Comparison of Machine Learning Tree-Based Algorithms to Predict Future Paratuberculosis ELISA Results Using Repeat Milk Tests.

Machine learning algorithms have been applied to various animal husbandry and veterinary-related problems; however, its use in Johne's disease diagnosis and control is still in its infancy. The following proof-of-concept study explores the application of tree-based (decision trees and random forest) algorithms to analyze repeat milk testing data from 1197 Canadian dairy cows and the algorithms' ability to predict future Johne's test results. The random forest models using milk component testing results alongside past Johne's results demonstrated a good predictive performance for a future Johne's ELISA result with a dichotomous outcome (positive vs. negative). The final random forest model yielded a kappa of 0.626, a roc AUC of 0.915, a sensitivity of 72%, and a specificity of 98%. The positive predictive and negative predictive values were 0.81 and 0.97, respectively. The decision tree models provided an interpretable alternative to the random forest algorithms with a slight decrease in model sensitivity. The results of this research suggest a promising avenue for future targeted Johne's testing schemes. Further research is needed to validate these techniques in real-world settings and explore their incorporation in prevention and control programs.

Prevalence of Microbial Isolates Cultured from Endometrial Swab Samples Collected from United Kingdom Thoroughbred Mares from 2014 to 2020.

Determining whether endometrial microbial isolates are pathogens, contaminants, or even part of the "normal" microbiome is extremely complex, particularly given the absence of "gold standard" tests for endometritis. Population-level benchmarking and temporal monitoring can provide novel insights and a wider context to improve understanding. This study aimed to (i) estimate the prevalence of endometrial isolates from swabs of Thoroughbred broodmares in Newmarket, UK between 2014 and 2020; and (ii) evaluate the effects of year, mare age, and cytology findings on isolate prevalence. Generalised linear mixed models with a logit link, both null models and models using year of sampling, mare age, or cytology findings as predictors, were fitted to estimate isolate prevalence. Over the 7-year period, data were available from 18,996 endometrial-swab samples from 6050 mares on 290 premises. The overall isolate prevalence was 35.5% (95% confidence interval (CI) 33.0-37.9), and this varied significantly between years. The most prevalent isolates were ß-hemolytic Streptococcus (17.9; 95% CI: 17-19) and E. coli (10.3%; 95% CI: 9.0-11.6). Isolate prevalence increased with mare age except for E. coli isolates, and with increasing category of cytology findings except for α-hemolytic Streptococcus isolates. The results provide novel estimates of isolate prevalence and highlight knowledge gaps around potential complexities in the interpretation of findings.

Comparison of 2 PCR assays on environmental samples cultured for Mycobacterium avium subsp. paratuberculosis.

Mycobacterium avium subsp. paratuberculosis (MAP) is the causal agent of paratuberculosis, a chronic, contagious, and incurable enteric disease of ruminants. An in-house IS900 PCR assay validated for MAP detection in sheep has been shown to have a higher sensitivity than a commercial PCR and fecal culture. We have now compared the performance of this in-house IS900 PCR assay with a commercial ISMap02 PCR assay for the detection of MAP DNA in bovine dairy farm environmental samples. We purposefully selected 30 culture-positive, 62 culture-negative, and 62 non-interpretable environmental samples. We applied the IS900 PCR assay directly to the frozen inoculum of these samples. Inocula were incubated in an automated system, and growth was confirmed by an acid-fast bacilli stain and the IS900 PCR assay. Among culture-positive samples before incubation, the IS900 PCR assay yielded significantly more positive results than the ISMap02 PCR assay; however, among culture-negative samples, the IS900 PCR assay yielded positive results both before and after incubation. The ISMap02 PCR assay did not flag positively among the culture-negative samples either before or after incubation. The IS900 PCR assay is a sensitive method that can be used to detect MAP DNA in environmental samples before incubation. The ISMap02 PCR assay is a specific method used to detect MAP DNA in environmental samples both before and after incubation.

Gestation Length is Associated With Early-Life Limb Deformities in Thoroughbred Foals.

