Genomic analysis of bovine respiratory disease and lung consolidation in preweaned Holstein calves using clinical scoring and lung ultrasound.

Bovine respiratory disease (BRD) is a leading cause of morbidity and mortality in dairy calves, with detrimental long-term effects that include stunted growth, increased age at first calving, and decreased milk production in first lactation. The objectives of this study were to establish a protocol for objective and efficient assessment of BRD phenotypes in preweaned dairy calves, develop a genomic reference population with well-defined clinical and subclinical phenotypes, identify chromosomal regions associated with BRD in a genome-wide association study, estimate genetic parameters of BRD, and predict genomic breeding values of dairy calves. A total of 1,107 Holstein calves from 6 dairy farms in southern Wisconsin were examined using clinical respiratory scoring and lung ultrasound at 3 and 6 wk of age. The clinical respiratory score was based on visual appraisal of eyes, nose, ears, cough, and temperature. Lung ultrasound scores were assigned based on the amount of consolidation present. Calves were genotyped with a commercially available SNP array and after quality control and imputation to higher density, 690,291 SNP markers and 1,014 individuals remained. Single-step genome-wide association study and single-step genomic best linear unbiased prediction were applied to binary 3- and 6-wk phenotypes considered as overall respiratory healthy versus affected (RESP3, RESP6) or as presence or absence of lung consolidation (CON3, CON6). Lung ultrasound combined with a clinical scoring system allowed for efficient and objective assessment for the prevalence of BRD. Proportions of variance attributed to 1-Mb non-overlapping windows suggested genomic regions that may contain putative candidate genes, most notably regions on Bos taurus autosomes 1, 6, 7, 10, 11, 12, 15, 17, 18, 27, and 28 that explained 0.70 to 1.45% of the genetic variance. Heritability estimates were higher at 3 wk (0.214 and 0.241 for CON3 and RESP3, respectively) than 6 wk (0.084 and 0.111 for CON6 and RESP6, respectively), and mean reliabilities of genomic estimated breeding vales for calves with genotypes and phenotypes ranged from 0.12 for CON6 to 0.30 for RESP3.

Bayesian estimation of sensitivity and specificity of systematic thoracic ultrasound exam for diagnosis of bovine respiratory disease in pre-weaned calves.

Among the different clinical presentations of bovine respiratory disease, active pneumonia, defined as an infection of the lower airway with signs of inflammation, is the most important to diagnose correctly so appropriate treatment can be initiated. Diagnostic tests that accurately identify cases of active pneumonia are lacking; however, thoracic ultrasonography (TUS) seems promising. The primary objective of this study was to estimate the accuracy of TUS compared to reference tests for the diagnosis of active pneumonia in pre-weaned calves, using a latent-class model method (LCM). The tests used for comparison were the Wisconsin Clinical Respiratory Scoring Chart (CRSC, positive if ≥5) and serum haptoglobin concentration (Hap, positive if ≥15 mg/dL). Secondary objectives were to assess the incremental value on TUS accuracy of combining TUS of the right cranial part and caudal parts, and to determine the accuracy of various thresholds for depth of consolidation (≥0 cm, ≥1 cm, or ≥3 cm) for diagnosis of active pneumonia. One population of veal calves (n = 209) and one of dairy calves (n = 301) were enrolled. TUS, CRSC and Hap were all performed on each calf on the same day. TUS was performed by screening the mid to ventral portion of the lung caudal of the heart (the caudal sites), as well as the right parenchyma cranial to the heart (the cranial site). The maximal depth of consolidation (DEPTH) on TUS was recorded and noted separately for caudal and cranial sites. Different TUS cases were defined according to site and DEPTH. The accuracy of TUS was estimated by LCM for three tests conducted in two populations. Prevalence of active pneumonia was low (0.05) in both populations. In general, higher minimal consolidation depth thresholds led to increased TUS specificity (Sp) estimates, with minimal effects on TUS sensitivity (Se). With a TUS DEPTH threshold of ≥3 cm, adding TUS of the cranial site had little effect on accuracy. Using the ≥3 cm threshold with caudal sites only, posterior Se and Sp median estimates of 0.89 (95%BCI: 0.55, 1.0) and 0.95 (95%BCI: 0.92, 0.98), respectively, were obtained. In conclusion, in populations with low active pneumonia prevalence, adding TUS of the cranial site did not enhance the performance of the test. We suggest using a DEPTH threshold of ≥3 cm solely on caudal sites to detect active pneumonia.

