Doctor of Philosophy / Department of Animal Sciences and Industry / J. S. Drouillard / The first chapter of this dissertation reviews factors affecting E. coli O157:H7 prevalence in the gastrointestinal tracts of cattle. Chapter 2 assessed E. coli O157:H7 ability to use bovine intestinal mucus and its constituents as substrates for growth in vitro in the presence and absence of fecal inoculum and exogenous enzymes. Whole mucus supported the greatest pathogen growth (P < 0.05), but all components tested were able to sustain E. coli growth. Chapter 3 evaluated the impact of crude glycerin feeding on E. coli O157 fecal shedding by cattle fed growing and finishing feedlot diets with corn or a combination of corn, distiller’s grains, and soybean hulls. Increasing levels of crude glycerin decreased incidence of E. coli O157 in growing cattle (linear effect, P < 0.01) and tended to do so in finishing cattle fed corn-based diets (P < 0.06). No effect of glycerin was observed in finishing cattle fed the byproduct-based diets (P > 0.05), highlighting potential for glycerin use as a means for controlling fecal prevalence of E. coli O157 in cattle fed conventional grain-based diets. Chapter 4 evaluated transportation and lairage effects on fecal shedding of E. coli in feedlot cattle by mimicking transport to the abattoir. Shedding patterns were influenced by transportation, with significantly lower E. coli O157 prevalence in transported animals 4 hours after transit (P < 0.05). Additional post-transit samplings are, however, needed to confirm effects of transport stress on pathogen prevalence and shedding patterns. The experiment summarized in chapter 5 evaluated the potential for utilizing fecal long-chain fatty acid (LCFA) profiles as an indicator of E. coli O157 status. Out of 39 LCFA evaluated, only eicosapentaenoic acid (EPA) concentration was associated with presence of the pathogen (P < 0.02). The final chapter assessed the impact of dietary menthol, up to 0.3% of diet DM, on antimicrobial resistance in commensal E. coli. Menthol addition affected prevalence of tetracycline resistant E. coli, but contrary to our hypothesis, increased their occurrence after 30 days of treatment (P < 0.006). No hypothesis on mechanism responsible for this increase could be made from the present study.

Doctor of Philosophy / Department of Animal Sciences and Industry / James S. Drouillard / Four studies evaluated effects of mineral supplementation on feedlot performance, carcass characteristics and ruminal fermentation of finishing cattle. Study 1 supplemented 0 or 3.3 g/d yeast combined with Cr propionate to steers separated into light and heavy groups. No treatment x weight group interactions were observed for ADG, DMI, final BW, carcass traits, or plasma glucose of lactate concentrations (P ≥ 0.06). A treatment x weight group interaction was observed for G:F (P = 0.03). In study 2, steers were supplemented 60 or 300 mg Zn/kg DM with or without zilpaterol hydrochloride (ZH). No interactions or effects of Zn or ZH were observed for IGF-1, plasma glucose, or lactate concentrations (P > 0.05). Plasma urea nitrogen (PUN) concentration decreased with ZH (P < 0.01). No interactions or effects of Zn or ZH were detected for ADG, DMI, final BW, G:F, and carcass traits were minimally affected (P ≥ 0.05). Study 3 evaluated effects of supplementing 30 or 100 mg Zn/kg DM (30 or 100Zn) with and without ractopamine hydrochloride (RH; 200 mg/d). No interactions or effects of Zn were observed for feedlot performance or PUN (P ≥ 0.07). Final BW, ADG, and HCW increased when heifers were fed RH (P ≤ 0.02). Zinc x RH interactions were observed for LM area and yield grade (P ≤ 0.01), but other carcass traits were not affected (P ≥ 0.08). In study 4, heifers were supplemented 0, 30, 60, or 90 mg Zn/kg DM. Zinc supplementation did not affect final BW, ADG, or DMI (P ≥ 0.07), but G:F increased linearly (P = 0.02). Carcass traits were not affected by Zn supplementation (P ≥ 0.07). Effects of in vitro Zn titration (0, 30, 60, 60, 90, 120, or 150 mg/kg Zn) were evaluated using ground corn and soybean meal as substrate. In vitro fermentation was not affected by added Zn (P ≥ 0.05). These studies suggest Cr and Zn supplementation minimally affected carcass traits, but Zn supplementation up to 60 mg/kg improved feed efficiency with minimal impact on ruminal fermentation. Supplementing increased Zn concentrations may alter fat and muscle deposition when fed with RH.