Flexural and angular limb deformities (LD) are an important cause of early-life morbidity and mortality/euthanasia in Thoroughbred foals. The majority are congenital in origin but, to date, their precise aetiology is poorly understood. We hypothesized that maternal- and pregnancy-level factors, particularly those with potential to influence in-utero growth and development, could play an important role. The aim of this study was therefore to investigate associations between such factors and early-life LD in Thoroughbred foals. A birth cohort was established on seven farms across the United Kingdom and Ireland and details of veterinary interventions for LD in foals in the first six months of life prospectively recorded. Details of dams' signalment, breeding history and reproductive and veterinary history in the breeding season(s) of interest were retrieved retrospectively from stud farm and veterinary records. Associations between mare- and pregnancy-level factors and LD in offspring were assessed using multivariable logistic regression. Records were available for 275 pregnancies in 235 mares, over two breeding seasons. Pregnancies resulted in the birth of 272 live foals, 21% of which (n = 57/272, 95% CI, 16-26) required veterinary intervention for LD in the first six months of life. Odds of LD decreased by 4% per day increase in gestation length between 314 and 381 days (OR 0.96, 95% CI, 0.93-0.99, P = .01). Longer gestation length appears to reduce the odds of early-life LD, including within the normal range of gestation length for Thoroughbred foals. Further work is required to elucidate biological mechanisms behind this association.

Incidence of disease, injury and death in Thoroughbred foals and yearlings on stud farms in the UK and Ireland.

BACKGROUND: Up-to-date estimates of early-life morbidity and mortality in Thoroughbreds are lacking. METHODS: A birth cohort was established on Thoroughbred stud farms across the UK and Ireland. All veterinary interventions for disease or injury between birth and 18 months of age or leaving the study were recorded. Multilevel Poisson regression models with farm and foal as random effects were fitted to estimate incidence rates. RESULTS: Data were available for 3328 foal-months at risk for 275 foals on seven farms. The overall rates of disease and injury requiring veterinary intervention and mortality were 11.9 cases/100 foal-months at risk (95% confidence interval [CI] 8.6-16.2) and 0.2 cases/100 foal-months at risk (95% CI 0.1-0.4), respectively. Almost half (n = 133/273, 49%, 95% CI 43-55) of the live-born cohort required veterinary intervention for musculoskeletal disease or injury, equating to 5.8 cases/100 foal-months at risk (95% CI 4.1-8.2), predominantly reported as developmental orthopaedic disease (DOD). LIMITATIONS: Convenience sampling of participants may affect the generalisability of the findings. CONCLUSIONS: Rates of musculoskeletal disease and injury, in particular DOD, on Thoroughbred stud farms were high. Further work to identify modifiable risk factors and further understanding of the economic impact of these conditions and long-term consequences for musculoskeletal health and performance is required.

Presence or severity of hypophosphatemia is not associated with survival outcome in postpartum downer dairy cows.

OBJECTIVE: To evaluate the association between serum phosphorus concentration and the outcome of postpartum downer cows. ANIMALS: Postpartum downer dairy cows presented over a 22-year period. PROCEDURES: In this cross-sectional study (1994 to 2016), medical records of all postpartum downer cows presented to a referral large animal hospital were reviewed. The association between serum inorganic phosphorus concentration and survival was assessed using a multivariable logistic regression. RESULTS: 907 postpartum downer dairy cows were included and classified as hypophosphatemic (mild: > 2.25 to < 3.25 mg/dL, moderate: > 1.50 to ≤ 2.25 mg/dL, and severe: ≤ 1.50 mg/dL), normophosphatemic (≥ 3.25 and ≤ 8.76 mg/dL) or hyperphosphatemic (> 8.76 mg/dL). Hypophosphatemia was observed in 19.4% of the cows (n = 176). Of those, 54.5% (n = 96) were also hypocalcemic. Overall, 58.4% cows (n = 530) survived after hospitalization. Hypophosphatemia was not significantly associated with the outcome of postpartum downer cows (mild: OR = 1.0, 95% CI: 0.6 to 1.8; moderate: OR = 0.5, 95% CI: 0.2 to 1.1; severe: OR = 1.0, 95% CI: 0.4 to 2.4). CLINICAL RELEVANCE: Low serum phosphorus concentration was frequently observed with hypocalcemia and was not associated with the outcome of postpartum downer cows.

