WSU Ag Animal Faculty Research Updates, April 2024

Comparative diagnoses of respiratory disease in preweaned dairy calves using sequential thoracic ultrasonography and clinical respiratory scoring

H R Hinnant, L A Elder, R Claus-Walker, C M Mandella, G S Slanzon, L M Parrish, S C Trombetta, C S McConnel.

DOI: 10.1111/avj.13309


Aims: Bovine respiratory disease (BRD) has serious impacts on dairy production and animal welfare. It is most commonly diagnosed based on clinical respiratory signs (CRS), but in recent years, thoracic ultrasonography (TUS) has emerged as a diagnostic tool with improved sensitivity and specificity. This study aimed to assess the alignment of BRD diagnoses based on a Clinical Respiratory Scoring Chart (CRSC) and weekly TUS findings throughout the progression of BRD of variable severity in preweaned Holstein dairy heifers.

Methods: A total of 60 calves on two farms were followed from the 2nd week of life through the 11th week of life and assessed on a weekly basis for CRS and lung consolidation via TUS. The alignment of BRD diagnoses based on CRSC scores and TUS findings was evaluated across disease progression (pre-consolidation, onset, chronic, or recovered) and severity (lobular or lobar lung consolidation) using receiver operator curves and area under the curves combined with Cohen’s kappa (κ), sensitivity, and specificity.

Results: The diagnosis of BRD using CRSC scores ≥5 aligned best with the onset of lobar lung consolidation (>1 cm in width and full thickness). This equated to an acceptable level of discrimination (AUC = 0.76), fair agreement (κ = 0.37), and a sensitivity of 29% and specificity of 99%. Similarly, there was acceptable discrimination (AUC = 0.70) and fair agreement (κ = 0.33) between CRSC ≥5 and the onset of a less severe threshold of disease based on lobular (1-3 cm2 but not full thickness) or lobar consolidation. Discrimination remained acceptable (AUC = 0.71) with fair agreement (κ = 0.28) between CRSC scores ≥2 for nasal discharge and/or cough (spontaneous or induced) and the onset of lobar consolidation. However, sensitivity was <40% across comparisons and outside of the onset of disease there tended to be poor discrimination, slight agreement, and lowered sensitivity between CRS and TUS diagnoses of lobular or lobar consolidation (pre-consolidation, chronic, or recovered). Conversely, specificity was relatively high (≥92%) across comparisons suggesting that CRSC diagnoses indicative of BRD and associated lung consolidation tend to result in few false positive diagnoses and accurate identification of healthy animals.

Conclusions and clinical relevance: Although we found the specificity of clinical signs for diagnosing lung consolidation to be ≥92% across all methods of TUS evaluations, the low levels of sensitivity dictate that clinical assessments lead to many false negative diagnoses. Consequently, depending on clinical signs alone to diagnose BRD within populations of dairy calves will likely result in overlooking a substantial proportion of subclinically affected animals that could inform the success of treatment and prevention protocols and guide management decisions.

Antimicrobial Susceptibility in Respiratory Pathogens and Farm and Animal Variables in Weaned California Dairy Heifers: Logistic Regression and Bayesian Network Analyses

Brittany L Morgan Bustamante, Munashe Chigerwe, Beatriz Martínez-López, Sharif S Aly, Gary McArthur, Wagdy R ElAshmawy, Heather Fritz, Deniece R Williams, John Wenz, Sarah Depenbrock