Herd-level prevalence of the ultrasonographic lung lesions associated with bovine respiratory disease and related environmental risk factors.

Bovine respiratory disease complex (BRD) is a major calf disease during the preweaning period. Thoracic ultrasound (TUS) has been recently described as a reliable tool for assessing BRD-associated lung lesions. The objectives of this study were to define the herd-level prevalence of lung consolidation assessed by TUS (CONSTUS). A total of 39 Québec dairy herds were randomly chosen to participate in this cross-sectional study. Between 6 and 12 preweaned calves were examined for signs of CONSTUS defined by any site with ≥3 cm consolidated lung tissue during 1 visit in summer and 1 visit in winter. Herd questionnaire focused on calf health and housing data [airborne bacteria (aerobic, coliform, yeasts and mold counts), air drafts, temperature, hygrometry, and ammonia levels] were also collected during these visits looking for potential association with CONSTUS prevalence. The median herd-level of CONSTUS prevalence (interquartile range) were 8% (0-22%) in summer and 15% (0-35%) in winter. Multivariable analyses showed that season was associated with an increased CONSTUS prevalence [10.0 vs. 19.3%; odds ratio (OR) = 2.16], as well as group housing during preweaned period (9.6 vs. 20.0%; OR = 2.37) and perceived BRD problem by the farmer (10.6 vs. 18.3%; OR = 1.89). Despite tremendous changes in calves' environment between winter and summer, none of the housing variables were associated with the CONSTUS prevalence in this study. Based on the observed CONSTUS prevalence ranges in the present study (herds in the lower prevalence quartile), an achievable goal of none of 12 calves with consolidation ≥3 cm can potentially be used to define a low-BRD risk herd.

Bayesian estimation of the accuracy of the calf respiratory scoring chart and ultrasonography for the diagnosis of bovine respiratory disease in pre-weaned dairy calves.

There is currently no gold standard method for the diagnosis of bovine respiratory disease (BRD) complex in Holstein pre-weaned dairy calves. Systematic thoracic ultrasonography (TUS) has been used as a proxy for BRD, but cannot be directly used by producers. The Wisconsin calf respiratory scoring chart (CRSC) is a simpler alternative, but with unknown accuracy. Our objective was to estimate the accuracy of CRSC, while adjusting for the lack of a gold standard. Two cross sectional study populations with a high BRD prevalence (n=106 pre-weaned Holstein calves) and an average BRD prevalence (n=85 pre-weaned Holstein calves) from North America were studied. All calves were simultaneously assessed using CRSC (cutoff used ≥ 5) and TUS (cutoff used ≥ 1cm of lung consolidation). Bayesian latent class models allowing for conditional dependence were used with informative priors for BRD prevalence and TUS accuracy (sensitivity (Se) and specificity (Sp)) and non-informative priors for CRSC accuracies. Robustness of the model was tested by relaxing priors for prevalence or TUS accuracy. The SeCRSC (95% credible interval (CI)) and SpCRSC were 62.4% (47.9-75.8) and 74.1% (64.9-82.8) respectively. The SeTUS was 79.4% (66.4-90.9) and SpTUS was 93.9% (88.0-97.6). The imperfect accuracy of CRSC and TUS should be taken into account when using those tools to assess BRD status.

Assessment of L-lactatemia as a predictor of respiratory disease recognition and severity in feedlot steers.