Interpretation and Analysis of Individual Diagnostic Tests and Performance.

Diagnostic tests are performed daily by bovine practitioners at the individual and population level. At the individual level, they help not only for making a diagnosis, but can also serve to rule in or rule out a specific condition, monitor treatment response, establish a prognosis, or to determine infection status. Performing an individual diagnostic test is technical; however, its interpretation and contextualization requires medical and epidemiologic skills that veterinary practitioners are able to master. This article shows the added value of the context of test prescription and correct interpretation highlighting the central role of the veterinary practitioner.

Multivariable analysis to determine risk factors associated with abortion in mares.

Risk factors associated with equine reproductive efficiency have been identified along with those associated specifically with early pregnancy loss (EPL). In contrast, no studies have reported risk factors associated with abortion (loss between day 70 and 300 post-cover). Given the causes of abortion differ to those of EPL, likely too will the risk factors. A retrospective cohort study was carried out to identify risk factors associated with abortion in UK and Irish based Thoroughbreds, collecting data on 20 exposure variables over a five-year period. A generalized linear mixed model was utilized to evaluate the associations between exposure variables and abortion, with clustering of observations accounted for at the mare and farm level. Variables with a likelihood ratio test (LRT) p value <0.2 were entered into the model in a forward stepwise approach. Pregnancy outcome was available on 4,439 pregnancies from 2,510 mares. Having had two or more prior abortions (odds ratio (OR) 7.91, 95% confidence interval (CI) 2.86, 21.88), conceiving on the second or subsequent covered estrous cycle (OR 1.84, 95% CI 1.22, 2.78) and conceiving multiple conceptuses (OR 1.68, 95% CI 1.02, 2.76) were associated with an increased risk of abortion compared to null parous, first estrous cycle covers and singleton conceptions respectively. Increasing paternal age (OR 0.95, 95% CI 0.90, 0.99) was associated with a decreasing risk of abortion. Mare and farm variance were not significant in the final model, LRT p=0.43. These findings provide evidence-based data to inform Thoroughbred breeding management practices to help mitigate abortion risk.

Bayesian Evaluation of Three Serological Tests for Diagnosis of Brucella infections in Dromedary Camels Using Latent Class Models.

Brucellosis is a zoonotic disease with significant economic and public health impacts. The disease has been found in ruminants, including camels, but clinical diagnosis of camel brucellosis is difficult due to the lack of clinical signs. Thus, this study aimed to estimate the sensitivity (Se) and specificity (Sp) of the Buffered Plate Antigen Test (BPAT), Rose Bengal Test (RBT), and indirect ELISA (i-ELISA) for the diagnosis of Brucella infection in dromedary camels imported from Sudan to Egypt. The secondary objective of the study was to calculate the animal-level true prevalence of Brucella infection in imported camels. A cross-sectional study was carried out on 921 apparently healthy camels randomly selected from those imported from Sudan and kept in the quarantine stations in the Shalateen area of the Red Sea Governorate, Egypt, between June 2018 and January 2019. Serum samples were collected and analyzed using BPAT, RBT, and i-ELISA. The posterior estimates [medians and 95% Bayesian probability intervals (95% BPI)] for Se and Sp of the three serological tests were obtained using Bayesian latent class models (BLCMs). The BLCM was fitted with the assumption that the BPAT and RBT tests were conditionally dependent on the true brucellosis status of camels. All tests had comparable and high Se (>86%) and Sp (>98%). The animal-level true prevalence of Brucella infection in imported camels was 8.6% (95% BPI: 6.8 - 10.7). Based on these findings, the three assays could be used for the initial screening of Brucella infection in camels. However, the BPAT and RBT are more suitable for use in camel brucellosis control and eradication program in Egypt because of their low unit cost and fast turnaround time compared to the i-ELISA. In addition, BPAT and RBT could be performed in the field where in-vivo tests are rarely used due to logistic and management constraints.

Date of birth and purchase price as foals or yearlings are associated with Thoroughbred flat race performance in the United Kingdom and Ireland.