DOI: 10.3390/antibiotics13010050


Weaned dairy heifers are a relatively understudied production group. Bovine respiratory disease (BRD) is the most common cause of antimicrobial drug (AMD) use, morbidity, and mortality in this production group. The study of antimicrobial resistance (AMR) is complicated because many variables that may affect AMR are related. This study generates hypotheses regarding the farm- and animal-level variables (e.g., vaccination, lane cleaning, and AMD use practices) that may be associated with AMR in respiratory isolates from weaned dairy heifers. A cross-sectional study was performed using survey data and respiratory isolates (Pasteurella multocida, Mannheimia haemolytica, and Histophilus somni) collected from 341 weaned dairy heifers on six farms in California. Logistic regression and Bayesian network analyses were used to evaluate the associations between farm- and animal-level variables with minimum inhibitory concentration (MIC) classification of respiratory isolates against 11 AMDs. Farm-level variables associated with MIC classification of respiratory isolates included the number of source farms of a calf-rearing facility, whether the farm practiced onsite milking, the use of lagoon water for flush lane cleaning, and respiratory and pinkeye vaccination practices. Animal-level variables associated with a MIC classification included whether the calf was BRD-score-positive and time since the last phenicol treatment.

An artificial intelligence approach of feature engineering and ensemble methods depicts the rumen microbiome contribution to feed efficiency in dairy cows

Hugo F Monteiro, Caio C Figueiredo, Bruna Mion, José Eduardo P Santos, Rafael S Bisinotto, Francisco Peñagaricano, Eduardo S Ribeiro, Mariana N Marinho, Roney Zimpel, Ana Carolina da Silva, Adeoye Oyebade, Richard R Lobo, Wilson M Coelho Jr, Phillip M G Peixoto, Maria B Ugarte Marin, Sebastian G Umaña-Sedó, Tomás D G Rojas, Modesto Elvir-Hernandez, Flávio S Schenkel, Bart C Weimer, C Titus Brown, Ermias Kebreab, Fábio S Lima

DOI: 10.1186/s42523-024-00289-5


Genetic selection has remarkably helped U.S. dairy farms to decrease their carbon footprint by more than doubling milk production per cow over time. Despite the environmental and economic benefits of improved feed and milk production efficiency, there is a critical need to explore phenotypical variance for feed utilization to advance the long-term sustainability of dairy farms. Feed is a major expense in dairy operations, and their enteric fermentation is a major source of greenhouse gases in agriculture. The challenges to expanding the phenotypic database, especially for feed efficiency predictions, and the lack of understanding of its drivers limit its utilization. Herein, we leveraged an artificial intelligence approach with feature engineering and ensemble methods to explore the predictive power of the rumen microbiome for feed and milk production efficiency traits, as rumen microbes play a central role in physiological responses in dairy cows. The novel ensemble method allowed to further identify key microbes linked to the efficiency measures. We used a population of 454 genotyped Holstein cows in the U.S. and Canada with individually measured feed and milk production efficiency phenotypes. The study underscored that the rumen microbiome is a major driver of residual feed intake (RFI), the most robust feed efficiency measure evaluated in the study, accounting for 36% of its variation. Further analyses showed that several alpha-diversity metrics were lower in more feed-efficient cows. For RFI, [Ruminococcus] gauvreauii group was the only genus positively associated with an improved feed efficiency status while seven other taxa were associated with inefficiency. The study also highlights that the rumen microbiome is pivotal for the unexplained variance in milk fat and protein production efficiency. Estimation of the carbon footprint of these cows shows that selection for better RFI could reduce up to 5 kg of diet consumed per cow daily, potentially reducing up to 37.5% of CH4. These findings shed light that the integration of artificial intelligence approaches, microbiology, and ruminant nutrition can be a path to further advance our understanding of the rumen microbiome on nutrient requirements and lactation performance of dairy cows to support the long-term sustainability of the dairy community.

Evaluating differences in milk production, reproductive performance, and survival associated with vaginal discharge characteristics and fever in postpartum dairy cows

C.C. Figueiredo, S. Casaro, F. Cunha, V.R. Merenda, E.B. de Oliveira, P. Pinedo, J.E.P. Santos, R.C. Chebel, G.M. Schuenemann, R.C. Bicalho, R.O. Gilbert, S. Rodriguez Zas, C.M. Seabury, G. Rosa, W.W. Thatcher, R.S. Bisinotto, K.N. Galvão

