DYNAMICS OF MYCOBACTERIUM AVIUM SUBSP. PARATUBERCULOSIS IN DAIRY HERDS: INSIGHTS INTO TRANSMISSION RISKS, BULK-MILK CONTAMINATION, AND ASSOCIATIONS BETWEEN DIAGNOSTIC TESTS

Johne’s disease, a severe granulomatous enteritis of ruminant animals, is caused by Mycobacterium avium subsp. paratuberculosis (MAP). MAP infections have detrimental consequences for animal health and reduce dairy-herd productivity. Bacterial fastidiousness and slow generation time encumber diagnostic testing strategies. MAP is also a potential etiologic agent of human Crohn’s disease, with the bulk-milk supply serving as a possible transmission vector. The objective of this dissertation is to explore MAP infection dynamics on dairy farms, with an emphasis on the routes of bulk-milk contamination, transmission risk across production type, and the interplay between diagnostic testing outcomes. Accordingly, we have applied statistical and mathematical approaches to both cross-sectional and longitudinal datasets. Using questionnaire data from 292 U.S. dairies, we conducted a comparative risk assessment of organic vs. conventional management and determined that organic herds were at higher risk for new MAP infections. We concluded, empirically, that organic farms were more susceptible to a synergism of risk factors within the maternity pen and should improve calving-area hygiene if electing to permit cow-calf contact. Bulk-milk testing was also conducted for these herds. Most high ELISA tanks were PCR negative, implying that ELISA is not a perfect predictor of bulk-milk MAP status; for accurate risk assessment, bulk-milk ELISA should be used in tandem with PCR. A combination of ELISA and PCR may also aid in determining the specific route of bulk-milk contamination (either environmental or direct shedding). To extend the investigation to individual animals, longitudinal data were obtained from 14 MAP-positive cows in 2 low-prevalence herds. Robust relationships between culture, fecal qPCR, and milk ELISA were revealed, using mixed linear modeling to adjust for cow characteristics. We explored temporal relationships and observed that spikes in fecal shedding were predictive of subsequent high milk ELISA results. We also noted that disease “Progressors,” (infected animals with increasing fecal MAP CFU over time) had higher antibody titers overall. Interestingly, the paucity of positive milk samples, from both individual and bulk- tank sources, suggests that milk contamination is not a chief concern in low-prevalence herds. Armed with insights from these studies, in addition to published literature, we developed a mathematical model to explore the interaction between categories of infection, environmental MAP burden, and bulk-tank contamination. Direct shedding into milk accounted for < 1% of the MAP CFU in the tank, with environmental contamination from high shedders as the primary driver of bulk-milk MAP burden. Culling of high shedders, cleaning of the maternity pen, and adherence to milking parlor cleanliness each had a strong influence on lowering the bulk-milk MAP load. A combination of these initiatives served to drive the MAP level below an acceptable threshold (< 103 CFU/L). While complete elimination of MAP may be an unrealistic target for high-prevalence herds, the production of bulk milk with a low MAP load appears feasible. In this work, we assess the significance of a variety of contamination routes, transmission risks, and intervention strategies. These efforts are directed toward improved understanding of testing schemes and an ultimate refinement of control measures and milk quality programs. The conclusions from the studies presented in this dissertation may be applied to mitigate the spread of MAP in dairy herds, reduce prevalence, and lower or eliminate MAP in the bulk-milk supply

A systematic review of the effects of early separation on dairy cow and calf health

There is a growing concern from the public regarding early cow-calf separation, yet proponents of this practice maintain that artificial rearing is critical for cow and calf health. Early separation is assumed to reduce the risk of transfer of pathogens from dam to neonatal calf, but a wide range of health benefits associated with extended cow-calf contact has also been documented. The aim of this systematic review was to report and synthesize conclusions from the literature on dairy cow and calf health in conventional rearing versus cow-calf contact systems. Peer-reviewed, published manuscripts, written in English, directly comparing dairy cow or calf health in artificial versus suckling systems, were eligible for inclusion. We conducted 7-targeted searches using Web of Science (WoS) to identify key literature on important health conditions. The resulting manuscripts underwent a 4-step appraisal process, and further manuscripts were sourced from reference lists. This process resulted in a final sample of 70 articles that addressed cow and calf health. Sufficient literature was available to assess mastitis in cows, and scours, Cryptosporidiosis, Johne’s disease, pneumonia, immunity, and mortality in calves. The results for Cryptosporidiosis, pneumonia, immunity, and mortality were mixed, with some differences between studies likely attributable to flawed comparisons between cohorts. Overall, the articles addressing calf scours and mastitis pointed to beneficial or no effects of suckling. The studies addressing Johne’s disease did not find cow-calf contact to be a significant risk factor. In conclusion, the scientific peer-reviewed literature on cow and calf health provides no consistent evidence in support of early separation

Moderate and heavy metabolic stress interval training improve arterial stiffness and heart rate dynamics in humans