Prevalence of antimicrobial resistance in fecal Escherichia coli isolates from feedlot cattle was characterized. Tetracycline resistance in isolates from newly weaned, auction market derived calves on arrival at the feedlot in a clinical trial was 9.8% and resistance to three or more antimicrobials was 2.1% compared to 17.6 % and 5.9% in a cohort study. The prevalence of tetracycline resistance at 78.3% and resistance to three or more antimicrobials at 52.5 % in isolates from spring calves submitted to a regional diagnostic laboratory were higher than those found on arrival at the feedlot. Of isolates from composite feedyard pen samples late in the feeding period, 39.4% were tetracycline resistant and 7.6% were resistant to three or more antimicrobials, somewhat higher than on arrival. Use of oxytetracycline in the feed for disease prophylaxis and the metaphylactic use of long-acting injectable oxytetracycline were associated with increased proportions of cattle with one or more resistant E. coli isolates early in the feeding period, while the use of individual animal treatments was not. The proportion of animals with one or more tetracycline resistant E. coli isolates was not different between the control, metaphylactic treatment and prophylactic treatment groups preslaughter; however, there were significantly more resistant animals in all groups preslaughter than at arrival. There were also no associations found between the total volume of parenteral antimicrobials used for disease treatment in individual animals and antimicrobial resistance in the cohort study. In addition, no strong associations were found between pen-level prevalence of antimicrobial resistance antimicrobial use or other variables. There was no significant difference between the proportion of isolates per pen resistant to tetracycline, one or more, two or more antimicrobials, or three or more antimicrobials when using 20, 15, 10 or 5 isolates from composite pen-level fecal samples. Variance for isolates resistant to three or more antimicrobials was partitioned as 12.7% at the feedyard-level and 28.7% at the pen-level. The use of diagnostic laboratory data for AMR surveillance was also discussed, and alternatives to antimicrobial treatment in the feedlot were also investigated. Overall a significant contribution to our understanding of antimicrobial resistance in feedlot cattle was achieved.

Two trials were conducted to evaluate the effects of titrated levels of wheat-based dried distillers grains on feedlot performance, carcass characteristics and rumen fermentation parameters of cattle fed wheat-based dried distillers grains with solubles (DDGS). In trial 1, a barley grain-based diet (0% DDGS) was used as a control. It was formulated to 12% CP and 1.52 and 0.93 Mcal kg-1 net energy of maintenance (NEm ) and net energy of gain( NEg) respectively, during the backgrounding period and to 13% crude protein (CP) and 1.90 and 1.26 Mcal kg-1 NEm and NEg respectively, during finishing. Wheat-based DDGS replaced on a dry matter basis (DM) barley grain at levels of 8, 16, 24 and 32% during backgrounding and 6, 12, 18 and 23% during finishing. During backgrounding dry matter intake (P = 0.02), ADG (P = 0.04), and ultrasounded (US) longissimus. dorsi gain (P = 0.02) exhibited a cubic response to DDGS inclusion level with theoretical minima at 6.9, 8.1 and 6.9% DDGS respectively, and theoretical maxima responses at 27.2, 30.8 and 23.9% DDGS, respectively. Feed efficiency exhibited a quadratic response (P = 0.02) to DDGS inclusion level with a theoretical poorest response at 13.1% DDGS. Similar responses were noted during the first 56 d of the finishing period, however over the course of the finishing period no effect of DDGS inclusion level was noted on average daily gain (ADG), DMI, feed efficiency (FE), ultrasound measurements or on any carcass traits. <p>Trial 2 examined the effects of graded levels of wheat-based DDGS (0, 7, 14, 21% DM basis) on rumen fermentation characteristics using rumen cannulated heifers. Rumen pH measurements indicated that the pH mean at or below 5.8 and 5.5 decreased as DDGS inclusion level increased to 14% DM. The highest values (P<0.05) for pH area between the benchmarks of 5.5 and 5.2, pH area below 5.2 and time below pH 5.2 were found at the 14% DDGS inclusion level, pointing to rumen fermentation characteristics associated with severe rumen acidosis. Ammonia nitrogen levels, percent acetate, percent butyrate and the acetate: propionate ratio increased linearly (P < 0.0001) with DDGS. Propionate concentration decreased linearly (P = 0.006) as the level of DDGS increased. In situ rumen degradation kinetics showed that the DM and CP soluble fraction of DDGS to be significantly higher than that of rolled barley, however effective degradability of dry matter (EDDM) and effective degradability of crude protein (EDCP) were greater for barley. The results of this trial indicate that wheat-based DDGS has an energy value at least equal to that of barley grain with no adverse effects on cattle performance or carcass quality. Furthermore, since all treatments showed equal susceptibility to sub-acute ruminal acidosis (SARA) and therefore, wheat-based DDGS as a dietary ingredient is unable to mitigate rumen fermentation conditions associated with SARA.

