Progress 01/06/16 to 01/05/21
Outputs
PROGRESS REPORT Objectives (from AD-416): The overall goal of this project is to determine the growth and inactivation kinetics of foodborne pathogens suspended in foods treated using thermal and nonthermal process interventions, with a strong emphasis on ExPEC. 1. Develop and validate models to simulate pathogen behavior under both growth and inactivation conditions. 2. Developing and validating non-thermal and thermal intervention technologies to inactivate pathogens and spoilage microorganisms in raw and ready-to-eat foods and food contact surfaces. 3. Examine any relationship between genotype (virulence factors) and pathogen resistance to interventions. The results of this research will be transferred to regulatory agencies (USDA Food Safety Inspection Service (FSIS), US Food and Drug Administration (FDA)) to develop genomic-based risk assessments. In addition, results will be transferred to women⿿s health groups, commercial entities, and the meat and poultry industry. This approach may be ultimately expanded to include other thermal and nonthermal intervention technologies and extraintestinal foodborne pathogens. Approach (from AD-416): Extraintestinal Escherichia coli (ExPEC) are common contaminants in food which includes fresh produce, fish, meat and poultry. Illness occurs after contaminated food is consumed, the ExPEC colonize the gastrointestinal tract, and are then accidentally transferred to the urethra. They then cause urinary tract infections (UTI), sepsis, and meningitis. Approximately 6-8 million cases of UTI and 23,000 deaths annually are attributed to ExPEC. ExPEC and other extraintestinal foodborne pathogens which are found in meat and poultry have been directly traced to illness in humans. In addition, these emerging foodborne pathogens are resistant to multiple antibiotics and are considered a national research priority as noted in the President⿿s Council of Advisors on Science and Technology (PCAST, 2014). As specifically noted by regulatory agencies this project addresses ⿿an area of growing concern to FSIS and the public health community which will help: 1) improve the ability to develop safe processing procedures and to evaluate the impact of processing deviations on pathogen growth in the impacted products; 2) provide insights into mechanisms that contribute to the survival of pathogens to commonly used microbial intervention and mechanisms that affect the severity of illness in humans, and antibiotic resistance in outbreak strains; and 3) provide a scientific foundation for the development of new Agency food safety policies. The Centers for Disease Control and Prevention (CDC) recommends the use of foods treated with appropriate intervention technologies to lessen the risk of foodborne illness for ⿿at risk individuals. There is little if any information about growth or inactivation kinetics of the ExPEC in food using both thermal and nonthermal food safety intervention technologies or how pathogen genotype affects their resistance to intervention technologies, hence we will generate such data to fill the informational void regarding these emerging pathogens as part of this unique food safety project. This is the final report for Project 8072-42000-078-00D, which ended January 05, 2021. This project focuses on assessing, characterizing, and killing the emerging pathogen extraintestinal pathogenic E. coli (ExPEC) in meat and poultry, with a genomics component to investigate the role that virulence factors and antibiotic resistance play in pathogen resistance to intervention technologies to aid in metagenomic risk assessments conducted by USDA Food Safety Inspection Service (FSIS). ExPEC is a diverse set of emerging pathogens that are present in poultry and red meat, in addition, to produce. The association of ExPEC with the disease in humans can be traced directly from food animals, produce, and food to humans through modern genetic analysis techniques. They are associated with illnesses such as sepsis (the 6th leading cause of death), ulcerative colitis and Crohn⿿s Disease (ca. 1 million cases), urinary tract infections (11 million cases annually, and 23,000 deaths), and meningitis (ca. 500 deaths annually). The ExPEC that causes illness in humans is categorized as Uropathogenic E. coli (UPEC), Sepsis-Associated Pathogenic E. coli (SEPEC), and Neonatal Meningococcal E. coli (NMEC). There is now very strong evidence these disease conditions are a form of foodborne illness. Many ExPEC is also resistant to multiple antibiotics, including the antibiotics of last resort. The total cost of ExPEC in foods may be as high as $25 billion annually. In contrast, there were only six confirmed cases of deaths associated with Shiga toxin-producing E. coli, such as O157:H7 in 2016. In continuing research on the presence of ExPEC in retail chicken meat, we isolated ExPEC Sequence Type (ST) 131 and ST 117 isolates involved in urinary tract infections. Both isolates are resistant to multiple antibiotics. We also isolated Klebsiella pneumoniae isolates which contained virulence factors necessary for infection in humans which are resistant to multiple antibiotics, as well as sanitizers used by both the hospital and food industries. Microbial Resource Announcements were published on these isolates and inactivation kinetic data presented at multiple scientific meetings and distributed to our stakeholders in FSIS as well as women⿿s health groups. We conducted a survey of E. coli types isolated from fresh herbs (e.g., mint, cilantro, basil, parsley) and found the E. coli ST were those associated with disease in humans, carried multiple ExPEC virulence factors, were resistant to multiple antibiotics, and industrial sanitizers. It appears E. coli on produce are being transferred there through animal waste as they are typically associated with both food and wild animals. The incidence of E. coli on the retail herbs ranged from zero to >10,000 per gram. The presence of E. coli with these virulence factors and antibiotics is concerning as each of the fore-mentioned fresh herbs is typically eaten raw. In cooperation with our collaborators at National Taiwan University (Taipei, Taiwan) and Tunghai University (Taichung, Taiwan), we have achieved the model development of HPP in combination with several food- grade antimicrobials, e.g., acetic acid, allyl isothiocyanate (AITC), and trans-cinnamaldehyde (tCinn), to assess/predict shiga toxin-producing Escherichia coli O157:H7 (STEC) and UPEC inactivation. We found that at high-pressure treatment (250-350 MPa; 10-20 min), AITC (0.03-0.09%, w/w) and tCinn (0.10-0.20%), a 5-log (i.e. 99.999%) reduction may be achieved. Therefore, a modest