Traditional continuous aerobic exercise training attenuates age-related increases of arterial stiffness, however, training studies have not determined whether metabolic stress impacts these favourable effects. Twenty untrained healthy participants (n = 11 heavy metabolic stress interval training, n = 9 moderate metabolic stress interval training) completed 6 weeks of moderate or heavy intensity interval training matched for total work and exercise duration. Carotid artery stiffness, blood pressure contour analysis, and linear and non-linear heart rate variability were assessed before and following training. Overall, carotid arterial stiffness was reduced (p  0.05). This study demonstrates the effectiveness of interval training at improving arterial stiffness and autonomic function, however, the metabolic stress was not a mediator of this effect. In addition, these changes were also independent of improvements in aerobic capacity, which were only induced by training that involved a high metabolic stress

A systematic review of the effects of prolonged cow-calf contact on behavior, welfare, and productivity

Separation of calves from cows within hours or days of birth is common on dairy farms. Stakeholders have conflicting perspectives on whether this is harmful or beneficial for the animals’ welfare and production. Our objective was to critically evaluate the scientific evidence for both acute and long-term effects of early separation versus an extended period of cow-calf contact. The outcomes investigated were the behavior, welfare (excluding physical health) and performance (milk yield and growth, respectively) of dairy cows and calves. Primary research papers were found through targeted Web of Science searches, the reference lists of recent reviews for each topic, and the reference lists of papers identified from these sources. Studies were included if they were published in English, the full text was accessible, and they compared treatments with and without contact between dairy cows and calves for a specified period. Early separation (within 24 h post-partum) was found to reduce acute distress responses of cows and calves. However, longer cow-calf contact typically had positive longer-term effects on calves, promoting more normal social behavior, reducing abnormal behavior and sometimes reducing responses to stressors. In terms of productivity, allowing cows to nurse calves generally decreased the volume of milk available for sale during the nursing period, but there was no consistent evidence of reduced milk production over a longer period. Allowing a prolonged period of nursing increased calf weight gains during the milk-feeding period. In summary, extended cow-calf contact aggravates the acute distress responses and reduces the amount of saleable milk while the calves are suckling, but can have positive effects on behaviors relevant to welfare in the longer term and benefit calf growth. The strength of these conclusions is limited, however, given that relatively few studies address most of these effects and that experimental design including timing of contact and observations are often inconsistent across studies. Few studies presented indicators of long-term welfare effects other than abnormal and social behavior of the calves

Modeling the effects of infection status and hygiene practices on Mycobacterium avium subspecies paratuberculosis contamination in bulk tank milk

Infectious diseases in dairy cattle are of significant concern to dairy industries because of their huge impact on animal health, milk production, and economics. Mycobacterium avium subsp. paratuberculosis (MAP)is a pathogenic bacterium that causes Johne's disease, one of the important endemic infectious diseases in dairy cattle. Contamination of bulk tank milk with MAP can occur through direct shedding into milk by infected cows (internal route), fecal contamination (fecal route), or introduction of soil and water containing MAP (environmental route). Humans can be exposed to MAP via raw milk consumption; additionally, there are reports of MAP survival in milk after pasteurization. The risk of human consumption is particularly important due to an association between MAP and human Crohn's disease. In the current study, we used a probabilistic modeling framework to predict the level of MAP contamination per liter in the bulk tank milk and weigh the relative importance of each contamination route. Our model focused on several different infection statuses and the contribution of each group to environmental and fecal contamination, in addition to internal route shedding. We assessed the influence of common hygiene practices, such as washing of udders before milking and the use of milk filters, on the concentration of MAP in bulk tank milk. We extracted parameters and their distributions from national surveys and thorough literature search. Our baseline model comprising all hygiene practices provided an average estimate of 0.76 log CFU/L for the final concentration of MAP in bulk tank milk, with a maximum of 6.70 log CFU/L and a minimum of 0.04 log CFU/L depending on herd size and the ratio of infection statuses. Results from sensitivity analyses indicated that the average fecal contamination showed the greatest impact on the final MAP concentration per liter in bulk tank milk, followed by herd size and washing efficiency. This study emphasized that good hygiene practices are crucial for maintaining the quality of raw milk in an endemically-infected dairy herd.</p

Modeling the effects of infection status and hygiene practices on Mycobacterium avium subspecies paratuberculosis contamination in bulk tank milk

