Browsing by Author "Belk, Keith, committee member"
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Item Embargo A comprehensive study of Salmonella infections and microbial analysis of probiotics on beef cattle(Colorado State University. Libraries, 2023) Thompson, Tyler Warren, author; Nair, Mahesh Narayanan, advisor; Geornaras, Ifigenia, committee member; Belk, Keith, committee member; Noyes, Noelle, committee member; Morley, Paul, committee memberNon-typhoidal Salmonella remains a significant concern for food safety in the United States, causing millions of infections, hospitalizations, and deaths yearly. The Healthy People 2030 initiative set forth by the U.S. Department of Health and Human Services aims to address this issue by establishing goals and objectives for national health promotion and disease prevention, including two objectives focused on Salmonella control in the food supply. The recent declaration of Salmonella as an adulterant in certain poultry products by the U.S. Department of Agriculture further highlights the urgency of this issue. To align with the Healthy People 2030 goals and achieve a 25% reduction in salmonellosis, the U.S. Department of Agriculture's Food Safety and Inspection Service (FSIS) implemented new performance standards for beef products. However, such policies must be supported by quantitative microbial risk assessments (QMRA) to determine their impact on Salmonella infections. Therefore, these analyses would benefit from a systematic review examining existing literature on Salmonella, considering factors such as illness rates, exposure, and bacterial loads. This review included 42 articles that provided data necessary for fitting a dose-response model to empirical data that describes how dose, virulence group, and food vector affect illness (attack) rates. Results from the mixed-effects logistic regression model showed significant impacts of log dose consumed, virulence group, and food vector on illness rates. Notably, Salmonella serogroups of "Higher" virulence were found to be associated with greater odds of illness than "Lower" virulence strains. The study highlights the need for improved data reporting and standardized outbreak investigations to enhance the fitting of models to outbreak data. By considering factors like serovar group and food vector in the modeling process, regulators can demonstrate what influences attack rate to frame more effective food safety policies. In conclusion, this systematic review provides valuable insights into Salmonella infection risk from food sources and emphasizes the importance of evidence-based policies to reduce the burden of Salmonella-related illnesses and improve food safety in the United States. Liver abscesses in beef cattle are a common problem associated with highly-fermentable carbohydrate diets during finishing, leading to decreased production efficiency and aggregate carcass value. Dietary antimicrobial supplementation, such as tylosin, helps to control liver abscesses but raises concerns about selection for antimicrobial resistance. This study examined the impact of a probiotic mixture of propionic and lactic acid bacteria on microbial communities and antimicrobial resistance genes (ARGs) in fecal and liver abscess samples from beef cattle alongside Salmonella populations of mesenteric lymphatic tissues. Treatment diets fed in this study included a probiotic mixture alone (DFM), inclusion of Tylosin (TYL), a combination of including both (DFM+TYL), and a control group diet that did not include any supplements (CON). Fecal samples were collected at the time that feeding started, and then 28 d before arriving at the abattoir, where liver abscesses and mesenteric lymph nodes were sampled. Fecal and liver abscess samples were subjected to 16S rRNA and targeted enriched shotgun metagenomics to evaluate microbial communities and resistance genes of bacteria present. A portion of the liver abscess and mesenteric lymph nodes were tested for presence of Salmonella using PCR with further analysis of enumeration and serotype classification for mesenteric lymph nodes. Results showed no differences (P > 0.05) between the fecal microbiomes of the different treatment groups, and the addition of tylosin or probiotic mixture did not impact the fecal resistome. Similarly, no differences (P > 0.05) were observed between the liver abscess microbiomes of the different (P > 0.05) treatment groups, with Fusobacteria and Bacteroidetes being the dominant phyla in liver abscesses. Results indicated that incorporating DFMs did not affect Salmonella prevalence