pressure level (i.e. 300-400 MPa vs. 500-600 MPa currently in use) hurdled with 0.05-0.15% (w/w) of several antimicrobials can deliver the 5-log reduction of ExPEC, UPEC, and STEC in chicken meat. The 5-log reduction is required by FDA to validate the non-thermal intervention technology. The effective high-pressure is much lower than that typically required at 500-600 MPa level, which can further reduce the food texture damages and HPP operation cost. Regression models to predict inactivation also have been developed and validated to include STEC, UPEC, Salmonella, and Listeria monocytogenes. All models have R^2 > 0.9, which indicated good predictions vs. experimental data. We also found that the foodborne pathogen resistance to HPP stress is (in order from high to low) STEC > UPEC > Salmonella > L. monocytogenes. Those models may assist the risk assessment task to control and enhance food safety. The HPP operation temperature impact on pathogen lethality was investigated and evaluated from -10 to +20 degrees Centigrade. We found the best temperature range to deliver inactivation is around 0- 6 degrees Centigrade for raw ground meats. This finding is in line with the meat process for safety concerns in terms of microbial growth potential. To reduce the meat quality damaged by high pressure (> 450 MPa), enzyme applications to improve meat texture have been studied and results demonstrated much-improved meat color (appearance) and texture could be achieved [via. Scanning Electron Microscopy (SEM) images observation/ evaluation]. The food industry may use those texture results and developed models to optimize the product, processing development, and cost reduction; in the meanwhile, the microbial risk (foodborne pathogens) can be properly assessed to meet the food safety concerns. Those results have been or are being prepared to be published in peer- review journals (e.g., Food Control with Impact Factor ca. 4) in 2020/ 2021. Record of Any Impact of Maximized Teleworking Requirement: Maximized telework from March 2020 until May 2021 prevented laboratory work from being performed during most of the reporting period. Based on guidance from the Agency, the Eastern Regional Research Center (ERRC) was able to resume operations at 25% capacity in the middle of May 2021 for some projects to do research experiments. The situation has imposed a negative impact on the project's progress. ACCOMPLISHMENTS 01 Models developed to predict the inactivation of Uropathogenic Escherichia coli (UPEC) and other Extraintestinal Pathogenic E.coli (ExPEC) in meats. Escherichia pathogens are commonly found in retail poultry meat and cause approximately ten million urinary tract infections and one million cases of inflammatory bowel Crohns disease each year, mostly in women. ARS scientists at Wyndmoor, Pennsylvania, worked with other scientists from the National Taiwan University and Tunghai University, Taiwan and determined that high-pressure processing and natural essential oil extracts inactivate Escherichia coli suspended in ground chicken meat.
Impacts
(N/A)
Publications
- Chuang, S., Sheen, S., Sommers, C.H., Sheen, L. 2020. Modeling the effect of simultaneous use of allyl isothiocyanate and cinnamaldehyde on high hydrostatic pressure inactivation of uropathogenic and shiga toxin- producing Escherichia coli in ground chicken. Journal of the Science of Food and Agriculture. https://doi.org//10.1002/jsfa.10731.
- Yang, Y., Dhakal, S., Chu, C.N., Wang, S., Xue, Q., Rudd, J.C., Ibrahim, A. M., Jessup, K., Baker, J., Fuentealba, M.P. 2020. Genome wide identification of QTL associated with yield and yield components in two popular wheat cultivars TAM 111 and TAM 112. PLoS ONE. 15(12). Article e0237293. https://doi.org/10.1371/journal.pone.0237293.
- Chuang, S., Sheen, S., Sommers, C.H., Sheen, L. 2021. Modeling the inactivation of salmonella and listeria monocytogenes in ground chicken meat subject to high pressure processing and trans-Cinnamaldehyde. LWT - Food Science and Technology. 139:110601. https://doi.org/10.1016/j.lwt. 2020.110601.
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Progress 10/01/19 to 09/30/20
Outputs
Progress Report Objectives (from AD-416): The overall goal of this project is to determine the growth and inactivation kinetics of foodborne pathogens suspended in foods treated using thermal and nonthermal process interventions, with a strong emphasis on ExPEC. 1. Develop and validate models to simulate pathogen behavior under both growth and inactivation conditions. 2. Developing and validating non-thermal and thermal intervention technologies to inactivate pathogens and spoilage microorganisms in raw and ready-to-eat foods and food contact surfaces. 3. Examine any relationship between genotype (virulence factors) and pathogen resistance to interventions. The results of this research will be transferred to regulatory agencies (USDA Food Safety Inspection Service (FSIS), US Food and Drug Administration (FDA)) to develop genomic-based risk assessments. In addition, results will be transferred to women⿿s health groups, commercial entities, and the meat and poultry industry. This approach may be ultimately expanded to include other thermal and nonthermal intervention technologies and extraintestinal foodborne pathogens. Approach (from AD-416): Extraintestinal Escherichia coli (ExPEC) are common contaminants in food which includes fresh produce, fish, meat and poultry. Illness occurs after contaminated food is consumed, the ExPEC colonize the gastrointestinal tract, and are then accidentally transferred to the urethra. They then cause urinary tract infections (UTI), sepsis, and meningitis. Approximately 6-8 million cases of UTI and 23,000 deaths annually are attributed to ExPEC. ExPEC and other extraintestinal foodborne pathogens which are found in meat and poultry have been directly traced to illness in humans. In addition, these emerging foodborne pathogens are resistant to multiple antibiotics and are considered a national research priority as noted in the President⿿s Council of Advisors on Science and Technology (PCAST, 2014). As specifically noted by regulatory agencies this project addresses ⿿an area of growing concern to FSIS and the public health community which will help: 1) improve the ability to develop safe processing procedures and to evaluate the impact of processing deviations on pathogen growth in the impacted products; 2) provide insights into mechanisms that contribute to the survival of pathogens to commonly used microbial intervention and mechanisms that affect the severity of illness in humans, and antibiotic resistance in outbreak strains; and 3) provide a scientific foundation for the development