Infectious diseases in dairy cattle are of significant concern to dairy industries because of their huge impact on animal health, milk production, and economics. Mycobacterium avium subsp. paratuberculosis (MAP)is a pathogenic bacterium that causes Johne's disease, one of the important endemic infectious diseases in dairy cattle. Contamination of bulk tank milk with MAP can occur through direct shedding into milk by infected cows (internal route), fecal contamination (fecal route), or introduction of soil and water containing MAP (environmental route). Humans can be exposed to MAP via raw milk consumption; additionally, there are reports of MAP survival in milk after pasteurization. The risk of human consumption is particularly important due to an association between MAP and human Crohn's disease. In the current study, we used a probabilistic modeling framework to predict the level of MAP contamination per liter in the bulk tank milk and weigh the relative importance of each contamination route. Our model focused on several different infection statuses and the contribution of each group to environmental and fecal contamination, in addition to internal route shedding. We assessed the influence of common hygiene practices, such as washing of udders before milking and the use of milk filters, on the concentration of MAP in bulk tank milk. We extracted parameters and their distributions from national surveys and thorough literature search. Our baseline model comprising all hygiene practices provided an average estimate of 0.76 log CFU/L for the final concentration of MAP in bulk tank milk, with a maximum of 6.70 log CFU/L and a minimum of 0.04 log CFU/L depending on herd size and the ratio of infection statuses. Results from sensitivity analyses indicated that the average fecal contamination showed the greatest impact on the final MAP concentration per liter in bulk tank milk, followed by herd size and washing efficiency. This study emphasized that good hygiene practices are crucial for maintaining the quality of raw milk in an endemically-infected dairy herd

The Freestall Reimagined: Effects on Stall Hygiene and Space Usage in Dairy Cattle

Modern freestall barns for dairy cattle have been constructed with considerations for dairy cow cleanliness; partitions and other stall features such as neck rails are designed to reduce manure contamination of bedding and decrease farm labor. However, cows prefer to lie in more open spaces, including on bedded packs and pasture. We created an “alternative” housing area by modifying a traditional freestall pen and including flexible partitions to create larger lying areas. We assessed cattle lying behaviour, including lying postures, in this alternative pen (ALT) compared to an open pack (OP) and freestalls (FS) with different stocking densities. We also assessed levels of manure contamination across systems. Cleanliness was highest in FS, but ALT provided substantial improvement compared to OP. Cattle spent more time lying down in OP and ALT compared to FS. There were few differences in postures (such as lying with limbs outstretched) between OP and ALT, but cows in both of these systems more often lay in extended positions compared to when they were housed in FS. Housing in OP and ALT was associated with reduced perching for cows with high body weight; perching has been linked to an increased prevalence of both hoof lesions and lameness. Thus, alternative lying areas can offer a solution for producers seeking to provide cattle with the advantages of a more open lying area, while improving hygiene relative to an open pack.Land and Food Systems, Faculty ofNon UBCReviewedFacult

Predicting Disease in Transition Dairy Cattle Based on Behaviors Measured Before Calving

Dairy cattle are particularly susceptible to metritis, hyperketonemia (HYK), and mastitis in the weeks after calving. These high-prevalence transition diseases adversely affect animal welfare, milk production, and profitability. Our aim was to use prepartum behavior to predict which cows have an increased risk of developing these conditions after calving. The behavior of 213 multiparous and 105 primiparous Holsteins was recorded for approximately three weeks before calving by an electronic feeding system. Cows were also monitored for signs of metritis, HYK, and mastitis in the weeks after calving. The data were split using a stratified random method: we used 70% of our data (hereafter referred to as the “training” dataset) to develop the model and the remaining 30% of data (i.e., the “test” dataset) to assess the model’s predictive ability. Separate models were developed for primiparous and multiparous animals. The area under the receiver operating characteristic (ROC) curve using the test dataset for multiparous cows was 0.83, sensitivity and specificity were 73% and 80%, positive predictive value (PPV) was 73%, and negative predictive value (NPV) was 80%. The area under the ROC curve using the test dataset for primiparous cows was 0.86, sensitivity and specificity were 71% and 84%, PPV was 77%, and NPV was 80%. We conclude that prepartum behavior can be used to predict cows at risk of metritis, HYK, and mastitis after calving.Land and Food Systems, Faculty ofOther UBCNon UBCReviewedFacult

Human-animal interactions and machine-animal interactions in animals under human care: A summary of stakeholder and researcher perceptions and future directions

Animals under human care are exposed to a potentially large range of both familiar and unfamiliar humans. Human-animal interactions vary across settings, and individuals, with the nature of the interaction being affected by a suite of different intrinsic and extrinsic factors. These interactions can be described as positive, negative or neutral. Across some industries, there has been a move towards the development of technologies to support or replace human interaction with animals. Whilst this has many benefits, there can also be challenges associated with increased technology use. A day-long Animal Welfare Research Network workshop was hosted at Harper Adams University, UK, with the aim of bringing together stakeholders and researchers (n = 38) from the companion, farm and zoo animal fields, to discuss benefits, challenges and limitations of human-animal interactions and machine-animal interactions for animals under human care and create a list of future research priorities. The workshop consisted of four talks from experts within these areas, followed by break-out room discussions. This work is the outcome of that workshop. The key recommendations are that approaches to advancing the scientific discipline of machine-animal interactions in animals under human care should focus on: (1) interdisciplinary collaboration; (2) development of validated methods; (3) incorporation of an animal-centred perspective; (4) a focus on promotion of positive animal welfare states (not just avoidance of negative states); and (5) an exploration of ways that machines can support a reduction in the exposure of animals to negative human-animal interactions to reduce negative, and increase positive, experiences for animals