Background: Thoroughbred breeders aim to have foals born early in the season, but scientific evidence on the advantages for race performance is scarce and contradictory. Methods: The association between date of birth and purchase price as foal/yearling, with race performance by the end of the second and third years of life of Thoroughbreds racing in flat races in the United Kingdom (UK) and Ireland (IRE) was assessed using negative binomial and zero-inflated negative binomial models on the entire 2014-2015 UK/IRE foal crops (n = 28,282). Results: In total, 6666 and 9456 horses raced in UK/IRE flat racing by the end of their second and third years of life. Prize money and prize money per start decreased with each additional day beyond 1 January that the foal was born. Purchase price as foal and yearling was negatively associated with the number of races run, while it was positively associated with prize money and prize money per start by the end of the third year of life. Conclusions: Foals born early in the season had higher earnings by the end of their second and third years of life than foals born later. Differences were more marked among males than females. The most expensive horses sold as foals or yearlings ran fewer races but earned more prize money and prize money per start than less expensive horses. Results from this population-based analyses may inform strategies and management practices aiming to maximise horses' racing performance potential and increase financial returns.

Bayesian accuracy estimates and fit for purpose thresholds of cytology and culture of endometrial swab samples for detecting endometritis in mares.

The overall aim of this work was to identify the potential impact of misclassification errors associated with routine screening and diagnostic testing for endometritis in mares. Using Bayesian latent class models (BLCM), specific objectives were to: 1) estimate the diagnostic accuracy of cytology and culture of endometrial swab samples to detect endometritis in mares; 2) assess the impact of different cytology thresholds on test accuracy and misclassification costs; and 3) assess the sensitivity (Se) and specificity (Sp) of a diagnostic strategy including both tests interpreted in series and parallel. Diagnostic and pre-breeding endometrial swab samples collected from 3448 mares based at breeding premises located in the South East of England between 2014 and 2020 were retrospectively analysed. Culture results were classified as positive according to three different case definitions: (A) > 90% of the growth colonies were a monoculture; (B) pathogenic or pathogenic and non-pathogenic bacteria were identified; and (C) any growth was observed. Endometrial smears were graded based on the percent of polymorphonuclear cells (PMN) per high power field (HPF). A hierarchical BLCM was fitted using the cross-tabulated results of the three culture case definitions with a cytology threshold fixed at > 0.5% PMN. Fit for purpose cytology thresholds were proposed using a misclassification cost analysis in the context of good antimicrobial stewardship and for varying endometritis prevalence estimates. Median [95% Bayesian credible intervals (BCI)] cytology Se estimates were 6.5% (2.2-11.6), 6.4% (2.2-10.8) and 6.3% (2.2-10.8) for scenario A, B and C, respectively. Median (95% BCI) cytology Sp estimates were 88.8% (83.1-94.8), 88.9% (83.9-93.8) and 88.8% (84.0-93.8) for scenarios A, B and C, respectively. Median (95% BCI) culture Se estimates were 37.5% (29.9-46.0), 42.3% (33.8-51.1) and 46.4% (35.7-55.9) for scenarios A, B and C, respectively. Median (95% BCI) culture Sp estimates were 92.8% (84.3-99.0), 91.5% (82.5-98.0) and 90.8% (80.1-97.4) for scenarios A, B and C, respectively. Regardless of the culture case definition, Se and Sp of cytology (> 0.5% PMN) was lower than previously reported for swab samples in studies using histology as the reference standard test. The misclassification cost term decreased as the cytology threshold increased for all scenarios and all prevalence contexts, suggesting that, regardless of the endometritis prevalence in the population, increasing the cytology threshold would reduce the misclassification costs associated with false positive mares contributing to good antimicrobial stewardship.

Descriptive Study of Medication Usage and Occurrence of Disease and Injury During Gestation in Thoroughbred Broodmares.