Prevalence of antimicrobial resistance in fecal Escherichia coli isolates from feedlot cattle was characterized. Tetracycline resistance in isolates from newly weaned, auction market derived calves on arrival at the feedlot in a clinical trial was 9.8% and resistance to three or more antimicrobials was 2.1% compared to 17.6 % and 5.9% in a cohort study. The prevalence of tetracycline resistance at 78.3% and resistance to three or more antimicrobials at 52.5 % in isolates from spring calves submitted to a regional diagnostic laboratory were higher than those found on arrival at the feedlot. Of isolates from composite feedyard pen samples late in the feeding period, 39.4% were tetracycline resistant and 7.6% were resistant to three or more antimicrobials, somewhat higher than on arrival. Use of oxytetracycline in the feed for disease prophylaxis and the metaphylactic use of long-acting injectable oxytetracycline were associated with increased proportions of cattle with one or more resistant E. coli isolates early in the feeding period, while the use of individual animal treatments was not. The proportion of animals with one or more tetracycline resistant E. coli isolates was not different between the control, metaphylactic treatment and prophylactic treatment groups preslaughter; however, there were significantly more resistant animals in all groups preslaughter than at arrival. There were also no associations found between the total volume of parenteral antimicrobials used for disease treatment in individual animals and antimicrobial resistance in the cohort study. In addition, no strong associations were found between pen-level prevalence of antimicrobial resistance antimicrobial use or other variables. There was no significant difference between the proportion of isolates per pen resistant to tetracycline, one or more, two or more antimicrobials, or three or more antimicrobials when using 20, 15, 10 or 5 isolates from composite pen-level fecal samples. Variance for isolates resistant to three or more antimicrobials was partitioned as 12.7% at the feedyard-level and 28.7% at the pen-level. The use of diagnostic laboratory data for AMR surveillance was also discussed, and alternatives to antimicrobial treatment in the feedlot were also investigated. Overall a significant contribution to our understanding of antimicrobial resistance in feedlot cattle was achieved.

