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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Meat Safety and Quality » Research » Research Project #430703

Research Project: Mitigation Approaches for Foodborne Pathogens in Cattle and Swine for Use During Production and Processing

Location: Meat Safety and Quality

2021 Annual Report

Objective 1: Develop and validate novel pre- and post-harvest intervention strategies to reduce or eliminate foodborne pathogen colonization and persistence in the animal and on carcasses and meat products. Sub-objective 1.A: Identify effective control measures to reduce pathogens and in the pre-harvest environment. Sub-objective 1.B: Identify and/or improve efficacious non-thermal post-harvest interventions to reduce contamination of processing plant surfaces, hides, carcasses, and meat products. Sub-objective 1.C: Determine if current processing interventions are equally effective on AMR bacteria and foodborne pathogens. Objective 2: Develop improved sampling, detection, and tracking technologies to identify points, including biofilms, where pathogens persist and contaminate in the production of red meat. Sub-objective 2.A: Characterization of bacterial and environmental components contributing to high event periods (HEP) of E. coli O157:H7 contamination at beef processing plants. Sub-objective 2.B: Identify improved sampling and detections technologies for foodborne pathogens associated with red meat. Sub-objective 2.C: Develop and evaluate indicator organisms as surrogates for tracking pathogens through beef processing. Objective 3: Identify environmental and management practices that influence antimicrobial resistance, colonization of lymph nodes, and colonization rates of cattle, veal, and swine. Sub-objective 3.A: Determine effects of season and production system on occurrence of antimicrobial resistance and foodborne pathogens associated with food animal production. Sub-objective 3.B: Identify environmental and management practices that influence Salmonella in lymph nodes. Sub-objective 3.C: Determine the prevalence of STEC and AMR in veal production systems and identify factors contributing to colonization.

Cattle and swine can serve as reservoirs of foodborne pathogens that can spread through the environment or to meat during harvest. Further, pharmacologic antimicrobial use in meat animal production is a concern due to the perceived possibility of emergence and transmission of antimicrobial resistant (AMR) bacteria to the environment and food supply. Research to develop ways to reduce the levels of foodborne pathogens such as Shiga-toxin producing Escherichia coli (STEC) and Salmonella on farms and in foods is important, as is understanding and reducing the risk posed to food safety by AMR bacteria present in the meat production system. To this end, the effects of animal vaccines and direct fed microbial feed additives will be investigated to reduce or eliminate foodborne pathogens in the pre-harvest environment. During the harvest process, chlorine dioxide gas, cold atmospheric plasma, and a unique nano-technology sprayer will be assessed to reduce contamination. Novel methods to detect and track pathogens will be designed and tested including examining processing plants for biofilms and determining their roles during times of widespread pathogen contamination. Environmental and animal management practices that influence antimicrobial resistance and colonization of meat animals by pathogens will be studied, with the goal of identifying management practices that influence Salmonella in beef carcass lymph nodes and the prevalence of STEC in veal production. Successful completion of the project objectives will increase the ability of producers and processors to monitor production and use improved interventions to control contamination and product loss, and clarify the risk of antimicrobial resistance in meat production, while providing meat consumers a decreased risk of foodborne illness.

