive assays for biothreat agents that can be used to detect intentionally contaminated foods, without the use of animal bioassay.  ARS scientists at Albany, California, designed new monoclonal antibodies for type A botulinum neurotoxin and ricin, and then used them to develop new immunoassay with sufficient sensitivity to detect subtoxic levels of these toxins in various food matrices.  The new antibodies have very high sensitivity, equivalent to the mouse bioassay, while others were found to protect mice from the effects of the toxins.  The availability of new test-tube assays with sufficient sensitivity to detect subtoxic levels in food matrices will help maintain the security and safety of the U.S. food supply.  New protective antibodies could prove useful in treating victims exposed to these toxins.


Determination of fluoroquinolone antibiotics in chicken.  Fluoroquinolones have recently been banned for use in chickens in the U.S.  The regulatory tolerance level, which had been set for enrofloxacin in chicken muscle, no longer applies, thus analytical methods for fluoroquinolones need to achieve lower detection limits.  Further, the marker matrix for analysis of chicken is no longer limited to muscle.  Using animal serum, ARS scientists at Wyndmoor, Pennsylvania, developed a liquid chromatography-fluorescence-tandem mass spectrometry method to easily detect 8 fluoroquinolones with good recoveries and low limits of detection.  Enrofloxacin and its metabolite, ciprofloxacin, were also detected in enrofloxacin-dosed animals for at least 2 days after withdrawal from dosing.  Serum is a much easier matrix to work with than muscle and the success of this method indicates a significant potential savings of time and effort in monitoring chickens for fluoroquinolones by the USDA Food Safety Inspection Service in their regulatory role.


Skinless, trimmed chicken has reduced PBDE contamination.  Studies in mammals have shown that tissues such as adipose and skin are major depots for persistent polybrominated diphenyl ethers (PBDE’s).  Since humans commonly consume cooked chicken skin of a chicken, ARS scientists at Fargo, North Dakota, conducted an adsorption, tissue disposition, metabolism, and excretion study with the most persistent PBDE found in the environment, that is, 2,2',4,4'-tetrabromodiphenyl ether (BDE-47).  Results demonstrated that BDE-47 was well absorbed by the chicken, was not readily metabolized (<1% of the dose), and was mainly distributed to adipose tissue and skin.  The data showed that the behavior of BDE-47 in chickens was similar to that observed in mammals. Therefore, to reduce human exposure to PBDEs from chicken consumption, the skin and fat should be trimmed before cooking.


Salmonella on almonds.  The California almond industry, which is the largest supplier of almonds in the world, has been affected by two international and one national outbreak of salmonellosis linked to raw almonds.  Propylene oxide (PPO) is the only effective dry treatment to decontaminate raw kernels, but these treated kernels cannot be exported to foreign countries due to a lack of standards about PPO residue levels in the product.  ARS scientists at Albany, California, developed an infrared heat-based technology that is at least as efficacious as fumigation in decontamination of raw kernels and involves a one-hour instead of a 5-day process, to achieve a reduction of over 99.99999% in Salmonella levels per kernel.  The Almond Board of California presently mandates a 99.99% reduction and consequently has shown considerable interest to commercially develop this non-chemical intervention process.  


Enhancing the activity of fungicides and antifungal drugs.  Fungal infection of crop plants poses a major problem to agricultural productivity, quality of agricultural products and food safety resulting from toxins that certain fungi produce.  Additionally, certain fungi are significant human pathogens, whose infection can lead to serious debilitation or death.  ARS scientists at Albany, California, have identified a number of safe, natural products that can significantly enhance the effectiveness of commercial fungicides, such as strobilurin and fludioxonil.  These compounds weaken the ability of the fungi to build their cell walls or to respire normally.  Once weakened by this “chemo-sensitization” the commercial products can be1000 fold more effective.  In collaboration with scientists at the University of Texas and the Institute of Hygiene and Tropical Medicine, Lisbon, Portugal, chemo-sensitization was also found to be effective against a number of human pathogenic fungi, when using the antifungal drugs, itraconazole or fluconazole.  Chemo-sensitization has significant potential in agriculture and medicine to help reduce environmental impact and costs of using fungicides and preventing or overcoming resistance. 


Zearalenone contamination. Zearalenone (ZEN) an estrogenic mycotoxin produced by Fusarium fungi has broad potential to contaminate many cereal crops. ARS scientists at Peoria, Illinois, developed a capillary electrophoresis (CE) method for detecting ZEN using cyclodextrins.  The cyclic oligosaccharide enhanced the fluorescence of ZEN, which permitted the development of the assay with vastly improved sensitivity.  The new technology permits the detection of ZEN at 5 parts per billion (ppb), a level well-suited for testing by both industry and regulatory agencies for compliance with the European Union guideline of 50 ppb.   




Last Modified: 10/17/2008