Comparison of classification algorithms to predict outcomes of feedlot cattle identified and treated for Bovine Respiratory Disease

Bovine respiratory disease (BRD) continues to be the primary cause of morbidity and mortality in feedyard cattle. Accurate identification of those animals that will not finish the production cycle normally following initial treatment for BRD would provide feedyard managers with opportunities to more effectively manage those animals. Our objectives were to assess the ability of different classification algorithms to accurately predict an individual calf’s outcome based on data available at first identification of and treatment for BRD and also to identify characteristics of calves where predictive models performed well as gauged by accuracy. Data from 23 feedyards in multiple geographic locations within the U.S. from 2000 to 2009 representing over one million animals were analyzed to identify animals clinically diagnosed with BRD and treated with an antimicrobial. These data were analyzed both as a single dataset and as multiple datasets based on individual feedyards and partitioned into training, testing, and validation datasets. Classifiers were trained and optimized to identify calves that did not finish the production cycle with their cohort. Following classifier training, accuracy was evaluated using validation data. Analysis was also done to identify sub-groups of calves within populations where classifiers performed better compared to other sub-groups. Accuracy of individual classifiers varied by dataset. The accuracy of the best performing classifier by dataset ranged from a low of 63% in one dataset up to 95% in a different dataset. Sub-groups of calves were identified within some datasets where accuracy of a classifiers were greater than 98%; however these accuracies must be interpreted in relation to the prevalence of the class of interest within those populations. We found that by pairing the correct classifier with the data available, accurate predictions could be made that would provide feedlot managers with valuable information

Antimicrobial use in 20 U.S. beef feedyards: 2018–2019

The objective of this study was to report antimicrobial use in a convenience sample of U.S. beef feedyards for the years 2018 and 2019. In addition to antimicrobial use metrics, also reported are the indications for antimicrobial use and outcomes related to these indications. Antimicrobial use is characterized at the study and feedyard levels for a total of 1,141,846 head of cattle in 20 U.S. feedyards. Antimicrobial use is reported as milligrams of active antimicrobial ingredient per kilogram of liveweight sold (mg/kg-LW) and regimens of antimicrobials per animal year (Reg/AY). Regimens are described by antimicrobial class within use category as characterized by mg of active antimicrobial product per regimen (mg/Reg) and calendar days of administration per regimen (CDoA/Reg). A total of 1,128,515 regimens of medically important antimicrobials were captured from records. The number of regimens/100 head-in (Reg/100 head-in) are described in a subset of 10 feedyards with adequate data granularity to directly determine indications for antimicrobial administration. For the indications of bovine respiratory disease (BRD), Lameness (Lame), Liver Abscess Control (LAC), and Other (e.g., central nervous system disease, cellulitis) the Reg/100 head-in study-level values are 37.1, 0.8, 98.4, and 0.7, respectively, for 2018, with similar values for 2019. The regimens for BRD are further categorized in these 10 feedyards by the use categories in-feed, control of BRD, and individual animal therapy, yielding study level values of 4.6, 19.6, and 12.9 Reg/100 head-in, respectively, for 2018, with similar values for 2019. Outcomes of therapy for individual animal treatment of BRD, Lame, and Other are reported as treatment success, retreatment, or mortality by 30 days after the initial therapy of an animal for a disease. Treatment success rates (no treatment or mortality in the next 30 days) for 2018 in the 10 feedyards with sufficient data granularity are 76.5, 86.5, and 83.0% for BRD, Lame, and Other, respectively. The comparison of these results with other reports of antimicrobial use in North American feedyards highlights how differing approaches in calculating metric values may result in substantially different conclusions regarding antimicrobial use, especially in relation to long-duration uses

Tracking Marsupial Evolution Using Archaic Genomic Retroposon Insertions

Genome-wide comparisons of shared retroposon insertion patterns resolve the phylogeny of marsupials, clearly distinguishing South American and Australian species and lending support to Didelphimorphia as the basal split

