Twenty-eight Holstein and crossbred calves of both genders were used to evaluate the effect of milk replacer antibiotics on abundance of selected antibiotic resistance genes (ARG) in the feces. Calves were blocked by breed, gender, and birth order, and assigned to one of three treatments at birth. Treatments were control (containing no antibiotics in the milk replacer), subtherapeutic (neomycin sulfate and oxytetracycline hydrochloride each fed at 10 mg/calf/d), and therapeutic (no antibiotics in the milk replacer until d 36, then neomycin sulfate and oxytetracycline hydrochloride each fed at 1000 mg/calf/d for 14 d). Calves were fed milk replacer twice daily at 0600 h and 1800 h. Fecal and respiratory scores and rectal temperatures were recorded daily. Calves were weighed at birth and weaning to calculate average daily gain. Beginning at six weeks of age fecal grab samples were collected from heifers at 0600 h, 1400 h, 2000 h, and 2400 h for 7 d, while bull calves were placed in metabolism crates for collection of all feces and urine. DNA was extracted from feces, and ARG corresponding to the tetracyclines (tetC, tetG, tetO, tetW, and tetX), macrolides (ermB, ermF), and sulfonamides (sul1, sul2) classes of antibiotics along with the class I integron gene, intI1, were measured by quantitative polymerase chain reaction (qPCR). No tetC or intI was detected. There was no significant effect of antibiotic treatment on the absolute abundance (gene copies/ g wet manure) of any of the ARG except ermF, which was lower in the antibiotic-treated calf manure probably because host bacterial cells carrying ermF were not resistant to tetracycline or neomycin. All ARG except tetC and intI were detectable in feces from 6 weeks onwards, and tetW and tetG significantly increased with time (P < 0.10), even in control calves. Overall, the majority of ARG analyzed for were present in the feces of the calves regardless of exposure to dietary antibiotic. Feed antibiotics had little effect on the ARG monitored; other methods for reducing the ARG pool should also be investigated. / Master of Science

Exposure to antibiotics has the potential to increase the incidence and proliferation of antibiotic resistance genes (ARG) in the gut and fecal microbiome. Non-saleable, antibiotic-containing milk from cows treated with antibiotics (waste milk) is commonly fed to dairy calves but the effects of ingestion of antibiotics at an early age on the gut microbiome and the development of ARG in the naive gut are not well understood. Pirlimycin, a lincosamide antibiotic acting against Gram positive bacteria through inhibiting protein synthesis by binding to the 50S ribosome, is commonly used as mastitis therapy. Lincosamides are also considered highly important in human medicine, often used against Staphylococcus aureus and Clostridium difficile infections. Emerging microbial resistance to pirlimycin is of concern for both animal and human health. The objective of this study was to determine the effect of early lincosamide antibiotic exposure on the abundance of ARG in feces of milk-fed calves. Eight female Holstein calves were blocked by age, paired by block, and randomly assigned to pasteurized whole milk (control; n = 4) or milk containing 0.2 mg/L of pirlimycin (treatment; n = 4). Calves were enrolled after receiving two colostrum feedings and were fed 5.68 L of pasteurized whole milk, treatment, or control, divided into two daily feedings, from d 1 to d 50 of age. After weaning calves were fed non-medicated starter grain ad libitum. Fecal samples were collected weekly until 85 d of age and freeze-dried. DNA was extracted using QiaAmp® Fast DNA Stool Mini Kit and qPCR was used to quantify the absolute abundance (gene copies/g of wet feces) and relative abundance (gene copies/copies of 16S rRNA genes) of erm(B), tet(O), tet(W) and 16S rRNA genes. Data was analyzed using PROC GLIMMIX in SAS. Abundance of 16S rRNA genes, tet(O) and tet(W) were not different between control and pirlimycin-fed calves nor were the relative abundance of tet(O) (mean = 0.050 tet(O) copies/16S rRNA genes) or tet(W) (0.561 tet(W) copies/16S rRNA genes). While abundance of erm(B) was higher in pirlimycin-fed calves compared to control calves (6.46 and 6.04 log gene copies/g wet feces; P = 0.04) the relative abundance of erm(B) (0.273 gene copies/16S rRNA genes) in feces of calves was not influenced by treatment. There was an effect of day (P < 0.10) for absolute abundance of tet(O), tet(W), and erm(B) indicating that the levels change with time as the fecal microbiome develops. This study suggests that feeding pirlimycin-containing non-saleable milk to growing calves may increase environmental loading of erm(B), which codes for resistance to highly important macrolide and lincosamide antibiotics. Additional research is needed on effects of feeding waste milk to calves on other fecal ARG and on the post-excretion and post-application fate of these genes. / Master of Science