of new Agency food safety policies. The Centers for Disease Control and Prevention (CDC) recommends the use of foods treated with appropriate intervention technologies to lessen the risk of foodborne illness for ⿿at risk individuals. There is little if any information about growth or inactivation kinetics of the ExPEC in food using both thermal and nonthermal food safety intervention technologies or how pathogen genotype affects their resistance to intervention technologies, hence we will generate such data to fill the informational void regarding these emerging pathogens as part of this unique food safety project. This project focuses on assessing, characterizing, and killing the emerging pathogen extraintestinal pathogenic E. coli (ExPEC) in meat and poultry, with a genomics component to investigate the role that virulence factors and antibiotic resistance play in pathogen resistance to intervention technologies to aid in metagenomic risk assessments conducted by USDA Food Safety Inspection Service (FSIS). ExPEC are a diverse set of emerging pathogens that are present in poultry and red meat, in addition to produce. The association of ExPEC with disease in humans can be traced directly from food animals, produce, and food to humans through modern genetic analysis techniques. They are associated with illnesses such as sepsis (the 6th leading cause of death), ulcerative colitis and Crohn⿿s Disease (ca. 1 million cases), urinary tract infections (11 million case annually, and 23,000 deaths), and meningitis (ca. 500 deaths) annually. The ExPEC that cause illness in humans are categorized as Uropathogenic E. coli (UPEC), Sepsis- Associated Pathogenic E. coli (SEPEC) and Neonatal Meningococcal E. coli (NMEC). There is now very strong evidence these disease conditions are a form of foodborne illness. Many ExPEC are also resistant to multiple antibiotics, including the antibiotics of last resort. The total cost of ExPEC in foods may be as high as $25 billion, annually. In contrast, there were only six confirmed cases of deaths associated with Shiga toxin- producing E. coli such as O157:H7 in 2016. In continuing research on the presence of ExPEC in retail chicken meat we isolated ExPEC Sequence Type (ST) 131 and ST 117 isolates which are involved in urinary tract infections. Both isolates are resistant to multiple antibiotics. We also isolated Klebsiella pneumoniae isolates which contained virulence factors necessary for infection in humans which are resistant to multiple antibiotics as well as sanitizers used by both the hospital and food industries. Microbial Resource Announcements were published on these isolates and inactivation kinetic data presented at multiple scientific meetings and distributed to our stakeholders in FSIS as well as women⿿s health groups. We conducted a survey of E. coli types isolated from fresh herbs (e.g. mint, cilantro, basil, parsley) and found the E. coli ST were those associated with disease in humans, carried multiple ExPEC virulence factors, were resistant to multiple antibiotics, and industrial sanitizers. It appears E. coli on produce are being transferred there through animal waste as they are typically associated with both food and wild animals. The incidence of E. coli on the retail herbs ranged from zero to >10,000 per gram. The presence of E. coli with these virulence factors and antibiotics are concerning as each of the fore-mentioned fresh herbs are typically eaten raw. In cooperation with our collaborators at National Taiwan University (Taipei, Taiwan) and Tunghai University (Taichung, Taiwan), we have achieved the model development of HPP in combination with several food grade antimicrobials, e.g. acetic acid, allyl isothiocyanate (AITC) and trans-cinnamaldehyde (tCinn), to assess/predict shiga toxin-producing Escherichia coli O157:H7 (STEC) and UPEC inactivation. We found that at high-pressure treatment (250-350 MPa; 10-20 min), AITC (0.03-0.09%, w/w) and tCinn (0.10-0.20%), a 5-log (i.e. 99.999%) reduction may be achieved. Therefore, a modest pressure level (i.e. 300-400 MPa vs. 500-600 MPa currently in use) hurdled with 0.05-0.15% (w/w) of several antimicrobials can deliver the 5-log reduction of ExPEC, UPEC and STEC in chicken meat. The 5-log reduction is required by FDA to validate the non-thermal intervention technology. The effective high-pressure is much lower than that typically required at 500-600 MPa level which can further reduce the food texture damages and HPP operation cost. Regression models to predict inactivation also have been developed and validated to include STEC, UPEC, Salmonella and Listeria monocytogenes. All models have R^2 > 0.9, which indicated good predictions vs. experimental data. We also found that the foodborne pathogen resistance to HPP stress is (in order from high to low) STEC > UPEC > Salmonella > L. monocytogenes. Those models may assist the risk assessment task to control and enhance food safety. The HPP operation temperature impact on pathogen lethality was investigated and evaluated from -10 to +20 degrees Centigrade. We found the best temperature range to deliver inactivation is around 0- 6 degrees Centigrade for raw ground meats. This finding is in line with the meat process for safety concern in terms of microbial growth potential. To reduce the meat quality damaged by high pressure (> 450 MPa), enzyme applications to improve meat texture has been studied and results demonstrated much improved meat color (appearance) and texture can be achieved [via. Scanning Electron Microscopy (SEM) images observation/ evaluation]. Food industry may use those texture results and developed models to optimize the product, processing development and cost reduction, in the meanwhile the microbial risk (foodborne pathogens) can be properly assessed to meet the food safety concerns. Those results have been or prepared to be published in peer-review journals (e.g. Food Control with Impact Factor ca. 4) in 2020/2021.
Impacts
(N/A)
Publications
- Chuang, S., Sheen, S., Sommers, C.H., Zhou, S., Sheen, L. 2020. Survival evaluation for salmonella spp. and listeria monocytogenes in ground chicken meat subject to high hydrostatic pressure and carvacrol using selective and nonselective media. Journal of Food Protection. 83(1):37-44.
- Hussain, S.A., Xu, A., Sommers, C.H., Sarker, M.I. 2020. Draft genome sequence of red heat-causing halomonas eurihalina MS1, a moderately halophilic bacterium isolated from saline soil in Alicante, Spain. Microbiology Resource Announcements.
- Zhou, S., Sheen, S., Zhao, G., Chuang, S., Han, L., Liu, L.S. 2020. Inactivation of Salmonella in tomato by combination treatment of high pressure and trans-cinnamaldeyde. Food Control.
