Multipopulational transcriptome analysis of post-weaned beef cattle at arrival further validates candidate biomarkers for predicting clinical bovine respiratory disease.

Bovine respiratory disease (BRD) remains the leading infectious disease in post-weaned beef cattle. The objective of this investigation was to contrast the at-arrival blood transcriptomes from cattle derived from two distinct populations that developed BRD in the 28 days following arrival versus cattle that did not. Forty-eight blood samples from two populations were selected for mRNA sequencing based on even distribution of development (n = 24) or lack of (n = 24) clinical BRD within 28 days following arrival; cattle which developed BRD were further stratified into BRD severity cohorts based on frequency of antimicrobial treatment: treated once (treated_1) or treated twice or more and/or died (treated_2+). Sequenced reads (~ 50 M/sample, 150 bp paired-end) were aligned to the ARS-UCD1.2 bovine genome assembly. One hundred and thirty-two unique differentially expressed genes (DEGs) were identified between groups stratified by disease severity (healthy, n = 24; treated_1, n = 13; treated_2+, n = 11) with edgeR (FDR ≤ 0.05). Differentially expressed genes in treated_1 relative to both healthy and treated_2+ were predicted to increase neutrophil activation, cellular cornification/keratinization, and antimicrobial peptide production. Differentially expressed genes in treated_2+ relative to both healthy and treated_1 were predicted to increase alternative complement activation, decrease leukocyte activity, and increase nitric oxide production. Receiver operating characteristic (ROC) curves generated from expression data for six DEGs identified in our current and previous studies (MARCO, CFB, MCF2L, ALOX15, LOC100335828 (aka CD200R1), and SLC18A2) demonstrated good-to-excellent (AUC: 0.800-0.899; ≥ 0.900) predictability for classifying disease occurrence and severity. This investigation identifies candidate biomarkers and functional mechanisms in at arrival blood that predicted development and severity of BRD.

Comprehensive at-arrival transcriptomic analysis of post-weaned beef cattle uncovers type I interferon and antiviral mechanisms associated with bovine respiratory disease mortality.

BACKGROUND: Despite decades of extensive research, bovine respiratory disease (BRD) remains the most devastating disease in beef cattle production. Establishing a clinical diagnosis often relies upon visual detection of non-specific signs, leading to low diagnostic accuracy. Thus, post-weaned beef cattle are often metaphylactically administered antimicrobials at facility arrival, which poses concerns regarding antimicrobial stewardship and resistance. Additionally, there is a lack of high-quality research that addresses the gene-by-environment interactions that underlie why some cattle that develop BRD die while others survive. Therefore, it is necessary to decipher the underlying host genomic factors associated with BRD mortality versus survival to help determine BRD risk and severity. Using transcriptomic analysis of at-arrival whole blood samples from cattle that died of BRD, as compared to those that developed signs of BRD but lived (n = 3 DEAD, n = 3 ALIVE), we identified differentially expressed genes (DEGs) and associated pathways in cattle that died of BRD. Additionally, we evaluated unmapped reads, which are often overlooked within transcriptomic experiments. RESULTS: 69 DEGs (FDR<0.10) were identified between ALIVE and DEAD cohorts. Several DEGs possess immunological and proinflammatory function and associations with TLR4 and IL6. Biological processes, pathways, and disease phenotype associations related to type-I interferon production and antiviral defense were enriched in DEAD cattle at arrival. Unmapped reads aligned primarily to various ungulate assemblies, but failed to align to viral assemblies. CONCLUSION: This study further revealed increased proinflammatory immunological mechanisms in cattle that develop BRD. DEGs upregulated in DEAD cattle were predominantly involved in innate immune pathways typically associated with antiviral defense, although no viral genes were identified within unmapped reads. Our findings provide genomic targets for further analysis in cattle at highest risk of BRD, suggesting that mechanisms related to type I interferons and antiviral defense may be indicative of viral respiratory disease at arrival and contribute to eventual BRD mortality.

Whole blood transcriptomic analysis of beef cattle at arrival identifies potential predictive molecules and mechanisms that indicate animals that naturally resist bovine respiratory disease.