Progress Report
This is the final report for the project titled “Mitigation Approaches for Foodborne Pathogens in Cattle and Swine for Use During Production and Processing”. It has been replaced with 3040-42000-021-00D “Holistic Tactics to Advance the Microbiological Safety and Quality of the Red Meat Continuum”. Under Objective 1, studies of novel intervention strategies to reduce or eliminate foodborne pathogens were completed. Two successful interventions were identified, while another was ruled out. A novel aqueous ozone treatment was identified as an efficacious spray chill intervention against Escherichia coli (E. coli) O157:H7 on fresh beef. The last step of beef processing is to rapidly cool the carcass by applying periodic sprays of cold water. Aqueous ozone was found to be 80% more effective than water alone when used for this spray. Ultraviolet Light (UV) light and ozone were used to sanitize food-contact surfaces and to reduce bacteria on food products. Exposing contaminated beef to UV light or UV with gaseous ozone reduced E. coli, Salmonella, and Listeria on the surfaces by 90 to 95%, without impairing the color or taste of the fresh beef. These new proven technologies will allow processors to replace water and energy intensive treatments and produce safer, greener, and more economical beef for consumers. The treatment of cattle hides with a bacteriophage before processing did not improve beef safety. It is established that cattle hides are the main source of beef carcass contamination during processing and that reductions in E. coli O157:H7 on the hides of cattle will lead to reductions in carcass contamination. Bacteriophage, viruses capable of killing bacteria, have been proposed as a novel technology to reduce the levels of E. coli O157:H7 on cattle hides. However, when a commercialized bacteriophage application was sprayed onto cattle hides prior to entering beef processing plants a significant reduction of E. coli O157:H7 on hides or beef carcasses was not found. Objective 2: Develop improved sampling, detection, and tracking technologies to identify points, like biofilms, where pathogens persist and contaminate in the production of red meat, resulted in numerous accomplishments. Novel pre-harvest and post-harvest continuous sampling device (CSD) and manual sampling device (MSD), sample collection methods were established. Rectal mucosal swab (RAM swabs) sampling for detection of pathogenic E. coli in beef cattle pre- or peri-harvest were validated. With RAMS swabs found equal to or better than grab samples for testing of pathogenic E. coli in cattle. Novel sampling methods for beef trim microbiological testing were developed. Traditional methods of beef sampling for pathogen testing examine less than one pound of trimmings from 2000 pounds of beef trimmings destined for ground beef. Two novel sampling technologies: the CSD and the MSD which sample a much greater proportion of the trim and are non-destructive were validated. Results from over 1400 samples demonstrated that both the CSD and MSD provide an equal or better level of performance for detecting pathogen contamination in beef trim compared to the existing methods. Implementation of these new trim sampling methods are resulting in improved beef safety with additional benefits in reduced labor and other costs, and improved worker safety. A novel approach using surface pH of fresh beef was developed to use as a validation parameter for lactic acid treatment against E. coli O157:H7 and Salmonella. The surface pH of a beef carcass after applying lactic acid was identified as an effective and inexpensive measurement of antimicrobial efficacy and this new practice can improve food safety in the beef industry while reducing costs to beef processors. Improved detection methods of E. coli O157:H7 and non-O157 Shiga Toxin-producing E. coli (STEC) were developed and validated. Many current tests cannot tell E. coli O157:H7 from other E. coli and, thus, produce false positive results. A new real-time Polymerase chain reaction (PCR) linked with melt peak analysis was developed and validated that can more accurately distinguish E. coli O157:H7 from the other E. coli. Two types of STEC are O26 and O111, but there are non-pathogen E. coli of these types that can cause false positive results in current tests. Working with collaborators at Florida State University two new tests that can detect STEC-O26 and STEC-O111 and distinguish them from the non-pathogen O26 and O111 were developed. When in use, these new tests will improve accuracy and implicate less beef products for disposition. Lastly under Objective 2, various E. coli (O157:H7, STEC-O113, and extremely heat resistant E. coli) were characterized to better understand their roles in contamination and disease. E. coli O157:H7 strains isolated during High Event Periods (HEP) of contamination were characterized and results showed that compared to control strains, the HEP strains had a higher