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Progress 10/01/18 to 09/30/19
Outputs
Progress Report Objectives (from AD-416): The overall goal of this project is to determine the growth and inactivation kinetics of foodborne pathogens suspended in foods treated using thermal and nonthermal process interventions, with a strong emphasis on ExPEC. 1. Develop and validate models to simulate pathogen behavior under both growth and inactivation conditions. 2. Developing and validating non-thermal and thermal intervention technologies to inactivate pathogens and spoilage microorganisms in raw and ready-to-eat foods and food contact surfaces. 3. Examine any relationship between genotype (virulence factors) and pathogen resistance to interventions. The results of this research will be transferred to regulatory agencies (USDA Food Safety Inspection Service (FSIS), US Food and Drug Administration (FDA)) to develop genomic-based risk assessments. In addition, results will be transferred to women⿿s health groups, commercial entities, and the meat and poultry industry. This approach may be ultimately expanded to include other thermal and nonthermal intervention technologies and extraintestinal foodborne pathogens. Approach (from AD-416): Extraintestinal Escherichia coli (ExPEC) are common contaminants in food which includes fresh produce, fish, meat and poultry. Illness occurs after contaminated food is consumed, the ExPEC colonize the gastrointestinal tract, and are then accidentally transferred to the urethra. They then cause urinary tract infections (UTI), sepsis, and meningitis. Approximately 6-8 million cases of UTI and 23,000 deaths annually are attributed to ExPEC. ExPEC and other extraintestinal foodborne pathogens which are found in meat and poultry have been directly traced to illness in humans. In addition, these emerging foodborne pathogens are resistant to multiple antibiotics and are considered a national research priority as noted in the President⿿s Council of Advisors on Science and Technology (PCAST, 2014). As specifically noted by regulatory agencies this project addresses ⿿an area of growing concern to FSIS and the public health community which will help: 1) improve the ability to develop safe processing procedures and to evaluate the impact of processing deviations on pathogen growth in the impacted products; 2) provide insights into mechanisms that contribute to the survival of pathogens to commonly used microbial intervention and mechanisms that affect the severity of illness in humans, and antibiotic resistance in outbreak strains; and 3) provide a scientific foundation for the development of new Agency food safety policies. The Centers for Disease Control and Prevention (CDC) recommends the use of foods treated with appropriate intervention technologies to lessen the risk of foodborne illness for ⿿at risk individuals. There is little if any information about growth or inactivation kinetics of the ExPEC in food using both thermal and nonthermal food safety intervention technologies or how pathogen genotype affects their resistance to intervention technologies, hence we will generate such data to fill the informational void regarding these emerging pathogens as part of this unique food safety project. This project focuses on assessing, characterizing, and killing the emerging pathogen extraintestinal pathogenic E. coli (ExPEC) in meat and poultry, with a genomics component to investigate the role that virulence factors and antibiotic resistance play in pathogen resistance to intervention technologies to aid in metagenomic risk assessments conducted by USDA Food Safety Inspection Service (FSIS). ExPEC are a diverse set of emerging pathogens that are present in poultry and red meat, in addition to produce. The association of ExPEC with disease in humans can be traced directly from food animals, produce, and food to humans through modern genetic analysis techniques. They are associated with illnesses such as sepsis (the 6th leading cause of death), ulcerative colitis and Crohn⿿s Disease (ca. 1 million cases), urinary tract infections (11 million case annually, and 23,000 deaths), and meningitis (ca. 500 deaths) annually. The ExPEC that cause illness in humans are categorized as Uropathogenic E. coli (UPEC), Sepsis-Associated Pathogenic E. coli (SEPEC) and Neonatal Meningococcal E.coli (NMEC). There is now very strong evidence these disease conditions are a form of foodborne illness. Many ExPEC are also resistant to multiple antibiotics, including the antibiotics of last resort. The total cost of ExPEC in Foods may be as high as $25 billion, annually. In contrast, there were only six confirmed cases of deaths associated with Shiga toxin-producing E. coli such as O157:H7 in 2016. In continuing research on the presence of ExPEC in retail chicken meat we isolated ExPEC Sequence Type (ST) 131 and ST 117 isolates which are involved in urinary tract infections. Both isolates are resistant to multiple antibiotics. We also isolated Klebsiella pneumoniae isolates which contained virulence factors necessary for infection in humans which are resistant to multiple antibiotics as well as sanitizers used by both the hospital and food industries. Microbial Resource Announcements were published on these isolates and inactivation kinetic data presented at multiple scientific meetings and distributed to our stakeholders in FSIS as well as women⿿s health groups. We conducted a survey of E.coli types isolated from fresh herbs (e.g. mint, cilantro, basil, parsley) and found the E. coli ST were those associated with disease in humans, carried multiple ExPEC virulence factors, were resistant to multiple antibiotics, and industrial sanitizers. It appears E. coli on produce are being transferred there through animal waste as they are typically associated with both food and wild animals. The incidence of E. coli on the retail herbs ranged from zero to >10,000 per gram. The presence of E. coli with these virulence factors and antibiotics are concerning as each of the fore-mentioned fresh herbs are typically eaten raw. In cooperation with our collaborators at National Taiwan University (Taipei, Taiwan) and the Department of Veterans Affairs (Minneapolis, Minnesota) we have determined the thermal inactivation kinetics of 18 individual ExPEC isolates and correlated the thermal resistance with the presence or absence of virulence factors. We found that ExPEC isolate difference in D-10 correlates with possessing or lacking the fdeC, sinH, cnf1, gad, ompT, iha, fimH and sat genes which are required for illness in humans and agricultural animals (e.g. avian colibacillosis). This may help some ExPEC survive cooking. We determined the thermal inactivation kinetics for multi-isolate cocktails of UPEC, NMEC, and food-source isolates at multiple temperatures and determined the thermal D-10 values or each ExPEC class, as well as the thermal z-values to generate mathematics based predictive equations that describe the heat resistance of the ExPEC over many temperatures. The mean D-10 values of the UPEC group were 7.34, 0.56, and 0.05 minutes at 55, 60, and 65 degrees Centigrade, respectively. The mean of the D-10 values of the NMEC group were 4.13, 0.47, and 0.08 minutes at 55, 60, and 65 degrees Centigrade, respectively. The z-values were 4.69, 5.89, and 5.53 degrees Centigrade/ min, respectively. Each of those processes is used commercially in the U. S. for food safety and shelf-life extension. This work was published in Food Control (Impact Factor = ca. 4) in 2019. In collaborative research with physicians and scientists at the Department of Veterans Affairs (Minneapolis, Minnesota) ARS scientists in Wyndmoor, Pennsylvania determined the ionizing radiation resistance of 25 ExPEC isolates suspended in refrigerated ground chicken meat. Irradiation of red and poultry meat is an FDA approved and commercialized process. We inoculated ground chicken meat with UPEC and NMEC, isolates from retail chicken meat (CM), as well as retail chicken-skin isolates identified in our laboratory (CS). We then determined their gamma radiation inactivation kinetics (D-10). The mean D-10 for all isolates (n=25) was 0. 30 kGy. The mean D-10 for the UPEC, NMEC, CM, and CS isolates were 0.25, 0.29, 0.29, and 0.39 kGy, respectively. The mean D-10 for the clinical isolates was 0.27 kGy vs. 0.34 kGy for the non-clinical isolates. Unlike the results for thermal processing of ExPEC mentioned previously there was no correlation between presence of virulence factors, antibiotic resistance, and radiation resistance. This research has been accepted for publication in Food Microbiology (Impact Factor = ca. 4) and will be published in 2019. Data from the studies listed above have been shared with stakeholders and customers including the Food and Drug Administration, the Centers for Disease Control and Prevention, FSIS, USDA-Economic Research Service, consumer groups, women⿿s health groups and the food processing industry through presentations at scientific meetings, published manuscripts and working groups. We participate in a FSIS working group which will address the risk posed from ExPEC in foods. Because of the high-profile nature of research on ExPEC in foods, ARS scientists in Wyndmoor, Pennsylvania organized and chaired the first ever symposium on the topic at a food safety meeting (Extraintestinal Pathogenic E.coli: Urinary Tract Infections and Sepsis)which was held at the International Association of Food Protection Meeting (Louisville, Kentucky) in July of 2019. Accomplishments 01 Radiation kills E. coli found in chicken meat that infect humans. Uropathogenic Escherichia coli (UPEC) and other Extraintestinal Pathogenic E. coli (ExPEC) cause approximately 10 million cases of urinary tract infections and 1 million cases inflammatory bowel disease (e.g. Crohns Disease) each year, disproportionately in women. UPEC and ExPEC are readily found in retail poultry meat. ARS scientists at Wyndmoor, Pennsylvania, working with physicians in the Department of Veterans Affairs in Minneapolis, Minnesota determined the radiation resistance, a Food and Drug Administration approved process, for UPEC and ExPEC suspended in ground chicken meat. They found a very modest radiation dose of 0.30 kGy kills 90% of UPEC and ExPEC in chicken meat. Irradiation of chicken meat will help food processors eliminate UPEC and ExPEC from retail poultry products and protect consumers, primarily women, from these deadly antibiotic resistant bacteria.