in the cattle's mesenteric lymph nodes or liver abscesses. Presence of Salmonella was found at low levels in only 22% of samples (91 positive out of 503 samples), just below 1 log CFU/g, and was predominantly represented by the C1 serogroup in mesenteric lymph nodes. These findings suggest that while diet interventions may not have a substantial impact, Salmonella can colonize mesenteric lymphatic tissues in cattle at low frequencies and concentrations. Treatment groups tested had no impact (P > 0.05) on fecal and liver abscesses microbiomes and resistance gene presence, along with no impact on Salmonella prevalence in liver abscesses or mesenteric lymphatic tissues.Item Open Access Assessment of rapid evaporative ionization mass spectrometry (REIMS) to characterize beef quality and the impact of oven temperature and relative humidity on beef(Colorado State University. Libraries, 2018) Gredell, Devin, author; Woerner, Dale, advisor; Belk, Keith, committee member; Engle, Terry, committee member; Prenni, Jessica, committee member; Heuberger, Adam, committee memberThe objective of experiment 1 was to evaluate the ability of rapid evaporative ionization mass spectrometry (REIMS) to predict beef eating quality characteristics. Striploin sections (5 cm in thickness; N = 292) from 7 beef carcass types (Select, Low Choice, Top Choice, Prime, Dark Cutter, Grass-fed, and Wagyu) were collected to achieve variation in fat content, sensory attributes, tenderness, and production background. Sections were aged for 14 d, fabricated into 2.54 cm thick steaks, and frozen until analysis. Trained descriptive panel rated tenderness, flavor, and juiciness attributes for sensory prediction models. Slice shear force (SSF) and Warner-Bratzler shear force (WBS) values were measured to predict tenderness classifications. A molecular fingerprint of each sample was collected via REIMS to build prediction models. Models were built using 80% of samples that were selected randomly for this purpose and tested for prediction accuracy using the remaining 20%. Partial least squares (PLS) discriminant analysis was used as a dimension reduction technique before building a linear discriminant analysis (LDA) model for classification. When Select and Low Choice samples, as well as Top Choice and Prime samples, were combined, balanced prediction accuracy reached 83.8%. Slice shear force and WBS tenderness classifications (tough vs tender) were predicted with 75.0% and 70.2% accuracy, respectively. Sensory models were built to assign samples into positive and negative classifications based on either all sensory attributes (i.e., tenderness, juiciness, and flavor) or only flavor attributes. Overall sensory class was predicted with 75.4% accuracy and flavor class with 70.3%. With future fine-tuning, these data suggest that REIMS produces a metabolic fingerprint to provide a method to meaningfully predict numerous beef quality attributes in an on-line application. The objective of the second study was to evaluate the roles of cooking rate and relative humidity on sensory development of beef strip steaks. Thirty USDA Choice beef strip loins were collected from a commercial packing facility. Each strip loin was cut into steaks and randomly assigned to 1 of 6 cooking methods utilizing 2 oven temperatures (80°C and 204°C) and 3 levels of relative humidity [zero (ZH), mid (MH), and high (HH)]. Cooked steaks were used to evaluate internal and external color, Warner-Bratzler and slice shear force, total collagen content, protein denaturation, and trained sensory ratings. Relative humidity greatly reduced cooking rate, especially at 80°C. Steaks cooked at 80°C-ZH had the greatest (P < 0.01) cook loss of all treatments, and cook loss was not affected (P > 0.05). Steaks cooked at 80C-ZH appeared the most (P < 0.01) well-done and had the darkest (P > 0.01) surface color. Total collagen was greatest (P < 0.01) in steaks cooked with ZH, regardless of oven temperature. Myosin denaturation was not affected (P > 0.05) by treatment. Increased (P = 0.02) sarcoplasmic protein denaturation was observed with ZH and MH, while increased (P = 0.02) actin denaturation was observed only with ZH. Oven temperature did not influence (P > 0.05) protein denaturation. Trained panelists rated steaks most tender (P < 0.01) when cooked at 80°C and with ZH and MH. Humidity did not affect (P > 0.05) juiciness at 204°C; however, MH and HH produced a juicier (P < 0.01) steak when cooked at 80°C. Humidity hindered (P < 0.01) the development of beefy/brothy and brown/grilled flavors but increased (P = 