This study was an extension of a study submitted in April 2014 by Sheldon D. Holt entitled “Ambient Temperature, Calf Intakes, and Weight Gains on Preweaned Dairy Calves”. A major component in a profitable dairy operation is the raising of female calves as replacement heifers; but since no direct income is generated by calf raising alone, it is often overlooked as a potential profit area on a dairy farm. Calf management practices that ultimately impact milk productivity and reproductive performance during a heifer’s lifetime begin at birth. This study examines the effect of calf starter intake on calf growth, measuring specifically calf weight. How calf starter intake affected production costs was also examined. Other factors included in the study were seasonal change, hip height, days since birth, and weather conditions. The cost of calf starter is one of the main contributors to total production cost in raising dairy calves. Since the amount of starter intake consumed by the calves in this study was measured by Holt, a cost analysis can be performed using these data. Therefore, the first two objectives of this study are to 1) develop a model which minimizes cost of starter feed (which is a variable controlled by the dairy producer) and 2) use the model developed under objective 1) to find the breakeven point (where the cost of an input is less than or equal to the value gained from that input) and conduct sensitivity analysis with respect to this point. Although an analysis was performed on the data at the close of its collection in 2014 by S.D Holt, there are several econometric issues that were not adequately addressed before these analyses were performed. The following problems have been found in the data: functional form, multicollinearity, heteroskedasticity, and serial correlation. Any interpretation or prediction based on these data, without these issues being resolved, is not reliable. In order for interpretations and predictions based on these data to be valid, the last two objectives of this study are to 3) define in detail the econometric problems that existed in Holt’s study and 4) find and implement solutions to econometric problems that existed in that study.

The objectives of this thesis were to investigate 1) the use of behavior and activity monitoring for the identification of heifers at risk of disease, 2) the use of group level management practices to reduce the risk of disease, and 3) the identification of long-term impacts of bovine respiratory disease complex (BRD). For objective 1, lying posture, a decreased willingness to approach an observer and high lethargy scores were associated with diarrhea in calves under 2 weeks of age and a high lethargy score in 4-6 week old calves was associated with decreased average daily gain (ADG) in the first 8 weeks of life (n = 744). In weaned calves (n = 74) increased activity (increase in steps and decrease in lying), standing at the bunk not eating, and lying far from other calves in the first 3 days post-weaning were associated with decreased post-weaning weight gain. For objective 2, separating social mixing from movement to a novel environment, and administering prophylactic antibiotics to calves at high risk of disease, were investigated. Both mixing and movement to a novel environment increased activity levels in newly weaned dairy calves (n = 64). When calves were mixed prior to movement to a novel environment they had a smaller increase in activity compared to calves that were simultaneously mixed and moved. No differences in weight gain or calf starter intake were observed. Administration of a prophylactic antibiotic, tulathromycin, to 3 day old calves upon arrival at a heifer raising facility (n = 788) and 8 week old calves at first movement to group housing (n = 1,392 ) was found to reduce diarrhea and otitis media, and BRD, respectively. Objective 3 was addressed by monitoring calves that received tulathromycin at 8 weeks of age to determine the long-term impacts of BRD. Bovine Respiratory Disease complex was associated with decreased growth to 9 months of age, decreased survival to first calving, increased risk of dystocia and a greater age at first calving. / Natural Sciences and Engineering Research Council of Canada & Pfizer Animal Health

Replacement heifer rearing is critical for the future of the dairy operation, especially to improve genetic merit and maintain herd size. A replacement heifer from the day she is born to the day she calves herself is generally a 2-year investment without potential income. A myriad of options exists on how to manage, fed, and ultimately raise replacement heifers. This study quantifies the costs associated with replacement heifer management decisions from birth to calving related to housing, labor, feed and health. The heifer rearing period can be broken into pre and post weaning sections to allow for more understanding the variation of these different biological time periods. Variation can influence the investment per day and breakdown of resources required from a dairy producer. Total heifer raising cost varied broadly across all management scenarios in our study, with feed and labor consistently representing over 60% of the total cost. After determining the true cost on an individual farm, or providing developed assumed cost for a change in management, producers can better manage current expenses and be more prepared for future investment.