Two trials were conducted to evaluate the effects of titrated levels of wheat-based dried distillers grains on feedlot performance, carcass characteristics and rumen fermentation parameters of cattle fed wheat-based dried distillers grains with solubles (DDGS). In trial 1, a barley grain-based diet (0% DDGS) was used as a control. It was formulated to 12% CP and 1.52 and 0.93 Mcal kg-1 net energy of maintenance (NEm ) and net energy of gain( NEg) respectively, during the backgrounding period and to 13% crude protein (CP) and 1.90 and 1.26 Mcal kg-1 NEm and NEg respectively, during finishing. Wheat-based DDGS replaced on a dry matter basis (DM) barley grain at levels of 8, 16, 24 and 32% during backgrounding and 6, 12, 18 and 23% during finishing. During backgrounding dry matter intake (P = 0.02), ADG (P = 0.04), and ultrasounded (US) longissimus. dorsi gain (P = 0.02) exhibited a cubic response to DDGS inclusion level with theoretical minima at 6.9, 8.1 and 6.9% DDGS respectively, and theoretical maxima responses at 27.2, 30.8 and 23.9% DDGS, respectively. Feed efficiency exhibited a quadratic response (P = 0.02) to DDGS inclusion level with a theoretical poorest response at 13.1% DDGS. Similar responses were noted during the first 56 d of the finishing period, however over the course of the finishing period no effect of DDGS inclusion level was noted on average daily gain (ADG), DMI, feed efficiency (FE), ultrasound measurements or on any carcass traits. <p>Trial 2 examined the effects of graded levels of wheat-based DDGS (0, 7, 14, 21% DM basis) on rumen fermentation characteristics using rumen cannulated heifers. Rumen pH measurements indicated that the pH mean at or below 5.8 and 5.5 decreased as DDGS inclusion level increased to 14% DM. The highest values (P<0.05) for pH area between the benchmarks of 5.5 and 5.2, pH area below 5.2 and time below pH 5.2 were found at the 14% DDGS inclusion level, pointing to rumen fermentation characteristics associated with severe rumen acidosis. Ammonia nitrogen levels, percent acetate, percent butyrate and the acetate: propionate ratio increased linearly (P < 0.0001) with DDGS. Propionate concentration decreased linearly (P = 0.006) as the level of DDGS increased. In situ rumen degradation kinetics showed that the DM and CP soluble fraction of DDGS to be significantly higher than that of rolled barley, however effective degradability of dry matter (EDDM) and effective degradability of crude protein (EDCP) were greater for barley. The results of this trial indicate that wheat-based DDGS has an energy value at least equal to that of barley grain with no adverse effects on cattle performance or carcass quality. Furthermore, since all treatments showed equal susceptibility to sub-acute ruminal acidosis (SARA) and therefore, wheat-based DDGS as a dietary ingredient is unable to mitigate rumen fermentation conditions associated with SARA.

This thesis demonstrates that optimal hedge ratios using futures contracts for Ontario and Alberta feedlot operators were low for live cattle and feeder cattle, and shows that the risk reduction from using US based live and feeder cattle futures was lower than 30% in most cases. Abstracting from the mean variance theoretical framework, constant optimal hedge ratios were estimated using OLS and SUR models. Time-varying optimal hedge ratios were estimated by GARCH models and the rolling window technique. Hedging effectiveness was measured by the variance reduction of hedged portfolios compared with a no-hedging position. Results suggested that hedging in the CME futures market reduced corn price variation by more than 50%. However, the optimal hedge ratios for cattle and barley in general were found to be low. Results also indicated that time-varying hedge ratios eliminated more risk than constant hedge ratios at the cost of frequently adjusting hedging positions. Higher optimal hedge ratios were obtained in the pre-BSE period than in the post-BSE period in both the commodity market and the currency market for joint hedging live cattle and the exchange rate. Both time-varying hedging and joint hedging strategies may generate additional transaction costs, which have negative impacts on the benefit from the potential higher risk reduction. / Ontario Ministry of Agriculture, Food and Rural Affairs (OMAFRA) Canadian Agricultural Trade Policy Research Network (CATPRN)