Impacts
(N/A)
Publications
- Xu, A., Mackay, W., Scullen, O.J., Ramos, R.V., Sheen, S., Sommers, C.H. 2019. Draft genomic sequence of Escherichia coli ST131 B7S75 isolated from retail chicken skin. Microbiology Resource Announcements.
- Xu, A., Johnson, J., Scullen, O.J., Chuang, S., Sheen, L., Sheen, S., Sommers, C.H. 2019. Thermal inactivation kinetics of extraintestinal pathogenic escherichia coli suspended in ground chicken meat. Food Control. 104:269-277.
- Chien, S., Sheen, S., Sommers, C.H., Sheen, L. 2018. Effects of combined treatments of high pressure processing, single-and multi-antimicrobial (Melissa officinalis extract)on the reduction of pathogenic Escherichia coli in ground beef. Food and Bioprocess Technology. 12:359-370.
- Xu, A., Abdul Wakeel, A.Y., Gunther, N.W., Sommers, C.H. 2019. Draft genomic sequence of Campylobacter coli isolated from chicken carcasses. Microbiology Resource Announcements. 8(28):e00564-19.
- Xu, A., Mackay, W., Sommers, C.H. 2019. Draft genomic sequence of multi- drug resistant Klebsiella peneumoniae B8S35, isolated from retail chicken skin. Microbiology Resource Announcements. 8(28):e00502-19.
- Xu, A., Scullen, O.J., Sheen, S., Johnson, J., Sommers, C.H. 2019. Inactivation of extraintestinal pathogenic E. coli clinical and food isolates suspended in ground chicken meat by gamma radiation. Food Microbiology.
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Progress 10/01/17 to 09/30/18
Outputs
Progress Report Objectives (from AD-416): The overall goal of this project is to determine the growth and inactivation kinetics of foodborne pathogens suspended in foods treated using thermal and nonthermal process interventions, with a strong emphasis on ExPEC. 1. Develop and validate models to simulate pathogen behavior under both growth and inactivation conditions. 2. Developing and validating non-thermal and thermal intervention technologies to inactivate pathogens and spoilage microorganisms in raw and ready-to-eat foods and food contact surfaces. 3. Examine any relationship between genotype (virulence factors) and pathogen resistance to interventions. The results of this research will be transferred to regulatory agencies (USDA Food Safety Inspection Service (FSIS), US Food and Drug Administration (FDA)) to develop genomic-based risk assessments. In addition, results will be transferred to women�s health groups, commercial entities, and the meat and poultry industry. This approach may be ultimately expanded to include other thermal and nonthermal intervention technologies and extraintestinal foodborne pathogens. Approach (from AD-416): Extraintestinal Escherichia coli (ExPEC) are common contaminants in food which includes fresh produce, fish, meat and poultry. Illness occurs after contaminated food is consumed, the ExPEC colonize the gastrointestinal tract, and are then accidentally transferred to the urethra. They then cause urinary tract infections (UTI), sepsis, and meningitis. Approximately 6-8 million cases of UTI and 23,000 deaths annually are attributed to ExPEC. ExPEC and other extraintestinal foodborne pathogens which are found in meat and poultry have been directly traced to illness in humans. In addition, these emerging foodborne pathogens are resistant to multiple antibiotics and are considered a national research priority as noted in the President�s Council of Advisors on Science and Technology (PCAST, 2014). As specifically noted by regulatory agencies this project addresses �an area of growing concern to FSIS and the public health community� which will help: 1) improve the ability to develop safe processing procedures and to evaluate the impact of processing deviations on pathogen growth in the impacted products; 2) provide insights into mechanisms that contribute to the survival of pathogens to commonly used microbial intervention and mechanisms that affect the severity of illness in humans, and antibiotic resistance in outbreak strains; and 3) provide a scientific foundation for the development of new Agency food safety policies. The Centers for Disease Control and Prevention (CDC) recommends the use of foods treated with appropriate intervention technologies to lessen the risk of foodborne illness for �at risk� individuals. There is little if any information about growth or inactivation kinetics of the ExPEC in food using both thermal and nonthermal food safety intervention technologies or how pathogen genotype affects their resistance to intervention technologies, hence we will generate such data to fill the informational void regarding these emerging pathogens as part of this unique food safety project. This project focuses on assessing, characterizing, and killing the emerging pathogen extraintestinal pathogenic E. coli (ExPEC) in meat and poultry, with a genomics component to investigate the role that virulence factors and antibiotic resistance play in pathogen resistance to intervention technologies to aid in metagenomic risk assessments conducted by USDA Food Safety Inspection Service (FSIS). ExPEC are a diverse set of emerging pathogens that are present in poultry and red meat, in addition to produce. The association of ExPEC with disease in humans can be traced directly from food animals, produce, and food to humans through modern genetic analysis techniques. They are associated with illnesses such as sepsis (the 6th leading cause of death), ulcerative colitis and Crohn�s Disease (ca. 1 million cases), urinary tract infections (11 million case annually, and 23,000 deaths), and meningitis (ca. 500 deaths) annually. The ExPEC that cause illness in humans are categorized as Uropathogenic E. coli (UPEC), Sepsis-Associated Pathogenic E. coli (SEPEC) and Neonatal Meningococcal E. coli (NMEC). There is now very strong evidence these disease