Master of Science / Department of Clinical Sciences / Daniel U. Thomson / Bovine respiratory disease (BRDC) is a multifaceted disease that causes considerable economic loss in both the beef and dairy industry. However, because there may be lingering effects of BRDC in the dairy industry, the full economic costs of the disease may not be realized. These lingering effects may include an increased departure from the herd, decreased milk production, and decreased reproductive performance. All of these outcomes are affected by multiple variables, but proper statistical modeling can control for many of the different influences. Few studies have attempted to look at the long term effects of calfhood BRDC but consistent associations have not been identified. The objective of this observational, retrospective study was to determine the association between calfhood BRDC prior to 120 d of age and departure from the herd, milk production, and reproductive performance. The association between the occurrence of BRDC with departure from the herd prior to first calving depended on the birth year, but for 5 of the 6 years, animals that contracted BRDC were 1.62 to 4.98 times more likely to leave the herd than animals that did not contract BRDC. In addition, animals that contracted BRDC were also 1.28 times more likely to leave the herd between first and second calving than animals that did not contract BRDC. Furthermore, the age at BRDC occurrence was associated with departure from the herd. Animals that contracted BRDC pre-weaning were 2.62 times more likely to leave the herd prior to first calving than animals that contracted BRDC post-weaning. However, age of BRDC occurrence was not significantly associated with departure from the herd between first and second calving. The occurrence of BRDC during the first 120 d of life was associated with a 233 kg decrease in lactation-one production, but was not significantly associated with production in subsequent lactations. Finally, calfhood BRDC was not significantly associated with a decreased reproductive performance measured by calving interval. In conclusion, calfhood BRDC negatively impacts productivity both prior to and after first calving.