The study aimed to (1) describe the use of reproductive therapeutics; (2) estimate the incidence of disease and injury; and (3) describe non-reproductive medications administered during pregnancy in Thoroughbred broodmares. A prospective birth cohort was established on seven farms across the UK and Ireland. Details of dams' signalment, breeding history, reproductive management during the breeding season(s) and veterinary-attended episodes of illness or injury and medication usage during gestation were retrieved retrospectively for 275 pregnancies in 235 mares over two breeding seasons. Results are reported at pregnancy-level of mares with data available. Preoestrus medications, ovulatory agents and post-covering treatments were administered to 55% (n = 85/155, 95% Confidence interval (CI) 47-62), 64% (n = 101/157, 95% CI 57-71) and 73% (n = 109/150, 95% CI 65-79) of mares respectively. Antibiotics were utilized in 69% (n = 75/109, 95% CI 60-77) of post-covering treatments. Of mares with no visible fluid on post-covering ultrasound, 37% (n = 24/65, 95% CI 26-49) still received treatment. Thirty-four percent (n = 70/203, 95% CI 28-41) of mares suffered at least one veterinary-attended episode of disease or injury, with conditions affecting the musculoskeletal system (23%, n = 46/203, 95%CI 17-29) and placentitis (5%, n = 10/203, 95% CI 3-9) most prevalent. Forty-seven percent (n = 95/203, 95% CI 40-54) of mares received at least one non-reproductive medication during gestation, antibiotics (25%, n = 51/203, 95% CI 20-31) and non-steroidal anti-inflammatory drugs (23%, n = 47/203, 95% CI 18-29) being most frequently prescribed. Post-covering treatments often included antibiotics and were sometimes given in the absence of fluid, highlighting a need to further understand therapeutic rationale. Disease occurrence and medication usage during gestation were frequent and warrant additional investigation.

Interpretation of cerebrospinal fluid analysis from recumbent cows using different thresholds of red blood cell count.

BACKGROUND: Hemodilution of the cerebrospinal fluid (CSF) could confound interpretation of results. Accurately predicting total nucleated cells count (TNCC) and total protein concentration (TPC) attributable to hemodilution is difficult. OBJECTIVE: To determine the effects of hemodilution on TPC and TNCC in bovine CSF. METHODS: Retrospective review of CSF analysis results of downer dairy cows treated at Centre hospitalier universitaire vétérinaire between January 2006 and December 2014. Descriptive statistics were performed using 3 scenarios. RESULTS: Among the 235 samples included, red blood cell (RBC) count (RBCC) ranged from 0 to 869 220 RBC/µL (median = 6.6), TPC ranged from 0.04 to 6.51 g/L (median = 0.27), and TNCC ranged from 0 to 7500 cell/µL (median = 1.1). Among the 157 samples that had <30 RBC/µL (a threshold used in other species), TPC and TNCC varied between 0.13 and 1.06 g/L (median = 0.27) and between 0 and 31.4 cell/µL (median = 0.6), respectively. Eighty-four samples had TPC <0.25 g/L and TNCC ≤4.5 cell/µL. Among those 84 samples, RBCC varied between 0 and 1290 RBC/µL (median = 4.7). In 20 samples, TNCC was 0 with a variation in RBCC between 0 and 840 RBC/µL (median = 3.9). No strong correlations between RBCC and TNCC and TPC were found. CONCLUSIONS: A cutoff around 200 RBC/µL is proposed as clinically meaninful in bovine CSF. Results between 200 and 1290 RBC/µL are equivocal.

Bayesian estimation of sensitivity and specificity of fecal culture, fecal PCR and serum ELISA for diagnosis of Mycobacterium avium subsp. paratuberculosis infections in sheep.