DOI: 10.3168/jds.2023-23905


The objective was to assess differences in productive and reproductive performance, and survival associated with vaginal discharge characteristics and fever in postpartum dairy cows located in Western and Southern states of the U.S.A. This retrospective cohort study included data from 3 experiments conducted in 9 dairies. Vaginal discharge was evaluated twice within 12 DIM and scored on a 5-point scale. The highest score observed for each cow was used for group assignment (VD group) as follows: VD 1 and 2 (VD 1/2; n = 1,174) = clear mucus/lochia with or without flecks of pus; VD 3 (n = 1,802) = mucopurulent with < 50% pus; VD 4 (n = 1,643) = mucopurulent with ≥50% of pus or non-fetid reddish/brownish mucous, n = 1,643; VD 5 = fetid, watery, and reddish/brownish, n = 1,800. All VD 5 cows received treatment according to each herd’s protocol. Rectal temperature was assessed in a subset of VD 5 cows, and subsequently divided into Fever (rectal temperature ≥39.5°C; n = 334) and NoFever (n = 558) groups. A smaller proportion of cows with VD 5 (67.6%) resumed ovarian cyclicity compared with VD 1/2 (76.2%) and VD 4 (72.9%) cows; however, a similar proportion of VD5 and VD 3 (72.6%) cows resumed ovarian cyclicity. A smaller proportion of VD 5 (85.8%) cows received at least one artificial insemination (AI) compared with VD 1/2 (91.5%), VD 3 (91.0%), or VD 4 (91.6%) cows. Although we did not detect differences in pregnancy at first AI according to VD, fewer cows with VD 5 (64.4%) were pregnant at 300 DIM than cows with VD 1/2 (76.5%), VD 3 (76.2%), or VD 4 (74.7%). Hazard of pregnancy by 300 DIM was smaller for VD 5 compared with VD 1/2, VD 3, or VD 4 cows. A greater proportion of VD 5 cows were removed from the herd within 300 DIM compared with other VD groups. There was 760 kg lesser milk production within 300 DIM for VD 5 compared with VD 2, VD 3, and VD 4, whereas VD 2, VD 3, and VD 4 had similar milk production. We did not detect an association between fever at diagnosis of VD 5 and reproductive performance or milk production. A greater proportion of VD 5 cows without fever were removed from the herd by 300 DIM compared with VD 5 cows with fever. Differences in productive and reproductive performance, and removal of the herd were restricted to fetid, watery, and reddish/brownish vaginal discharge, which was independent of fever.

MicroRNAs and Their Associated Genes Regulating the Acrosome Reaction in Sperm of High- versus Low-Fertility Holstein Bulls

V. Kasimanickam, R Kasimanickam 

DOI: 10.3390/ani14060833  


Bioinformatics envisage experimental data as illustrated biological networks, exploring roles of individual proteins and their interactions with other proteins in regulation of biological functions. The objective was to identify differentially expressed miRNAs and their associated genes regulating the acrosome reaction in capacitated sperm of high- compared to low-fertility dairy bulls and to elucidate biological functional pathways using a systems biology approach, featuring miRNA-mRNA cluster analysis. Categorized bovine-specific miRNAs (n = 84) were analyzed by RT-PCR; 19 were differentially expressed in high- compared to low-fertility sperm (p ≤ 0.05, fold regulation ≥ 2 magnitudes). Six miRNAs (bta-miR-129-5p, bta-miR-193a-3p, bta-miR-217, bta-mir-296-5p, bta-miR-27a, and bta-miR-320a) were highly upregulated (p < 0.05; fold regulation ≥ 5 magnitudes) in high- compared to low-fertility sperm. Highly scored integrated genes of differentially expressed miRNAs predicted associations with pathways regulating acrosome vesicle exocytosis, acrosome reaction, and sperm-oocyte binding. The mRNA expressions of genes associated with the acrosome reaction (including hub genes) were greater, ranging from 2.0 to 9.1-fold (p < 0.05) in high- compared to low-fertility capacitated bull sperm. In conclusion, differentially expressed miRNAs in high-fertility bovine sperm regulating acrosome functions have potential for predicting bull fertility.