<p>Heart rate variability (<b>HRV</b>), or the variation in time between adjacent heart beats over time, is a non-invasive proxy measure of autonomic nervous system (<b>ANS</b>) function that has been used regularly in studies focused on evaluating livestock stress and welfare. The autonomic nervous system regulates involuntary physiological processes (<i>e.g.</i> respiration and heart rate) and consists of two main components, the parasympathetic (<b>PNS</b>), and sympathetic (<b>SNS</b>) branches, which act to maintain bodily homeostasis (PNS) or stimulate the “fight-or-flight” response after exposure to a stressor (SNS). Traditional linear HRV measures provide an estimation of overall autonomic activity or changes to the balance between the PNS and SNS branches by evaluating changes to the mean, variance, or frequency spectra of the R-R intervals. </p><p>To interpret HRV data obtained via linear HRV measures, particularly spectral HRV analysis, a linear assumption has to be assumed where SNS and PNS activity act in a purely antagonistic manner. However, this assumption is not always met. In many cases, ANS activity is altered in a nonlinear manner, which is reflected to some degree in the variability of heart rate output. Therefore, HRV measures that evaluate nonlinear changes to organizational or structural aspects of the R-R interval variability may be a useful compliment to traditional linear HRV measures for distinguishing between stressed and non-stressed states. The purpose of this dissertation was to evaluate the use of nonlinear HRV measures for evaluating dairy calf disbudding pain, piglet castration pain, growing pig heat stress, and as potential indicators of the subsequent immune response to a lipopolysaccharide (<b>LPS</b>) challenge in growing pigs.</p><p>Chapter 1 provides a knowledge base for understanding HRV and its use as a measure of autonomic stress in studies with livestock species. A brief explanation of animal welfare science, measures used to evaluate an animal’s welfare, and a demonstration of need for non-invasive physiological measures is provided before discussing the physiological basis of HRV. Relevant linear and nonlinear HRV measures are explained and examples of their use in livestock stress research are provided. Finally, a rationale for the studies conducted in this dissertation is presented.</p><p>Chapter 2 evaluates the use of HRV as an indicator of castration pain in 9-d-old piglets over a 3-d experimental period. Compared to sham castrated piglets, surgically castrated piglets exhibited greater low frequency to high frequency ratios (<b>LF/HF</b>), reduced sample entropy (<b>SampEn</b>), and greater percent determinism (<b>ÞT</b>) during the post-castration period. However, postural behavior was not different between treatments and serum cortisol concentrations only tended to differ between treatments at 1 and 24 h post-castration treatment, with surgically castrated pigs having numerically greater serum cortisol concentrations at both timepoints. These results demonstrate the ability of nonlinear HRV measures (SampEn and ÞT) to complement the physiological interpretation of linear HRV measures (LF/HF) in response to castration. Specifically, pigs who were surgically castrated exhibited more regularity (SampEn) and periodicity (ÞT) in their HRV data, and potentially more sympathetic activity (LF/HF) compared to sham castrated piglets, indicating greater pain-related stress. Additionally, HRV was a more sensitive measure of the stress response to castration than readily identifiable behaviors such as posture and the serum cortisol response.</p><p>Chapter 3 evaluates the use of HRV as an indicator of disbudding pain in dairy heifer calves (4 to 7-wk of age) over a 5-d experimental period. Calves who were given lidocaine and meloxicam prior to disbudding exhibited lower mean R-R interval (<b>RR</b>) values and a greater short-term detrended fluctuation analysis scaling exponent (<b>DFAα₁</b>) than sham disbudded calves. Together, these results indicate that calves who received pain mitigation exhibited greater pain-related stress (RR) and reduced physiological complexity in their heart rate signal (DFAα₁). Calves who were disbudded without pain mitigation had an intermediate response compared to sham disbudded calves and calves provided lidocaine and meloxicam. However, their numerical values closely followed those of calves provided lidocaine and meloxicam. These results demonstrate the usefulness of nonlinear HRV measures (DFAα₁) for evaluating nonlinear and correlational aspects of physiological complexity in response to disbudding. Additionally, the HRV results suggest that the provision of meloxicam does not reduce the amount of pain-related stress experienced by calves following disbudding.</p><p>Chapter 4 evaluates the use of HRV as an indicator of heat stress in growing pigs exposed to an acute heat episode. Heat stressed pigs exhibited greater body temperatures and spent less time in an active position compared to thermoneutral control pigs. Additionally, heat stressed pigs displayed an altered nonlinear HRV response to the acute heat phase compared to non-heat stressed control pigs. Specifically, heat stressed pigs exhibited lower SampEn and tended to exhibit greater ÞT, but no alterations to linear measures were observed in response to the acute heat episode. The low frequency to high frequency ratio was higher in heat stressed pigs during the period following the acute heat phase. Therefore, nonlinear HRV measures (particularly SampEn) may be more sensitive to the immediate physiological stress response to increased environmental temperature than traditional linear HRV measures.</p><p>Chapter 5 evaluates the use of baseline HRV as a potential indicator of the subsequent cortisol and pro-inflammatory cytokine response to an LPS challenge in growing pigs. The time for a pig to approach a human (<b>approach time)</b> prior to LPS administration was inversely related to baseline standard deviation of the R-R intervals (<b>SDNN</b>), and directly related to RR and the mean length of diagonal lines in a recurrence plot (<b>Lmean</b>). This result may have implications for the use of HRV as a measure of temperament in livestock species, since pigs with lower baseline SDNN (<i>i.e.</i> greater stress) and greater baseline Lmean (<i>i.e.</i> increased periodicity length in HRV data; greater stress) values took longer to approach a human observer before LPS administration (which occurred 1 d after HRV measurement). Area under the curve values for approach time following LPS administration were inversely related to high frequency spectral power (<b>HF</b>) and directly related to body weight, where pigs with low baseline HF values (<i>i.e. </i>lower parasympathetic activity) and higher body weights were slower to approach a human observer following LPS administration. Additionally, pigs with greater Lmean values had a greater change in body temperature following LPS administration. In conclusion, while baseline HRV measures were not directly representative of the cortisol or cytokine response following an LPS challenge, HF and Lmean may be useful indicators for evaluating certain aspects (sickness behavior and fever) of the innate immune response to an LPS challenge. <b></b></p><p> In conclusion, these studies demonstrate the usefulness of nonlinear HRV measures for evaluating livestock stress. Measures such as sample entropy and those derived from recurrence quantification analysis (ÞT, Lmean) seem to be particularly useful for complementing traditional linear HRV measures and, in some cases, are more sensitive measures of the physiological stress response (see chapter 4). Therefore, their inclusion in future studies on livestock HRV is warranted. However, further work is needed to fully elucidate the physiological significance of nonlinear HRV measures and their response to stress.</p>