0.01) metallic/bloody intensity. Lower oven temperatures and moderate levels of humidity could be utilized to maximize tenderness, while minimally affecting flavor development.Item Open Access Capabilities of rapid evaporative ionization mass spectrometry to predict lamb flavor and overview of feeding genetically modified grain to livestock(Colorado State University. Libraries, 2019) Gifford, Cody Lynn, author; Woerner, Dale, advisor; Belk, Keith, committee member; Engle, Terry, committee member; Prenni, Jessica, committee member; Heuberger, Adam, committee memberThe objective of experiment 1 was to evaluate the ability of rapid evaporative ionization mass spectrometry (REIMS) to predict characteristics of cooked sheep meat flavor using metabolomic data from raw samples. Boneless leg samples were obtained from 150 carcasses of sheep representing three age classifications (n=50 per age classification), at three USDA inspected harvest facilities located in Colorado and California, between October 2017 to June 2018. A trained descriptive panel rated seven flavor attributes. Metabolomic data from fat, lean and ground patties from legs of sheep carcasses were captured through the REIMS platform. Principal component analysis factor scores were used in hierarchical cluster analysis to assess two-level and three-level sensory clusters. Partial least squares (PLS) was used to reduce dimensionality of data before the linear discriminant analysis (LDA) model was built. Eighty percent of the samples were randomly selected to train models and the remaining 20% were used to test prediction accuracy. Mutton carcasses were identified with 88.9% sensitivity and 80.0% precision using external fat of the leg and with 100% sensitivity and 90.9% precision using ground patties. Yearling carcasses were identified with 85.7% precision using lean and lambs were predicted with 70% precision using lean and fat tissue. Greater than 80% accuracy (overall and balanced), sensitivity and precision was achieved in models using lean and ground patties to identify production background (whether the live animal that produced the lean or ground patties was grain-finished or grass-finished). Prediction accuracies of age classification, production background and two-level flavor performance categories were 68% or higher with various machine learning algorithms coupled with data dimension reduction approaches. Further work is warranted to validate use of this technology in an on-line production setting and additional datasets could be used to further refine or create additional prediction models with better understanding of data processing characteristics. The review was conducted to assess the scientific literature for evidence of altered health effects in livestock species that have been fed genetically modified grain and any health effects discussed in reference to human consumption of meat products from those animals. Public concern still exists for feeding genetically modified (GM) or genetically engineered (GE) corn to animals that produce animal protein foods. In the U.S., 90% of all corn acres planted in 2013 were from single herbicide or insect resistance GE corn varieties. Regulation of GE crops is mandatory in the U.S. and consists of review and approval by three different Federal agencies. Substantial equivalence is a principle used in evaluating the safety of GE crops to establish that transgenic (GE or GM) varieties are nutritionally similar and as safe as non-transgenic crops. Animal feeding trials can provide further information to establish the safety of GE crops for human and animal consumption. No publications were found that had reported human metabolic effects from consuming beef cattle fed genetically modified grains. No consistent conclusions have been made that feeding GE corn to mice or rats, beef or dairy cattle, swine, or poultry causes any adverse effects to health. Parameters regarding sample size, diet treatments and specified controls exist to guide researchers in designing animal feeding trials with GE crops, but many criticisms of the scientific literature still exist. Additionally, published feeding trials conducted with transgenic corn grain and silage in beef cattle are limited.Item Open Access Carcass bruising location and bruise trim loss in finished steers, cows, and bulls at five commercial slaughter facilities(Colorado State University. Libraries, 2018) Kline, Helen Carter, author; Grandin, Temple, advisor; Edwards-Callaway, Lily, advisor; Belk, Keith, committee member; Engle, Terry, committee member; Rollin, Bernard, committee memberDetermining