Lameness continues to cause significant problems in profitability, productivity, and animal welfare in the feedlot industry. Toe tip necrosis syndrome (TTNS) is a new name for a previously reported condition. By definition, TTNS is separation of the apical white line with tissue necrosis and clinical lameness. This definition includes complications such as pedal (P3) osteitis, middle (P2) and proximal (P1) phalangeal osteomyelitis, tendonitis, tenosynovitis, cellulitis, and embolic pneumonia. Anecdotal experiences from practitioners report this lameness in feedlot cattle will develop within weeks after feedlot entry. Often the hindlimbs, specifically the lateral claw, are affected where a separation of the dorsal wall and sole will be noticed. Secondary infections will progress deeper into the foot and become systemic. Unfortunately, despite treatment, these animals can become very lame and will need to be euthanized. The overall objective of this project was to describe the epidemiology of TTNS in western Canadian feedlot cattle. The specific objectives were 1) to use clinical examinations, imaging modalities, and necropsy findings to aid in description, classification, and characterization of TTNS lesions, 2) to describe the epidemiology of TTNS in feedlot cattle, and 3) to evaluate risk factors for TTNS. Upon further investigation into this arrival related condition it became apparent that there were many different descriptors: P3 necrosis, toe abscess, apicus necrotica, apical pedal bone necrosis or toe necrosis. These names and descriptors of toe tip lesions were based on anecdotal experiences and previous case reports. As a result, traditional epidemiological approaches that included field investigations, clinical and necropsy examinations were implemented to identify, characterize and describe this condition. Based on clinical findings, imaging modalities, and necropsy specimens examined during September to December 2012, inclusive, a more specific name and descriptive case definition were introduced. TTNS descriptive epidemiology was described by use of a retrospective database analysis from Feedlot Health Management Services (FHMS) with 702 veterinarian confirmed TTNS cases by necropsy examination. From this database, there were 30% (210/702) of necropsy cases treated for TTNS and 70% of cases (492/702) that were not treated. Of those animals treated, the mean and standard deviation (median) interval from feedlot arrival to first treatment was 18.9 ±1.7 d (12 d). The mean (standard deviation) days on feed until death from TTNS was the earliest in grass-fed calves (32.4 ± 22.1 d), followed by auction-derived (40.6 ± 40.6 d), ranch direct (44.1 ± 53.1 d), and back-grounded calves (69.0 ± 75.6 d) (P < 0.001). Yearlings were on feed for a mean (standard deviation) days of 37.1 ± 32.0 d when compared to calves at 49.5 ± 57.0 d before death (P < 0.001). The greatest proportion of deaths occurred from September to November. There were 96.2% (1,832/1,904) of lots without one case of TTNS and 3.8% (72/1,904) of lots had one or more TTNS cases. A prospective case-control study to identify TTNS risk factors consisted of 148 total necropsy submissions (82 cases, 66 controls) from three feedlot veterinary practices and 16 feedlots during October 2012 to January 2013, inclusive. Confirmation of feet samples by the principal investigator at the Western College of Veterinary Medicine reduced the total to 135 animals: 67 cases and 68 controls. The measure of agreement (kappa) on classification of TTNS cases and controls between the veterinary practice and WCVM was 0.778 (P < 0.001). Bacterial culture results revealed that 75% of pure isolates in TTNS cases were attributed to Escherichia coli, Streptococcus spp., Trueperella pyogenes, Fusobacterium necrophorum. TTNS cases were 3.8 times more likely than control animals to have BVDV isolated (95% CI 1.7-8.5; P < 0.001). TTNS animals were 2.2 times more likely than control animals to have histopathological evidence of vasculitis (95% CI 1.0-4.6; P = 0.04). BVDV samples were 11.2 times more likely to show histopathological evidence of vasculitis than non-BVDV samples (95% CI 4.7-27.0; P < 0.001). A decreased difference was found in sole thickness at the toe tip (P < 0.001). There was no evidence of pedal bone rotation between case and control animals (P = 0.15). In summary, TTNS is a specific term for apical white line separation with tissue necrosis and clinical lameness. A practitioner's field diagnosis of TTNS based on apical white line separation and tissue necrosis is accurate on clinical signs alone. TTNS is a transport or arrival related condition in feedlot cattle that has a propensity for cases to cluster together. Pure bacterial isolates provide an understanding of the pathogens responsible for TTNS and that environmental pathogens contribute to an ascending infection. BVDV, vasculitis and apical sole thickness were risk factors associated with TTNS; however, their exact role requires further investigation.