The bovine respiratory disease complex (BRD) is a major health issue in feedlot cattle and one of the primary reasons for antimicrobial use in the North American feedlot industry. The purpose of the present study was to assess blood L-lactate levels of feedlot steers at high risk of developing BRD during the early feeding period. Blood samples were obtained at initial processing and again after BRD confirmation (using bronchial lavage or thoracic ultrasound exam). The study involved 232 recently weaned steers received at a single research feedlot that were processed without metaphylactic antimicrobial treatment. Blood samples were obtained for determination of L-lactatemia and temperament scores (very quiet or stoic [score 1], average [score 2] and very excited [score 3]) were systematically assigned at initial processing. A subsample of calves that were later confirmed as cases of BRD were sampled at first pull (day 0), and at subsequent observation points on days 3, 6, 9 and 15 following initial BRD diagnosis for blood lactate determination as a potential indicator of subsequent death. The clinical BRD cumulative incidence in the cohort was 38% (87/232). Temperament was associated with the probability of becoming a BRD case during the early feeding period. Stoic or very excited calves showed 2.2 times higher odds (95%CI: 1.3, 3.8) of becoming BRD cases compared to calves with average temperament. The impact of L-lactatemia differed by temperament strata. In calves with a temperament score of 2 (average temperament) every 1-log unit increase of lactatemia at processing resulted in 1.9 times higher odds (95% CI: 1.2, 3.1) of becoming a BRD case; this relationship was not significant in calves with a score of either 1 or 3. Twenty-nine confirmed BRD cases were studied for the dynamic lactate assessment analysis. L-lactate at first pull was not significantly different between survivors (median 3.3mmol/L; range 0.8-7.8mmol/L) and non-survivors (median 2.7mmol/L; range: 1.6-5.4mmol/L) steers. However, the dynamic assessment of L-lactatemia was associated with the hazard of death using Cox proportional hazard survival analysis. A 1-log increase of lactatemia increased the hazard of dying prior to the next observation by a factor of 36.5 (95% CI: 3.5-381.6). For calves showing a normal temperament score (i.e. temperament score of 2), a misclassification cost term analysis was conducted to identify potential L-lactate test thresholds for identifying future BRD steers. When planned test usage was for informing decision of administering or not a metaphylactic treatment at processing, experts agreed that false-negative (not treating a calf that would have benefit from treatment) to false-positive (wrongfully treating a calf that would have remained healthy) health costs ratio ranged from 8:1 to 20:1. In this situation, a threshold of 5mmol/L would have best informed treatment decision. When using L-lactate for informing the type of antimicrobial used at processing, false-negative to false-positive health costs ratio ranging from 1:1 to 3:1 could be expected and, again, a L-lactate threshold of 5.0mmol/L would have minimized the costs associated with calves' misclassification and could be used to identify calves that would benefit from a more efficient metaphylactic treatment. This study provides an interesting perspective on the potential application of chute-side markers or diagnostic tests to stratify the risk of future pull for BRD in cattle during processing in order to adapt antimicrobial treatments accordingly.

Short communication: ultrasonographic assessment of the thorax as a fast technique to assess pulmonary lesions in dairy calves with bovine respiratory disease.

The aim of this study was to assess inter- and intraoperator agreement when assessing lung consolidation secondary to bovine respiratory disease (BRD) by thoracic ultrasonography. Ten calves were blindly assessed by 3 operators with varying expertise in thoracic ultrasound to look for lung consolidation and the presence of comet-tail artifacts (COMT). Systematic ultrasonography of the thorax was performed using an 18-site per side assessment with a linear 8.5-MHz probe. The status of the calves [healthy (n=4) vs. treated for BRD (n=6)] was not known by the operators. The interoperator kappa agreement for detecting consolidation was moderate to almost perfect (from 0.6 to 1.0) depending on the operator's experience (diagnosis of consolidation if depth ≥1cm). The intraclass correlation coefficient for consistency was 0.71 for a single measurement and 0.88 for average measurement. The intraclass correlation coefficient for agreement was 0.73 for single measurements and 0.89 for average measurements. These values were considered good for single measurements and excellent for average measurements. Systematic ultrasonography of the thorax can be used routinely to assess lung consolidation in dairy calves and can therefore be of importance, especially for assessment of subclinical BRD.