the location of, and investigating possible causes of, bruising in beef carcasses is critical for addressing animal well-being concerns in the livestock industry—as well as understanding losses in value that are a consequence of carcass defects. This study was conducted in five commercial slaughter facilities, located in multiple regions of the U.S., that slaughter fed steers/heifers, cows and bulls. At each plant, animals from thirty trailers, at least one animal from each utilized compartment. In total, approximately 50 animals were marked each night, providing 150 marked animals over the three days of sampling at each facility. Individual carcasses were followed through the slaughtering process and were evaluated before carcass splitting for: presence/absence and location of bruising, and the weight of bruised meat that was removed from carcasses during trimming. This study found that 28.1% of carcasses observed were visibly bruised. Regions of the carcass that had the highest bruise incidence were the round, rib, and loin beef cuts, respectively. However, some carcasses had deep tissue bruises that were not visible on the surface of the carcass, but trim loss was collected once these bruises were exposed and averaged 1.0 kg per carcass. Cattle in the top deck compartment were less likely to be bruised when compared to cattle in the belly compartment (P = 0.03). Reduction of bruising enhances animal well-being and reduction in trim loss adds economic efficiency along the entire beef supply chain.Item Open Access Control of Escherichia coli O157:H7 and Listeria monocytogenes in meat and poultry products with chemicals and heating treatments(Colorado State University. Libraries, 2010) Shen, Cangliang, author; Sofos, John, advisor; Kendall, Patricia, committee member; Belk, Keith, committee member; Scanga, John A., committee memberObjectives of studies included in this dissertation were to evaluate the effects of chemical antimicrobials, such as cetylpyridinium chloride, lactic acid, hops beta acids, commercial salad dressings, and heat treatments including cooking with various appliances and microwave oven heating to control Escherichia coli 0157:H7 in moisture enhanced noninact beef and Listeria monocytogenes on ready-to-eat (RTE) meat and poultry products. In the first study, the effect of different cooking appliances on thermal inactivation of E. coli 0157:H7 in nonintact beef steaks of different thickness was evaluated. In general, the thicker the steaks, the higher the reduction levels reached, and roasting in a standard kitchen oven showed the best inactivation effect compared to the other cooking appliances. The second study evaluated thermal inactivation of E. coli 0157:H7 in nonintact beef steaks with pan-broiling or roasting appliances set at different temperatures. Results showed that setting the cooking appliances at higher temperatures resulted in higher reduction levels of E. coli 0157:H7 cells in nonintact beef steaks compared to the lower ones. The third study involved comparison of inactivation of different types of stress-adapted or unstressed E. coli 0157:H7 cells, inoculated in moisture enhanced nonintact beef steaks with various brining solutions and cooked by pan-broiling on an electric skillet. It was evident that acid stress-adapted cells were more resistant to heat treatment, while cold or desiccation stress-adapted cells were more Hi sensitive to heat treatment than controls. The lowest pathogen counts survived during cooking of beef steaks moisture enhanced to include cetylpyridinium chloride or lactic acid for all stressed inocula tested, thus, indicating that cetylpyridinium chloride and lactic acid could be considered as potential antimicrobial agents for use in beef brining solutions. An additional study evaluated the antilisterial activity of hops beta acids (HBA) in broth medium. HBA exhibited promising antilisterial activity in culture broth, and its activity was increased with increasing concentrations (0.5 to 5.0 pg/ml), and when combined with potassium lactate (1%), sodium diacetate (0.25%), or acetic acid (0.1%), at 4°C. In a subsequent study, HBA applied as dipping solutions (0.03 to 0.10%) on frankfurters, inoculated with L. monosytogenes, vacuum packaged and stored at 4 or 10°C, inhibited pathogen growth for 30 to 50 (4°C) or 20 to 28 days (10°C). The last two studies were designed to detect the antilisterial effects of commercial salad dressings, oil with vinegar or lemon juice, on artificially inoculated frankfurters, diced ham and turkey breast during simulated home storage, without