The objective of the present study was to evaluate the diagnostic accuracy of the individual fecal culture (IFC), fecal PCR (FPCR), and serum ELISA for the detection of Mycobacterium avium subsp. paratuberculosis (MAP) infections in sheep from four governorates in Egypt, using a latent class model (LCM) fitted within a Bayesian framework. Furthermore, the within-governorate prevalence of MAP infection in sheep was estimated as a secondary objective. Fecal and blood samples were collected from 370 sheep in four Egyptian governorates. Fecal samples were analyzed by IFC and RT-PCR based on ISMav2 gene, while ELISA was performed on serum samples. The sensitivity (Se) and specificity (Sp) of the three diagnostic tests were estimated using a three-tests-four-populations Bayesian LCM to obtain posterior estimates [medians and 95% Bayesian credible intervals (95% BCI)] for each parameter. The median Se estimates (95% BCI) for IFC, FPCR, and serum ELISA were 31.8% (22.8-41.4), 49.7% (31.8-79.9), and 61.2% (39.8-81.4), respectively. The median Sp estimates (95% BCI) for IFC, FPCR, and serum ELISA were 97.7% (96.1-98.9), 97.7% (95.6-99.5), and 98.4% (96.9-99.3), respectively. The median within-governorate paratuberculosis prevalence (95% BCI) was 5.2% (1.1-13.6), 8.4% (2.9-17.7), 9.4% (3.0-20.7), and 18.2% (10.5-29.5) for the Gharbia, Menoufia, Qalyubia, and Kafr El-Sheikh governorates, respectively. In conclusion, at a ratio of the optical density (OD) sample/OD positive control threshold of > 45%, ELISA showed the highest Se among the three tests and comparable Sp to IFC and FPCR. The test ELISA evaluated in this study is an interesting alternative for detecting MAP in sheep due to its higher Se, lower cost, and shorter turnaround laboratory time compared to IFC and FPCR.

Bayesian accuracy estimates of environmental sampling for determining herd paratuberculosis infection status and its association with the within-herd individual fecal culture prevalence in Québec dairies.

The objectives of this retrospective analysis were to: 1) estimate the diagnostic sensitivity (Se) and specificity (Sp) of bacterial culture of environmental samples for determining Mycobacterium avium subsp. paratuberculosis (MAP) infection status in Québec dairies, using a Bayesian Latent Class Model (BLCM); and 2) determine the association between the number of positive environmental samples and the individual fecal culture (IFC) apparent and true MAP within-herd prevalence. Environmental and individual fecal samples were collected from 87 commercial dairy herds participating in previous research projects. Environmental samples included two composite samples of 20 g collected from different locations within each of the following sites: an area where manure from the majority of adult cattle accumulates, a manure storage area and another site of manure accumulation chosen by the veterinarian. Samples were cultured using the MGIT Para TB culture liquid media and the BACTEC MGIT 960 system. The Se and Sp of environmental sampling were estimated using a one-test-one-population BLCM. Herds were considered positive for environmental sampling if at least one out of the six samples collected was positive. The apparent and true IFC within-herd MAP prevalence estimates for each herd were obtained using a two-stage cluster BLCM, then merged in a single dataset with the environmental sample results. The association between the within-herd MAP prevalence results (apparent and true), and the number of positive environmental samples was assessed using a zero-inflated negative binomial (ZINB) model. In all BLCMs, median posterior estimates and 95 % Bayesian credible intervals (BCI) were obtained with OpenBUGS statistical freeware. Se and Sp of environmental sampling were 43.7 % (95 % BCI: 32.5-55.5) and 96.2 % (95 % BCI: 84.2-99.8), respectively. Overall, the number of positive environmental samples increased with the apparent and true MAP within-herd prevalence. The true prevalence was higher than the apparent prevalence for a given number of positive environmental samples. The probability of not observing a positive environmental sample decreased with the prevalence. Despite its imperfect accuracy, environmental sampling is an inexpensive and non-invasive sampling method to determine MAP infection status in tie-stall herds that can be used as a proxy to estimate the true within-herd prevalence. The absence of positive environmental samples in a single sampling visit is likely an indicator of a very low within-herd prevalence rather than being MAP exempt.

Survival and prognostic indicators in downer dairy cows presented to a referring hospital: A retrospective study (1318 cases).