Diagnosis and management of bovine respiratory disease

Doctor of PhilosophyDepartment of Diagnostic Medicine and PathobiologyBrad J. White and Robert L. LarsonBovine respiratory disease (BRD) is the most costly disease of cattle in US feedyards and diagnosis based on clinical signs of illness is challenging. Over the course of five independent studies we evaluated the precision of multiple observers assigning clinical illness scores (CIS) to calves with induced Mycoplasma bovis pneumonia. We also evaluated the accuracy of CIS in relation to lung lesions at necropsy. Agreement among observers over all five studies was slight ({kappa]= 0.16; 95% confidence interval, 0.10 to 0.24) and ranged from 0.10 to 0.21 for individual trials. The accuracy of CIS varied based on the pulmonary consolidation score chosen to represent a truly ill animal. Inflammation associated with BRD can lead to significant pulmonary damage and reduced lung function. Treatment for BRD frequently involves antimicrobial administration and occasionally non-steroidal anti-inflammatory drugs. We evaluated how calves experimentally challenged with Mannheimia haemolytica respond to treatment with flunixin meglumine, alone or in combination with the antimicrobial florfenicol. Individual calf response to bacterial pneumonia was highly variable in this study. None of the changes in serum biomarkers, CBC or chemistry parameters provided reliable indicators of the pulmonary inflammation associated with the mild severity of bronchopneumonia in our study. Metaphylaxis is frequently administered to manage the risk of BRD within cohorts of cattle. We evaluated the impact of metaphylactic antimicrobial administration 10 days prior to experimental Mannheimia haemolytica inoculation to mitigate pulmonary lesions. We found that calves receiving tildipirosin had less lung damage and fewer clinical signs of illness compared to calves treated with tulathromycin or saline. Finally, the ability to predict those animals that would not finish the production cycle normally would provide benefits in effectively managing cattle. We evaluated the ability of classification algorithms to accurately predict an individual calf’s outcome based on data available at first identification of and treatment for BRD. We found accuracy of classifiers was dependent on the data recorded by the feedyard and there are sub-groups of calves within feedyard populations where classifiers were highly accurate. These data suggest the importance of pairing the proper classifier with the data available

Predictive Models for Weekly Cattle Mortality after Arrival at a Feeding Location Using Records, Weather, and Transport Data at Time of Purchase

Feedlot mortality negatively affects animal welfare and profitability. To the best of our knowledge, there are no publications on predictive models for weekly all-cause mortality in feedlot cattle. In this study, random forest models to predict weekly mortality for cattle purchase groups (n = 14,217 purchase groups; 860,545 animals) from arrival at the feeding location (Day 1) to Day 42 and cumulative mortality from Day 43 until slaughter were built using records, weather, and transport data available at the time of purchase. Models were evaluated by calculating the root mean squared error (RMSE) and accuracy (as defined as the percent of purchase groups that had predictions within 0.25% and 0.50% of actual mortality). The models had high accuracy (>90%), but the RMSE estimates were high (range = 1.0% to 4.1%). The best predictors were maximum temperature and purchase weight, although this varied by week. The models performed well among purchase groups with low weekly mortality but performed poorly in high mortality purchase groups. Although high mortality purchase groups were not accurately predicted utilizing the models in this study, the models may potentially have utility as a screening tool for very low mortality purchase groups after arrival. Future studies should consider building iterative models that utilize the strongest predictors identified in this study

Highly dynamic animal contact network and implications on disease transmission

Contact patterns among hosts are considered as one of the most critical factors contributing to unequal pathogen transmission. Consequently, networks have been widely applied in infectious disease modeling. However most studies assume static network structure due to lack of accurate observation and appropriate analytic tools. In this study we used high temporal and spatial resolution animal position data to construct a high-resolution contact network relevant to infectious disease transmission. The animal contact network aggregated at hourly level was highly variable and dynamic within and between days, for both network structure (network degree distribution) and individual rank of degree distribution in the network (degree order). We integrated network degree distribution and degree order heterogeneities with a commonly used contact-based, directly transmitted disease model to quantify the effect of these two sources of heterogeneity on the infectious disease dynamics. Four conditions were simulated based on the combination of these two heterogeneities. Simulation results indicated that disease dynamics and individual contribution to new infections varied substantially among these four conditions under both parameter settings. Changes in the contact network had a greater effect on disease dynamics for pathogens with smaller basic reproduction number (i.e. R0 \u3c 2)