or with prior microwave heating for 30 s or 45 s. Results indicated that microwave heating followed by immersing in salad dressings, especially oil with vinegar, could potentially contribute to control of L monocytogenes on RTE meat and poultry products in the home environment. The results of all studies in this dissertation indicated that certain chemical antimicrobials and heating treatments could be effectively to control E. coli 0157:H7 and L. monocytogenes in meat and poultry products.Item Open Access Effects of potential Tylosin substitutes on Salmonella prevalence and the microbiome of subiliac lymph nodes of beef feedlot cattle(Colorado State University. Libraries, 2017) Holzer, Katlyn, author; Martin, Jennifer, advisor; Belk, Keith, committee member; Metcalf, Jessica, committee member; Schountz, Tony, committee memberTylosin, a macrolide antibiotic, is fed to feedlot cattle for liver abscess prevention. Tylosin alternatives are currently being investigated as pressures to reduce the amount of antibiotics used in livestock increase. Understanding effects of various feeding strategies on the safety of beef products is a priority as alternatives are investigated. This study investigated the effect of Tylosin, and two Tylosin alternatives on the prevalence of Salmonella in subiliac lymph nodes (SLN) and the microbiome of SLN from feedlot cattle. Salmonella harborage in the lymph node is a challenge for the beef industry as ground beef is made from beef trimmings that commonly contain lymph nodes. Consumption of contaminated ground beef is one of the possible foodborne routes of Salmonella infection. SLN (n=600) were collected from feedlot cattle (n = 5,481) at the time of slaughter. Overall 84.6% of the SLN were positive for Salmonella and the treatment did not influence prevalence (P > 0.8402). Samples from each pen of feedlot cattle (15 SLN/pen) were composited for microbiome analysis using 16s rRNA amplicon sequencing. Samples were analyzed using the open-source software Quantitative Insights Into Microbial Ecology (QIIME). The treatment did not influence the microbiome of the SLN (P = 0.223; P= 0.267). The top three phyla present were Proteobacteria (67.3%), Actinobacteria (10.2%), and Acidobacteria (9.5%). Although Salmonella was culturally isolated, it was not identified in the microbiome analysis because the genus could not be resolved for 18.9% of the Enterobacteriaceae family. Understanding why Salmonella is detectable in the lymph nodes may hold the key for prevention, and characterizing the microbiome is crucial for this process.Item Open Access Exploration of novel antimicrobials and comparative genomic analysis for the control of foodborne pathogens(Colorado State University. Libraries, 2020) Jia, Mo, author; Yang, Hua, advisor; Belk, Keith, committee member; Martin, Jennifer, committee member; Abdo, Zaid, committee memberTo view the abstract, please see the full text of the document.Item Open Access Management strategies to improve beef feedlot performance and assessment of nutrient composition of beef retail cuts(Colorado State University. Libraries, 2011) Schutz, Jennifer Sue, author; Engle, Terry, advisor; Belk, Keith, committee member; Archibeque, Shawn, committee member; Van Campen, Hana, committee memberTo view the abstract, please see the full text of the document.Item Open Access Survival and inactivation of Listeria monocytogenes, shiga toxin-producing Escherichia coli, and multidrug-resistant and susceptible Salmonella serovars exposed to heat and antimicrobials on food contact and food surfaces(Colorado State University. Libraries, 2013) Fouladkhah, Aliyar, author; Sofos, John, advisor; Nightingale, Kendra, advisor; Kendall, Patricia, committee member; Belk, Keith, committee memberTo view the abstract, please see the full text of the document.Item Open Access The effect of tylosin exposure or exclusion on liver abscess prevalence, fecal pathogen populations, and the microflora of finished beef products from feedlot cattle(Colorado State University. Libraries, 2018) Weissend, Carla Jane, author; Martin, Jennifer, advisor; Belk, Keith, committee member; Bryant, Tony, committee member; Metcalf, Jessica, committee member; Weir, Tiffany, committee memberThere is great pressure to reduce use of, and find alternatives to, antibiotics in animal production. More than 70% of feedlot cattle in 1000+ head lots are currently exposed to tylosin phosphate, a macrolide antibiotic used for the reduction and prevention of liver abscesses. As such, its potential removal from cattle feeding strategies could have