conditions are a form of foodborne illness. Many ExPEC are also resistant to multiple antibiotics, including the antibiotics of last resort. In contrast, there were only six confirmed cases of deaths associated with Shiga toxin-producing E. coli such as O157:H7 in 2016. There has been substantial progress in the second year of the project. In collaboration with ARS scientists in Beltsville, Maryland, we obtained a number of ExPEC isolated from dairy cattle which have already been subjected to whole genome sequencing. We completed whole genome sequencing of twenty ExPEC clinical and food isolates, and published three Genome Announcements. In cooperation with our collaborators at National Taiwan University (Taipei, Taiwan) and the Department of Veterans Affairs (Minneapolis, Minnesota) we have determined the high pressure processing, thermal processing, and ionizing radiation inactivation kinetics for those twenty isolates suspended in ground chicken meat. We found that, in general, the Uropathogenic E. coli clinical isolates to be the most heat, high pressure, and irradiation resistant while the meningitis-causing E. coli tended to be the most sensitive, with the food isolates covering a wide range of sensitivity and resistances to the processing technologies. Inactivation kinetics are typically described as a D-10 value, or the processing condition needed to kill 90% of a microorganism. Overall, for the ExPEC tested, the thermal D-10 at 55 degrees Centigrade ranged from 0.5 to 7.6 min, the HPP D-10 at 400 MPa (4 degrees Centigrade) ranged from 0.5 to 9.6 min, and the ionizing radiation D-10 from 0.18 to 0.68 kGy. Of the ca. 53 ExPEC isolates characterized to date, over 45 were resistant to multiple antibiotics. In cooperation with our collaborators at National Taiwan University (Taipei, Taiwan) and the Department of Veterans Affairs (Minneapolis, Minnesota) we determined the thermal inactivation kinetics for multi-isolate cocktails of UPEC, NMEC, and food-source isolates at multiple temperatures and determined the thermal D-10 values or each ExPEC class, as well as the thermal z-values to generate mathematics- based predictive equations that describe the heat resistance of the ExPEC over many temperatures. The mean D-10 values of the UPEC group were 7.34, 0.56, and 0.05 minutes at 55, 60, and 65 degrees Centigrade, respectively. The mean of the D-10 values of the NMEC group were 4.13, 0.47, and 0.08 minutes at 55, 60, and 65 degrees Centigrade, respectively. The z-values were 4.69, 5.89, and 5.53 degrees Centigrade/min, respectively. Each of those processes is used commercially in the U.S. for food safety and shelf-life extension. Substantial progress has been made on determining the incidence and prevalence of ExPEC in retail chicken parts. We found that ca. 12% of the E. coli isolated from retail chicken skin were ExPEC. Those ExPEC (ca. 33) were then characterized by whole genome sequencing. This will enable food processors to apply appropriate thermal processing conditions to meat and poultry to control ExPEC. Data from the studies listed above have been shared with stakeholders and customers including the Food and Drug Administration, the Centers for Disease Control and Prevention, USDA-FSIS, USDA-Economic Research Service, consumer groups, and the food processing industry through presentations at scientific meetings, published manuscripts and working groups. As a result, we have been asked to participate in a USDA-FSIS working group which will address the risk posed from ExPEC in foods. In addition, we are now collaborating as part of an ExPEC working group with scientists from the Pennsylvania Department of Health (Harrisburg, Pennsylvania), Penn State University (State College, Pennsylvania), University of Pennsylvania (Philadelphia, Pennsylvania), the Centers for Disease Control and Prevention (Atlanta, Georgia) and the US-FDA (Food and Drug Administration) (Washington, District of Columbia). Accomplishments 01 Heat kills E. coli in chicken meat that infects women. Uropathogenic Escherichia coli (UPEC) causes approximately 11 million cases of urinary tract infections (UTI) each year, primarily in women. UPEC are found mostly in retail chicken meat and are linked to UTI in women. ARS scientists at Wyndmoor, Pennsylvania, working with scientists in the Department of Veterans Affairs (Minneapolis, Minnesota) and National Taiwan University (Taipei, Taiwan) determined that cooking at 65 degrees centigrade for 30 seconds, or 60 degrees for 150 seconds, killed almost all UPEC in ground chicken meat. These cooking conditions define the time and temperature needed to kill UPEC in chicken meat.
Impacts
(N/A)
Publications
- Sommers, C.H., Huang, C., Sheen, L., Sheen, S., Huang, L. 2018. Growth modeling of uropathogenic Escherichia coli in ground chicken meat. Food Control. 86:397-402.
- Sheen, S., Huang, C., Ramos, R.V., Chien, S., Scullen, O.J., Sommers, C.H. 2018. Lethality prediction for Escherichia coli 0157:H7 and Uropathogenic E. coli in ground chicken treated with high pressure processing and trans- cinnamaldehyde. Journal of Food Science. 83(3):740-749.
- Xu, A., Hertrich, S.M., Needleman, D.S., Sheen, S., Sommers, C.H. 2018. Draft genome sequences of four uropathogenic escherichia coli 04:H5 isolates (ATCC 700414,700415,700416 and 700417). Genome Announcements. 6(11):e00134-18.
- Xu, A., Johnson, J., Sheen, S., Needleman, D.S., Sommers, C.H. 2018. Draft genomic sequencing of six potential extraintestinal pathogenic Escherichia coli isolates from retail chicken meat. Genome Announcements.
- Xu, A., Johnson, J., Sheen, S., Sommers, C.H. 2018. Draft genome sequences of six neonatal meningitis-causing escherichia coli isolates (SP-4, SP-5, SP-13, SP-16, SP-46, and SP-65). Genome Announcements.