biofilm-forming ability and lower sanitizer susceptibility. Moreover, the HEP strains retained higher copy numbers of the pO157 plasmid suggesting that it might be the genetic basis for the HEP strains’ enhanced ability to survive in the meat plants and cause contamination. STEC-O113 are commonly found in U.S. beef but little disease is reported in the U.S. for this STEC. In other countries STEC O113 have caused outbreaks of severe disease. In collaboration with the U.S. Food and Drug Administration and the French Agency for Food, Environmental and Occupational Health & Safety, STEC O113 isolated from beef and cattle in the U.S. were compared to the disease-causing strains from other countries. Results showed U.S. strains of STEC O113 form two related groups, with a small portion of one of the groups overlapping with the disease causing STEC O113. However, these had been isolated from imported beef products and are not found in U.S. beef and cattle. Extremely heat resistant (XHR) E. coli can survive in beef patties cooked to 160F and raised concerns regarding food safety. Therefore, the prevalence of XHR E. coli and other heat resistant bacteria present in the feces of U.S. feedlot cattle, cull dairy, and cull beef cows at harvest were examined. Results showed that XHR bacteria and their respective genes are present in feces of all cattle types and in all geographical regions across the U.S. The prevalence is, however, very low and none of the heat resistant bacteria were identified as food-borne pathogens so they do not currently pose any food safety risk. Objective 3 addressed environmental and management practices that influenced antimicrobial resistance, colonization of lymph nodes, and colonization rates of veal. Antimicrobial use in livestock production is under intense scrutiny in the U.S. due to potential contributions to antimicrobial resistance. Multiple studies were performed and reported that showed prophylactic in-feed treatment of chlortetracycline administered for five days to calves entering feedlots is judicious as this therapy reduced animal illnesses, reduced the use of antimicrobials more critical to human health, and had no long-term impact on the occurrence of antimicrobial resistance. Likewise, in-feed tylosin phosphate administration to feedlot cattle was found to have little to no impact on antimicrobial resistance where human health is concerned. Lastly, the occurrence of antimicrobial resistance in beef cows was found not associated with antimicrobial use indicating that other factors more strongly influenced the observed levels of antimicrobial-resistant bacteria in beef cows. It was concluded that, beef cattle production without any antibiotics would not be expected to reduce the amount of antimicrobial resistance (AMR) contributed to the environment compared to conventional production. Meat products are considered by some consumers, regulators, and public health officials to transmit antibiotic resistance from animals to humans. Studies were performed and reported that found pork chops produced from swine “raised without antibiotics” (RWA) had similar levels of antibiotic resistant bacteria and antibiotic resistance genes as pork chops produced from “conventionally” (CONV) raised swine where the animals receive antibiotics. In the case of ground beef, CONV and RWA ground beef products contained similar levels of antimicrobial resistances. This is mounting evidence that antimicrobial uses in U.S. cattle and swine production do not significantly impact the antibiotic resistance present in beef and pork products; and that claims of detrimental impacts of antibiotic use during cattle and swine production on human health from eating beef or pork are without merit. Beef carcass lymph nodes have been identified as a potential source of human exposure to Salmonella when fat trim containing these nodes is mixed with lean trim and incorporated into ground beef. Salmonella were found in peripheral lymph nodes of healthy cattle at slaughter but the majority were neither resistant to any antimicrobial agents, nor of serotypes commonly identified in human disease. The processing and harvest of bob veal and formula-fed veal calves were studied for E. coli O157:H7, non-O157 STEC, and Salmonella. Significantly more non-O157 STEC were found on veal hides and carcasses than E. coli O157:H7, as compared to beef where the opposite has been reported. Further, a greater proportion of bob veal was found to be contaminated by STEC compared to formula-fed veal. In regard to Salmonella, bob veal products were at higher risk of Salmonella contamination than formula fed veal. However, the strains of Salmonella from bob veal were types rarely seen in human illness, and although formula-fed veal had a lower incidence of Salmonella, the strains were types more often linked to human illnesses. The study was repeated a year later, and processing had improved with less STEC and Salmonella detected on carcasses.