<p>The first four months of a dairy calf’s life provide the foundation for future production and health. Therefore, it is critical that calves are managed to optimize both health and growth, to maximize their potential. Calf morbidity, which leads to less productive animals and is an economic impact on producers, continue to be areas of opportunity in the dairy industry. In addition, the animal agricultural community is working to reduce the use of antibiotics, due to a growing concern regarding antibiotic resistant bacteria. This provides researchers with the challenge of identifying strategies to reduce calf morbidity and mortality, while also decreasing reliance on antibiotics. The objective of this dissertation was to evaluate nutritional strategies supplemented to calves as well as maternal factors that impact colostrum. The studies focused on strategies to improve the innate and adaptive immune responses and growth of the calf, ultimately reducing reliance on antibiotics. Chapters 2 and 3 discuss feeding dairy calves <i>Saccharomyces cerevisiae</i> fermentation products in milk replacer and solid feeds until 4 months of age. This study concluded that feeding <i>Saccharomyces cerevisiae</i> fermentation products to calves improves average daily gain and feed efficiency post-weaning and reduces antibiotic treatment incidence for respiratory disease. It also increases the evenness of the fecal microbiome and the acute innate immune response, as determined by increased TNF-α, glucose, and respiration rate during a lipopolysaccharide challenge. Chapter 4 evaluated the effects of feeding dairy calves medium chain fatty acids (C8:0 and C10:0) in milk replacer until 60 days of age. Feeding C8:0 and C10:0 to calves reduced plasma NEFA concentrations around weaning, suggesting the mobilization of less adipose tissue to meet the energy demands of the calf. This trial also determined that vaccinating calves at 3 weeks of age with ovalbumin combined with an aluminum hydroxide adjuvant, is an effective way to evaluate their adaptive immune responses. </p> <p>Supplementing calves directly is not the only way to impact calf growth and health, maternal factors also impact calf nutrition through colostrum consumption. Last, chapter 5 explored maternal factors that influence the lipidome of colostrum and therefore the lipid intake of the newborn calf. This study concluded that the metabolic status of the cow affects circulating lipids and the lipid content of colostrum. Also, the lipidome of colostrum is distinct from the circulating lipidome of the calf, which is similar to the circulating lipidome of the cow, except for phosphatidylglycerol, where it appears that colostrum serves as the source for the phosphatidylglycerol present in the circulation of the calf. There are many different nutritional strategies that can impact the health and productivity of calves. Calves can be directly supplemented with nutraceuticals like <i>Saccharomyces cerevisiae</i> fermentation products or medium chain fatty acids, or calf nutrition can be influenced by the maternal factors through the consumption of colostrum. </p>

The objective of this study was to measure the effects of both a nutritional (water nipple) and social (partner calf) enrichment on calf body weight, grain intake, water intake, behavior and learning. The enrichments included 1) water provided from a nipple vs. a bucket (nutritional) and 2) visual and tactile access to a partner vs. isolated rearing with no visual or tactile access to a partner calf (social). A total of 72 Holstein and Jersey dairy calves were pseudo-randomly distributed into 4 treatments at birth [Individual/Bucket (IB), Paired/Bucket (PB), Individual/Nipple (IN), Paired/Nipple (PN)]. Socially and nutritionally enriched calves drank more water than non-enriched calves (Social: 5.02 ± 0.27 kg/d vs 3.723 ± 0.27 kg/d respectively; P = 0.0009; Nutritional: 4.93 ± 0.27 kg/d vs. 3.81 ± 0.26 kg/d respectively; P = 0.004). No difference in daily grain intake was found between individual or pair reared calves except during wk 8 (1.31 ± 0.07 kg/d vs 1.60 ± 0.07 respectively kg/d; P= 0.04). There were no differences in average body weight among treatments (P > 0.20). Pre-milk delivery, calves reared on a water bucket spent more time standing (P= 0.03) and when paired, less time non-nutritively suckling compared to water nipple reared calves (P = 0.05). Grooming time was highest during period 2 (wk 3, 4, 5; P = 0.01)) pre-milk delivery. Post-milk delivery, calves reared on a water bucket spent more time drinking milk (7.13 ± 0.40 vs 5.37 ± 0.39 min; P = 0.005)and grooming (P= 0.05), and less time drinking water (P < 0.001)and lying (6.17 ± 1.02 vs 9.19 ± 0.97 min, respectively; P= 0.04)than water nipple reared calves. Water nipple calves when paired exhbited longer drinking times (P = 0.04)..The most notable behavior was cross suckling post-milk delivery, as the weeks progressed water bucket reared calves increased time spent cross-suckling while water nipple calves maintained the amount of time spent cross-suckling. At wk 8 a subset of 24 calves (6 from each treatment) were trained over 14-d period to differentiate between an “X” and “O” cue to receive a milk reward (visual discrimination task). Learning (% correct choices) was compared using a Wilcoxon-signed rank test. Calves individually reared had greater overall correct choices than pair reared calves (0.63 ± 0.02 % correct/total choices vs 0.57 ± 0.02 % correct/total choices respectively: P = 0.05), while calves reared with a nutritional enrichment (water nipple) had greater overall correct choices compared to water bucket reared calves (0.64 ± 0.02 % vs 0.56 ± 0.02 %, P = 0.02). These results indicate that social and nutritional enrichments positively influence calf cognitive performance, water intake, and lying, cross-sucking, grooming behaviors.

No description available.