a marked impact on both the economics of the beef industry and food safety. Additionally, little is known about the effect of tylosin exposure or exclusion on the microbiome of finished beef products. In light of these facts, a blinded, randomized, controlled field trial was conducted to evaluate the impact on the prevalence of liver abscesses and the characterization of the microbiome of feces, liver abscesses, carcasses, and finished beef products through 16S rRNA gene sequencing and shotgun sequencing from feedlot cattle with and without exposure to tylosin. Overall, liver abscess rates were lower among cattle exposed to tylosin. However, there were no differences among treatment groups for any of the sample types, suggesting that removal of tylosin from current feeding strategies will not upend the safety of the beef supply. The information gained in this study will provide valuable insight as the search for alternative feeding strategies to antibiotics continues.Item Open Access The effects of a Saccharomyces cerevisiae fermentation product on liver abscess prevalence, microbiomes, and resistomes of cattle raised to produce natural-branded beef(Colorado State University. Libraries, 2018) Huebner, Katherine Louise, author; Morley, Paul, advisor; Belk, Keith, committee member; Metcalf, Jessica L., committee member; Sischo, William M., committee memberUse of antibiotics in livestock production has received increased scrutiny due to public health concerns over the development and dissemination antimicrobial resistance. As a result, there are efforts to replace the use of medically important antimicrobial drugs in food producing animals with novel non-antimicrobial alternatives to treat disease. One target for antimicrobial drug reduction and replacement within the beef cattle industry is the use of tylosin, a macrolide antibiotic, which is widely included within diets of feedlot cattle to reduce incidence of liver abscesses. Tylosin is considered medically important for human health, and therefore tylosin use in feedlot operations may be limited in the future. Liver abscesses are a leading cause of liver condemnation at slaughter, and result in significant financial losses to the beef cattle industry. Exposure of cattle to high concentrate diets is associated with rumen acidosis and rumenitis, leading to the formation of liver abscesses. Several non-antimicrobial strategies for the treatment of liver abscesses have been evaluated, including nutritional management, vaccines, other antimicrobial drugs, and feed additive products, although none have been shown to reduce liver abscesses as effectively as treatment with tylosin. The studies in this thesis evaluated effects of a Saccharomyces cerevisiae fermentation product (SCFP) on cattle performance, health, and microbiology outcomes. Yeast products have been shown to benefit rumen fermentation and improve cattle performance; and therefore, SCFP were hypothesized to reduce the occurrence of liver abscesses when included in diets of beef cattle raised without antibiotics. The first chapter of this thesis reviews current information about liver abscess pathogenesis, microbiology, and the use and efficacy of antimicrobial and non-antimicrobial interventions. There is a significant impact of diet, treatment, and other management factors on rumen microbial ecology, including shifts in microbiomes attached to the rumen epithelium, rumen acidosis, and microbiology of liver abscesses. The second chapter focuses on a randomized block clinical trial conducted to evaluate the effects of SCFP on animal health, growth and production, liver abscess prevalence, fecal microbiomes, and fecal resistomes in cattle raised without antibiotics using 16S rRNA gene sequencing and shotgun metagenomic sequencing. In a randomized block clinical trial, there were no statistically significant, detectable differences of SCFP supplementation on any of the tested outcomes. The third chapter characterized the liver abscess microbial community from liver abscess contents using 16S rRNA marker gene sequencing. The liver abscess microbiome was diverse and polymicrobial, and shifts in liver abscess microbiomes across cattle enrollment group demonstrates that there is a potential impact of cattle source, feedlot environment, and other factors on liver abscess microbiomes. Given the diversity of the liver abscess microbiome demonstrated in this study, more work is needed to understand the role of liver abscess microbiomes for disease severity as pre-harvest feeding strategies are investigated further in feedlot cattle.