1. Environmental biofilms help Escherichia coli (E. coli) O157:H7 survive sanitation. E.coli O157:H7 is a foodborne pathogen that causes outbreaks of severe disease in humans. Inside meat processing plants a wide variety of bacteria, and occasionally E. coli O157:H7, are found. Floor drains at meat plants catch all of these bacteria, where many survive as a protected community in the form of a biofilm. USDA-ARS scientists in Clay Center, Nebraska, tested biofilm samples from floor drains at two meat plants with different E. coli O157:H7 contamination histories. They found the biofilm forming ability and the bacterial species that made up the biofilms were different between the two plants. Certain bacterial species in the drain biofilms helped E. coli O157:H7 survive and persist by protecting it from sanitation. This new knowledge will inform plant sanitation procedures to disrupt biofilms, making E. coli O157:H7 and other potentially harmful bacteria more susceptible to sanitation and disinfection procedures in the packing plant, which will improve the safety of meat and further protect public health.

2. Shiga toxin-producing Escherichia coli (E. coli) on pork carcasses. Escherichia coli (E. coli) that produce Shiga toxin are pathogenic, making them a food safety threat. Beef processors routinely test for Shiga toxin-producing E. coli, however, the presence of these pathogenic E. coli throughout pork processing is not well known. USDA-ARS scientists in Clay Center, Nebraska, tested pork carcasses each season at two pork processing plants and determined that pathogenic E. coli prevalence was 40 to 100% on pigs coming into the processing plant regardless of season. Although, pork processing steps and antimicrobial interventions reduced pathogenic E. coli levels and prevalence significantly, some types of E. coli capable of causing human illness were identified on the finished pork carcasses. Based on this study, pork processors may need to consider Shiga toxin-producing E. coli a potential contaminate in order to improve pork food safety and to better protect public health.

3. Prevalence of antibiotic resistance in cull cow processing plants. Dairy cows make up about 18% of the cattle harvested in the United States each year. Published studies show antibiotic use has little effect on antibiotic resistance in fed beef cattle and their products, but little data exists regarding culled cows that are typically many years older when harvested for beef. To address this data gap, USDA-ARS scientists in Clay Center, Nebraska, in collaboration with scientists from Colorado State University, Fort Collins, Colorado, tested culled beef cows (conventional beef), culled dairy cows (conventional dairy), and culled organic dairy cows cared for without using antibiotics (organic dairy). Results indicate that all groups had very low levels of antibiotic resistance and that cows managed without antibiotics were not significantly different in measured antimicrobial resistance on their beef products when compared to both conventional beef and dairy cows. These data demonstrate that human exposure to antibiotic resistance through beef is insignificant and not different between conventional and organic production systems.

Review Publications
Dass, S.C., Bosilevac, J.M., Weinroth, M., Elowsky, C.G., Zhou, Y., Anandappa, A., Wang, R. 2020. Impact of mixed biofilm formation with environmental microorganisms on E. coli O157:H7 survival against sanitization. NPJ Science of Food. 4:16.
Schmidt, J.W., Vikram, A., Arthur, T.M., Belk, K.E., Morley, P.S., Weinroth, M.D., Wheeler, T.L. 2020. Antimicrobial resistance at two United States cull cow processing establishments. Journal of Food Protection. 83(12):2216-2228.
Nastasijevic, I., Schmidt, J.W., Boskovic, M., Glisic, M., Kalchayanand, N., Shackelford, S.D., Wheeler, T.L., Koohmaraie, M., Bosilevac, J.M. 2020. Seasonal prevalence of Shiga toxin-producing Escherichia coli on pork carcasses for three steps of the harvest process at two commercial processing plants in the United States. Applied and Environmental Microbiology. 87(1):e01711-20.
Schmidt, J.W., Vikram, A., Doster, E., Thomas, K., Weinroth, M.D., Parker, J., Hanes, A., Geornaras, I., Morley, P.S., Belk, K.E., Wheeler, T.L., Arthur, T.M. 2021. Antimicrobial resistance in U.S. retail ground beef with and without label claims regarding antibiotic use. Journal of Food Protection. 84(5):827-842.