BACKGROUND: Downer cow syndrome, a common problem in dairy cattle, represents a diagnostic and therapeutic challenge for the attending veterinarian. Identifying prognostic indicators and assessing the odds of survival may improve the accuracy of the clinician's prognosis at the time of diagnosis. OBJECTIVE: To describe a population of downer dairy cows referred to a hospital and investigate predictors of outcome. ANIMALS: Recumbent adult dairy cows (cows unable or unwilling to stand without help) treated at a referral hospital. METHODS: Data at the time of admission were collected from medical records of downer dairy cows treated at the Centre Hospitalier Universitaire Vétérinaire between 1994 and 2016. Simple and multivariable logistic regression analyses were performed to assess the association of predictors with the outcome. RESULTS: Among 1318 cows included, 727 (55%) cows were discharged, and 591 (45%) cows died or were euthanized. Cows with longer time of recumbency before referral (odds ratio [OR] = 3.6), tachycardia (100-120 beats per minute [bpm], OR = 1.93; >120 bpm, OR = 2.92), tachypnea (OR = 1.76), hypothermia (OR = 2.08), anemia (OR = 3.30), neutropenia (OR = 1.7), high aspartate aminotransferase activity (500-1000 U/L, OR = 2.16; >1000 U/L, OR = 6.69), and increased serum creatinine concentration (OR = 1.75) had higher odds of nonsurvival. CONCLUSIONS AND CLINICAL IMPORTANCE: These findings may help the practitioner to consider treatment options and decide if referral is likely beneficial based on the odds of success. Early recognition of low chance of survival may facilitate an early decision for euthanasia.

Retrospective analysis of the population dynamics and racing outcomes of the 2014 and 2015 UK and Ireland Thoroughbred foal crops.

BACKGROUND: Up-to-date figures on early losses of Thoroughbreds from the racing industry can inform strategies to improve retention and incentivise traceability of Thoroughbreds during this early life period. METHODS: Data on Thoroughbred mares bred in 2013-2014 and training, racing and sales information of their live offspring were analysed. The proportions and 95% confidence intervals (95% CI) of the entire 2014-2015 United Kingdom and Ireland foal crops that entered training, raced, were imported and/or exported between birth and the end of their third year of life, as well as the racing performance of these horses as 2- and 3-year-olds were described. RESULTS: A total of 20,661 mares produced 28,282 live foals. Of them, 47.2% (95% CI: 46.7-47.8; n = 13,354) entered training by the end of their third year of life. Of these, 10,595 (79.3%; 95% CI: 78.7-80.0) raced at least once. Around 20% (n = 5712) of horses were exported by the end of their third year of life, of which 3526 (61.7%) had been in training. The overall mortality during the study period was 7.6% (n = 2123). CONCLUSION: A considerable proportion of Thoroughbreds had not entered training by 3 years of age but of those that had, the proportion that raced at least once was high. Further research is needed to establish reasons for premature losses from the industry.

Accuracy of leukocyte esterase test, endometrial cytology and vaginal discharge score for diagnosing postpartum reproductive tract health status in dairy cows at the moment of sampling, using a latent class model fit within a Bayesian framework.

The objectives of this retrospective study were: 1) to determine the sensitivity (Se) and specificity (Sp) of leukocyte esterase test (LE), endometrial cytology (CYTO) and vaginal discharge score (VDS) for diagnosis of reproductive tract diseases in dairy cows at the moment of sampling; 2) to assess the impact of different thresholds on test accuracy and misclassification costs; and 3) to quantify herd prevalence of reproductive tract diseases in dairy farms from Québec, Canada. Data from 2092 cows (39 herds) enrolled in two randomized control trials were included. Cows were examined at 35 (± 7) days in milk using LE, CYTO, and VDS to determine their reproductive tract health status. A latent class model assuming conditional dependence of CYTO and LE was fit within a Bayesian framework. Non-informative priors were used for the Se and Sp of LE, CYTO, and VDS, while prior information for disease prevalence was obtained from expert opinions (mode = 20%, 5th percentile = 10%). Posterior inferences (median and 95% Bayesian credible intervals; BCI) were obtained using the WinBUGS statistical freeware. An initial model was built using thresholds of ≥ 1 (small amount of leukocytes), of ≥ 6%, and of ≥ 3 (mucopurulent discharge) for the LE, CYTO, and VDS, respectively. Then, the impact on tests accuracy and misclassification costs of using different thresholds was explored. Optimal thresholds balancing the need for good antimicrobial stewardship and animal health considerations were proposed. The optimal thresholds obtained in the final model were: LE ≥ 2 (moderate amount of leukocytes), CYTO ≥ 6%, and VDS ≥ 2 (mucus with flecks of pus). In the final model, median (95% BCI) Se for LE, CYTO and VDS were 42.6% (38.8-47.0), 45.9% (41.9-50.7), and 64.2% (59.1-70.3), respectively. Median Sp was 90.9% (88.0-93.6) for LE, 92.2% (89.2-94.9) for CYTO and 96.6% (91.3-99.8) for VDS. Median within-herd prevalence of reproductive tract disease was estimated at 47.9% (39.0-56.7). At a threshold ≥ 2 (mucus with flecks of pus), VDS had the highest Se and Sp among the tests evaluated. The LE is an interesting diagnostic alternative for detecting reproductive tract disease in dairy cows. At a threshold ≥ 2 (moderate amount of leukocytes), LE Se and Sp were comparable to those of CYTO. This is the first study reporting the accuracy of LE, CYTO, and VDS for diagnosing reproductive tract diseases in dairy cows at the moment of sampling.