A new species of eriophyoid mite (Acari : Eriophyidae) on sugarcane in Australia

Seven species of eriophyoid mites (Acari: Eriophyoidea) are known to attack sugarcane plants (Saccharum spp., Poaceae) and related grasses in various parts of the world, but except for unconfirmed reports of Aceria sacchari and Abacarus sacchari, Australia had been thought to be free of these pests. Herein, Abacarus queenslandiensis n. sp. (Eriophyidae), vagrant on leaf surfaces of sugarcane in Australia, is described. Also, Cathetacarus n. gen. is erected for the distinctive mite, Catarhinus spontaneae Mohanasundaram, 1984. In addition, a key to the eriophyoid mites known to occur on sugarcane plants in the world is given

Predicting Bovine Respiratory Disease Risk in Feedlot Cattle in the First 45 Days Post Arrival

Bovine respiratory disease (BRD) is the leading cause of morbidity in feedlot cattle. The ability to accurately identify the expected BRD risk of cattle would allow managers to detect high-risk animals more frequently. Five classification models were built and evaluated towards predicting the expected BRD risk (high/low) of feedlot cattle within the first 45 days on feed (DOF) and incorporate an economic analysis to determine the potential health cost advantage when using a predictive model compared with standard methods. Retrospective data from 10 U.S. feedlots containing 1733 cohorts representing 188,188 cattle with known health outcomes were classified into high- (≥15% BRD morbidity) or low- (<15%) BRD risk in the first 45 DOF. Area under the curve was calculated from the test dataset for each model and ranged from 0.682 to 0.789. The economic performance for each model was dependent on the true proportion of high-risk cohorts in the population. The decision tree model displayed a greater potential economic advantage compared with standard procedures when the proportion of high-risk cohorts was ≤45%. Results illustrate that predictive models may be useful at delineating cattle as high or low risk for disease and may provide economic value relative to standard methods

Multimodal assessment of biometric changes in injection sites and physiology and behavior in beef calves receiving two different clostridial immunizations compared to negative controls

Clostridial immunizations are commonly administered to cattle, and understanding the physiologic and behavioral effects of vaccination may influence preventative health program design. A randomized, controlled, blinded clinical trial was conducted using multimodal assessment of injection sites, physiologic, and behavioral changes in calves receiving one of two clostridial vaccinations and negative controls. Calf response after injection was monitored daily utilizing physiologic parameters (rectal temperature, pulse, respiratory rate, and body weight), measurements of injection site reaction (lesion surface area, depth, and volume), skin surface temperature (thermography), and avoidance response to pressure at injection site (algometer). Calf behavior was remotely monitored using pedometers, accelerometers, and a remote triangulation system. Calves vaccinated with the clostridial products had larger injection site lesions and greater injection site surface temperature ratios compared to saline controls. The pressure required to stimulate a reaction differed among treatments and this effect was modified by treatment group with control calves requiring more pressure to stimulate avoidance response early in the trial. The percent of time calves spent standing was greater in one of the vaccine groups relative to controls as measured by the accelerometers. The location monitoring system revealed differences among treatment groups relative to time spent at the hay and grain feeding areas. This research illustrates that clostridial vaccination induced multiple changes in injection site, physiological, and behavioral variables as compared to negative controls. The biometric profile generated by the combination of multimodal assessment tools employed in this project demonstrates the advantages of objective assessment to describe effects of vaccine administration

Associations of various physical and blood analysis variables with experimentally induced Mycoplasma bovis pneumonia in calves

Objective-To determine associations of blood analysis variables and orbit and nasal planum surface temperatures with the onset and severity of Mycoplasma bovis pneumonia in calve