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Progress 10/01/16 to 09/30/17
Outputs
Progress Report Objectives (from AD-416): The overall goal of this project is to determine the growth and inactivation kinetics of foodborne pathogens suspended in foods treated using thermal and nonthermal process interventions, with a strong emphasis on ExPEC. 1. Develop and validate models to simulate pathogen behavior under both growth and inactivation conditions. 2. Developing and validating non-thermal and thermal intervention technologies to inactivate pathogens and spoilage microorganisms in raw and ready-to-eat foods and food contact surfaces. 3. Examine any relationship between genotype (virulence factors) and pathogen resistance to interventions. The results of this research will be transferred to regulatory agencies (USDA Food Safety Inspection Service (FSIS), US Food and Drug Administration (FDA)) to develop genomic-based risk assessments. In addition, results will be transferred to women�s health groups, commercial entities, and the meat and poultry industry. This approach may be ultimately expanded to include other thermal and nonthermal intervention technologies and extraintestinal foodborne pathogens. Approach (from AD-416): Extraintestinal Escherichia coli (ExPEC) are common contaminants in food which includes fresh produce, fish, meat and poultry. Illness occurs after contaminated food is consumed, the ExPEC colonize the gastrointestinal tract, and are then accidentally transferred to the urethra. They then cause urinary tract infections (UTI), sepsis, and meningitis. Approximately 6-8 million cases of UTI and 23,000 deaths annually are attributed to ExPEC. ExPEC and other extraintestinal foodborne pathogens which are found in meat and poultry have been directly traced to illness in humans. In addition, these emerging foodborne pathogens are resistant to multiple antibiotics and are considered a national research priority as noted in the President�s Council of Advisors on Science and Technology (PCAST, 2014). As specifically noted by regulatory agencies this project addresses �an area of growing concern to FSIS and the public health community� which will help: 1) improve the ability to develop safe processing procedures and to evaluate the impact of processing deviations on pathogen growth in the impacted products; 2) provide insights into mechanisms that contribute to the survival of pathogens to commonly used microbial intervention and mechanisms that affect the severity of illness in humans, and antibiotic resistance in outbreak strains; and 3) provide a scientific foundation for the development of new Agency food safety policies. The Centers for Disease Control and Prevention (CDC) recommends the use of foods treated with appropriate intervention technologies to lessen the risk of foodborne illness for �at risk� individuals. There is little if any information about growth or inactivation kinetics of the ExPEC in food using both thermal and nonthermal food safety intervention technologies or how pathogen genotype affects their resistance to intervention technologies, hence we will generate such data to fill the informational void regarding these emerging pathogens as part of this unique food safety project. Progress was made on all objectives, all of which fall under National Program 108 � Food Safety, Component I Foodborne Contaminants. Progress on this project focuses on Problem Statement 5, Intervention and Control Strategies Including Mycotoxins; and Problem Statement 6, Predictive Microbiology/Modeling: Data Acquisition. This project focuses on assessing, characterizing, and killing the emerging pathogen extraintestinal pathogenic E. coli (ExPEC) in meat and poultry, with a genomics component to investigate the role that virulence factors and antibiotic resistance play in pathogen resistance to intervention technologies to aid in metagenomic risk assessments conducted by USDA Food Safety Inspection Service. ExPEC are a diverse set of emerging pathogens that are present in poultry and red meat, in addition to produce. The association of ExPEC with disease in humans can be traced directly from food animals, produce, and food to humans through modern genetic analysis techniques. They are associated with illnesses such as sepsis (the 6th leading cause of death), ulcerative colitis and Crohn�s Disease (ca. 1 million cases), urinary tract infections (10.5 million case annually, and 23,000 deaths), and meningitis (ca. 500 deaths) annually. The ExPEC that cause illness in humans are categorized as Uropathogenic E. coli (UPEC), Sepsis-Associated Pathogenic E. coli (SEPEC) and Neonatal Meningococcal E. coli (NMEC). There is now very strong evidence these disease conditions are a form of foodborne illness. Many ExPEC are also resistant to multiple antibiotics, including the antibiotics of last resort. In contrast, there were only six confirmed cases of deaths associated with Shiga toxin-producing E. coli such as O157:H7 in 2016. There has been substantial progress in the first year of the project. In collaboration with scientists at Penn State University (State College, PA) we obtained a number of ExPEC clinical isolates associated with disease in humans and others from the American Type Culture Collection (Manassas, VA.) We obtained a number of food and animal ExPEC isolates from our collaborators at the Veterans Administration (St. Paul, MN). Substantial progress has been made on isolation of ExPEC from ground chicken and chicken parts, determining their status as ExPEC by polymerase chain reaction (PCR)-based phylogrouping and virulence factor profiling, and subjecting those isolates to genetic analysis. Isolates have been subjected to whole genome sequencing with our collaborators from Drexel University (Philadelphia, PA). Food processing technologies used by industry include thermal processing (cooking), and US Food and Drug Administration approved nonthermal processing technologies including high pressure processing, ionizing radiation, and ultraviolet light. Each of these technologies is commercialized and used by the food processing industry. High pressure processing (HPP) kills E. coli by crushing it. The D10 value, the HPP time and pressure parameters required to reduce ExPEC levels in ground chicken by 90%, were determined to be 30.6, 8.37, and 4.43 min at 300, 400, and 500 MPa, respectively. Furthermore, in experiments conducted in collaboration with scientists from National Taiwan University, we determined that natural antimicrobials mixed in with ground meat such as thymol essential oil and other essential oil mixtures substantially enhanced the killing of ExPEC and E. coli O157:H7, and a predictive model was developed to describe the essential oil/HPP killing process. Gamma radiation kills bacteria by damaging their DNA and proteins. We determined the gamma radiation inactivation kinetics for ExpEC suspended in ground chicken, with the gamma radiation D10 value being 0.28 and 0.36 kGy at 4 degrees C and -20 C, respectively. Ultraviolet light also kills bacteria by damaging their DNA and proteins. The ultraviolet light D10 for ExPEC suspended in poultry purge and placed on stainless steel and plastic food contact surfaces ranged from 11.4 to 12.9 mJ/cm2. We also completed a growth model for ExPEC suspended