Frequency and distribution of foot lesions identified during cattle hoof trimming in the Province of Antioquia, Colombia (2011-2016).

Lameness is a severe welfare problem in cattle and has a detrimental effect on longevity, productivity, and reproductive performance. This study aimed to describe the frequency and distribution of foot lesions in cattle using hoof trimming records over a period of 6 years in the Province of Antioquia (Colombia). The data collection instrument enabled differentiation between limbs, digits, and views. The Claw Lesion Identification in Dairy Cattle brochure was the reference for foot lesion identification. A total of 1814 foot lesions observations, recorded from 1120 cows in 71 herds, were analyzed and 11 different foot lesions were identified. Non-infectious foot lesions were more common than infectious (94.4 vs 5.6%). White line disease was more frequently observed in the hind limbs (79.6%) compared to the front limbs (20.4%), and more frequent in medial claws of the front limbs (70.3%) compared to lateral claws (29.7%). In hind limbs, the lateral claws were more commonly affected (65.7%) compared to the medial claws (34.3%). Claw zone 3 was affected in 61.3% of the cases, followed by zones 2 (21.7%) and 1 (17%). Although our data are from a limited area of the country, they are consistent with published and anecdotal reports of foot lesions in cattle in Colombia and worldwide. Our results suggest that there is need for additional prospective research under Colombian dairy cattle management conditions to better understand the lameness and benefit of trimming intervention.

Estimating diagnostic accuracy of fecal culture in liquid media for the detection of Mycobacterium avium subsp. paratuberculosis infections in Québec dairy cows: A latent class model.

A latent class model fit within a Bayesian framework was used to estimate the sensitivity and specificity of individual fecal culture (IFC) in liquid medium (Para TB culture liquid medium and BACTEC MGIT 960 system) for the detection of Mycobacterium avium subsp. paratuberculosis (MAP) infections in Québec dairy cows. As a secondary objective, the within-herd paratuberculosis prevalence was estimated. A dataset including 21 commercial Québec dairy herds participating in previous research projects was retrospectively analyzed. In total, 1386 adult cows on which both IFC and serum-ELISA were available were included. The selected latent class model assumed conditional dependence between the tests. Non-informative priors for IFC accuracy and paratuberculosis prevalence were used while informative priors, obtained from the literature, were used for serum-ELISA accuracy. The WinBUGS statistical freeware was used to obtain posterior estimates (medians and 95% Bayesian credibility intervals (95% BCI)) for each parameter. The sensitivity and specificity estimates for IFC were 34.4% (95% BCI: 20.3-66.1) and 99.5% (95% BCI: 98.6-100), respectively. Sensitivity and specificity for serum-ELISA were 27.3% (95% BCI: 18.1-38.3) and 97.4% (95% BCI: 96.6-98.0). Median paratuberculosis within herd prevalence was estimated to be 0.3% (0-3.3). In conclusion, a higher sensitivity of IFC compared to serum-ELISA was observed both in the unconditional and conditional dependent models. Since the sensitivity of both IFC and serum-ELISA was relatively low, conditional dependence between the tests is more likely in the true disease positive animals. We hypothesize that conditional dependence arises because an unmeasured covariate influences the performance of both tests among disease positive animals causing both tests to incorrectly misclassify the animal as negative. One limitation of this study was the very low within herd prevalence of the participant herds.