Master of Science / Department of Animal Sciences and Industry / James S. Drouillard / Three studies evaluated effects of high-amylase corn (Enogen® Feed Corn, EFC) on ruminal digestive characteristics using different processing methods; a 4th study evaluated performance of finishing cattle fed steam-flaked EFC. In study 1, mill-run corn (CON) and EFC were ground through 9-, 6-, or 4 -mm screens, blended to contain 0, 33.3, 66.7, or 100% EFC, and heated to 50, 75, or 100⁰C (plus a non-heated control). No 2- or 3-way interactions occurred (P > 0.05). Increasing EFC in blends linearly improved in situ dry matter disappearance (ISDMD; P < 0.01) and in vitro gas production (IVGP; P = 0.02). Study 2 used blends of EFC and CON containing 0, 25, 50, 75, or 100% EFC, which were reconstituted to 27, 30, or 33% moisture, and ensiled. High-amylase corn did not affect ISDMD (P = 0.19) but IVGP increased linearly (P < 0.01) in response to greater amounts of EFC. Acetate:propionate ratio and total volatile fatty acid (VFA) production by in vitro fermentation improved linearly by increasing EFC (P < 0.02). Study 3 used the same blends of EFC and CON as study 2. Grains were tempered with 0, 3, or 6% moisture, steam conditioned 15, 30, or 45 min, and flaked. No 2- or 3-way interactions occurred. Starch availability, ISDMD, IVGP, and in vitro production of acetate, propionate, and total VFA increased linearly (P < 0.01) with greater flaked EFC in blends. Study 4 fed finishing diets consisting of steam-flaked CON, or EFC, for 136 d to 700 crossbred beef heifers (394 ± 8.5 kg initial BW). Compared to CON, cattle fed EFC had similar DMI (P = 0.78) but had greater ADG (P < 0.01) and a 5% improvement in feed efficiency (P < 0.01). Carcass weight was 6 kg greater for EFC cattle (P < 0.01), which also had 8% fewer liver abscesses (P = 0.03) than CON. Marbling score was greater in CON cattle (P = 0.04) than EFC; no differences in USDA Quality Grade (P = 0.33), Yield Grade (P = 0.13), LM area (P = 0.89), or 12th-rib fat thickness (P = 0.21) were evident. Improvements in digestion associated with EFC are likely confined to that component of grain mixtures due to a lack of quadratic effects. Improvements in feed efficiency, carcass weight, and potential liver abscess mitigation may be of advantageous use for producers.

Doctor of Philosophy / Department of Diagnostic Medicine/Pathobiology / Daniel U. Thomson / With the concerning predicted growth of the world population for the next decades it is evident that farmers, ranchers, and cattle feeders need to find alternative ways to increase food production globally and assure food provision for future generations. The United States has an impressive reputation in global beef production. Beef cattle production in the United States is a complex industry with thousands of operations differing in geographical location, environmental conditions, management practices, operative systems, feedstuffs used, type of cattle raised or fed, production type, cattle capacity, and design of facilities. Beef cattle feeding operations exist all across the United States, but the majority of the larger feedlot operations are located in the Great Plains region. Feeding cattle is considered a high-risk business driving cattle feeders to implement all technologies available with best management practices with the goal of improving sustainability and profitability of their operations through biological and economical efficiencies. Thus, it is theorized that profitability in the feedlot industry is achieved when cattle feeders meet the requirements of the basic production management factors, such as cattle health, nutrition, and welfare in an equilibrated fashion. The first objective of this research was to describe recommended practices made by veterinary consultants and practitioners who service clients with commercial beef cow-calf operations in the US and Canada in terms of vaccine protocols, health practices, and production practices to establish a benchmark for standard operating procedures used in the beef cattle industry. The second objective of this research was to provide a thorough description of outdoor cattle feeding facilities currently being used by feedlots in the High Plains region of the United States that would serve as a benchmark for those looking to build a new facility or enhance an existing cattle feedlot. The third objective of this research was to obtain descriptive data regarding feedlot cattle management practices and cattle health and use it as a tool to make comparisons of cattle management practices between feedlots that might explain the difference in AIP incidence between feedlots in multiple locations. The fourth objective of this research was to evaluate the effects of periodic feeding of low-quality long-stemmed roughage in Holstein steers fed a steam-flaked corn-based finishing diet on dry-matter intake, ruminal dynamics, ruminal fermentation parameters, and fecal starch concentration.