in ground chicken in collaboration with scientists from National Taiwan University. Data from the studies listed above have been shared with stakeholders and customers including the Food and Drug Administration, USDA Food Safety Inspection Service, consumer groups, and the food processing industry through meeting presentations scientific manuscripts, working groups. As a result, we have been asked to participate in a USDA FSIS working group which will address the risk posed from ExPEC in foods. Accomplishments 01 Inactivation of Uropathogenic Escherichia coli (UPEC) in ground chicken or chicken purge by high pressure processing, gamma radiation, and ultraviolet light. High pressure processing, gamma radiation, and ultraviolet light are sustainable food safety technologies that can kill harmful bacteria in meat and poultry. Uropathogenic Escherichia coli are an emerging and common contaminant in poultry meat and are associated with urinary tract infections which affect over 10 million people, primarily women, each year including 23,000 deaths. ARS researchers at Wyndmoor, Pennsylvania found that High pressure processing (500 MPa, 4 C, 4.43 min), gamma radiation (1.3 kGy at 4 C or 1.6 kGy at -20 C), or ultraviolet light (125 mJ/cm2) killed 99.999% of UPEC in chicken meat or chicken purge. The results of this study will allow regulatory agencies and food processing industries to conduct risk analysis and provide safer poultry meat to consumers. Consumers, especially those who are immuno-compromised (e.g. women, cancer patients, diabetics, and the HIV/AIDS population) will benefit from having more information about foods treated with alternative processes which kill harmful bacteria such as UPEC. 02 Growth kinetics for Uropathogenic Escherichia coli in ground chicken meat. Uropathogenic Escherichia coli (UPEC) are an emerging and common contaminant in poultry meat and are associated with urinary tract infections which affect over 10 million people, primarily women, each year including 23,000 deaths. ARS researchers at Wyndmoor, Pennsylvania, in collaboration with scientists from National Taiwan University, completed a growth model to describe the ability of UPEC to grow in ground chicken. UPEC was unable to grow at proper refrigeration temperature (4C), but was able to grow significantly at the mild abuse temperature of 10C. Food processors and risk assessors will be able to provide safer ground poultry meat to consumers. Consumers, especially those who are immuno-compromised (e.g. women, cancer patients, diabetics, and the HIV/AIDS population) will benefit from having more information about foods treated with alternative processes which kill harmful bacteria such as the UPEC.
Impacts
(N/A)
Publications
- Chien, S., Sheen, S., Sommers, C.H., Sheen, L. 2016. Modeling the inactivation of Escherichia coli 0157:H7 and uropathogenic E.coli in ground chicken by high pressure processing and thymol. Frontiers in Microbiology. 7(920):1-11.
- Chien, S., Sheen, S., Sommers, C.H., Sheen, L. 2016. Modeling the inactivatin of Escherichia coli 0157:H7 and uropathogenic E. coli in ground beef by high pressure processing and citral. Food Control. 73:672- 680.
- Sommers, C.H., Scullen, O.J., Mackay, W. 2016. Inactivation of Staphylococcus saprophyticus in chicken meat and exudate using high pressure processing, gamma radiation, and ultraviolet light. Food Control. 75:78-82.
- Li, C., Hsu, H., Wang, Y., Cassidy, J.M., Sheen, S., Liu, S. 2017. Effects of heat treatment on antioxidative and anti-inflammatory properties of orange by-products. The Royal Society of Chemistry. doi: 10.1039/ C7FO00188F.
- Sommers, C.H., Gunther, N.W., Sheen, S. 2016. Inactivation of foodborne pathogens in chicken purge or skin using a 405-nm LED array. Food Microbiology. 64:135-138.
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Progress 10/01/15 to 09/30/16
Outputs
Progress Report Objectives (from AD-416): The overall goal of this project is to determine the growth and inactivation kinetics of foodborne pathogens suspended in foods treated using thermal and nonthermal process interventions, with a strong emphasis on ExPEC. 1. Develop and validate models to simulate pathogen behavior under both growth and inactivation conditions. 2. Developing and validating non-thermal and thermal intervention technologies to inactivate pathogens and spoilage microorganisms in raw and ready-to-eat foods and food contact surfaces. 3. Examine any relationship between genotype (virulence factors) and pathogen resistance to interventions. The results of this research will be transferred to regulatory agencies (USDA Food Safety Inspection Service (FSIS), US Food and Drug Administration (FDA)) to develop genomic-based risk assessments. In addition, results will be transferred to women�s health groups, commercial entities, and the meat and poultry industry. This approach may be ultimately expanded to include other thermal and nonthermal intervention technologies and extraintestinal foodborne pathogens. Approach (from AD-416): Extraintestinal Escherichia coli (ExPEC) are common contaminants in food which includes fresh produce, fish, meat and poultry. Illness occurs after contaminated food is consumed, the ExPEC colonize the gastrointestinal tract, and are then accidentally transferred to the urethra. They then cause urinary tract infections (UTI), sepsis, and meningitis. Approximately 6-8 million cases of UTI and 23,000 deaths annually are attributed to ExPEC. ExPEC and other extraintestinal foodborne pathogens which are found in meat and poultry have been directly traced to illness in humans. In addition, these emerging foodborne pathogens are resistant to multiple antibiotics and are considered a national research priority as noted in the President�s Council of Advisors on Science and Technology (PCAST, 2014). As specifically noted by regulatory agencies this project addresses �an area of growing concern to FSIS and the public health community� which will help: 1) improve the ability to develop safe processing procedures and to evaluate the impact of processing deviations on pathogen growth in the impacted products; 2) provide insights into mechanisms that contribute to the survival of pathogens to commonly used microbial intervention and mechanisms that affect the severity of illness in humans, and antibiotic resistance in outbreak strains; and 3) provide a scientific foundation for the development of new Agency food safety policies. The Centers for Disease Control and Prevention (CDC) recommends the use of foods treated with appropriate intervention technologies to lessen the risk of foodborne illness for �at risk� individuals. There is little if any information about growth or inactivation kinetics of the ExPEC in food using both thermal and nonthermal food safety intervention technologies or how pathogen genotype affects their resistance to intervention technologies, hence we will generate such data to fill the informational void regarding these emerging pathogens as part of this unique food safety project. This new Project Plan was recently certified through the ARS Office of Scientific Quality Review (OSQR). For further details on current work see the 2016 annual report for project 8072-42000-073-00D.
Impacts
(N/A)
Publications
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