Bovine respiratory disease (BRD) is a multifactorial disease complex and the leading infectious disease in post-weaned beef cattle. Clinical manifestations of BRD are recognized in beef calves within a high-risk setting, commonly associated with weaning, shipping, and novel feeding and housing environments. However, the understanding of complex host immune interactions and genomic mechanisms involved in BRD susceptibility remain elusive. Utilizing high-throughput RNA-sequencing, we contrasted the at-arrival blood transcriptomes of 6 beef cattle that ultimately developed BRD against 5 beef cattle that remained healthy within the same herd, differentiating BRD diagnosis from production metadata and treatment records. We identified 135 differentially expressed genes (DEGs) using the differential gene expression tools edgeR and DESeq2. Thirty-six of the DEGs shared between these two analysis platforms were prioritized for investigation of their relevance to infectious disease resistance using WebGestalt, STRING, and Reactome. Biological processes related to inflammatory response, immunological defense, lipoxin metabolism, and macrophage function were identified. Production of specialized pro-resolvin mediators (SPMs) and endogenous metabolism of angiotensinogen were increased in animals that resisted BRD. Protein-protein interaction modeling of gene products with significantly higher expression in cattle that naturally acquire BRD identified molecular processes involving microbial killing. Accordingly, identification of DEGs in whole blood at arrival revealed a clear distinction between calves that went on to develop BRD and those that resisted BRD. These results provide novel insight into host immune factors that are present at the time of arrival that confer protection from BRD.

A randomized controlled trial to test the effect of on-arrival vaccination and deworming on stocker cattle health and growth performance.

Our objective was to determine the effect of vaccination and deworming at arrival (d 0) on bovine respiratory disease (BRD) incidence, mortality, and growth of stocker calves. Calves (n=80) were stratified by d -3 weight and fecal egg count (FEC) into 20 pens of 4 calves. Pens were randomly assigned to treatments in a 2×2 factorial design, testing d 0 vaccination (modified-live respiratory virus and clostridial vaccine, or not) and deworming (oral fenbendazole and levamisole, or not). Body weights were measured on days 0, 14, 28, 42, 56, 70, and 85, and FEC were measured on days -3, 28, 56, and 85. Incidence of BRD was greater for d 0 vaccination (RR=3.2), high fever (≥104°F, ≥40°C) at d 0 (RR=6), and higher d -3 FEC (RR=1.2 per 100 epg). Mortality was greater for d 0 vaccination (OR=8.3) and high fever (OR=41.6). Growth was 10.3 lb (4.7 kg) lower for d 0 vaccination, 24 lb (11 kg) and 16 lb (7.3 kg) lower for moderate (103°F to 103.9°F; 39.4°C to 39.9°C) and high fever, respectively, and 17.6 lb (8 kg) lower for each additional BRD treatment a calf received. Deworming was neither beneficial nor detrimental to any health or performance factors. Health and growth performance of stocker calves may be adversely affected by vaccination at arrival, higher arrival FEC, and fever at arrival.

Notre objectif était de déterminer l'effet de la vaccination et de la vermifugation à l'arrivée (j0) sur l'incidence du complexe respiratoire bovin (CRB), la mortalité et la croissance des veaux d'élevage. Les veaux (n=80) ont été stratifiés selon le poids et le compte d'œufs fécaux (COF) à j-3 et placés dans 20 enclos avec chacun quatre veaux. Les enclos étaient assignés aléatoirement aux traitements selon un plan factoriel 2×2 avec la vaccination à j0 (avec ou sans vaccin anti-clostridial avec virus respiratoires vivants modifiés) et la vermifugation (avec ou sans injection orale de fenbendazole et de lévamisole) comme facteurs. Le poids corporel a été mesuré aux jours 0, 14, 28, 42, 56, 70 et 85 et le COF a été fait aux jours −3, 28, 56 et 85. L'incidence du CRB était plus élevée suivant la vaccination à j0 (RR=3.2), lorsque la fièvre était élevée à j0 (≥104°F, ≥40°C) (RR=6) et lorsque le COF était plus élevé à j-3 (RR=1.2 par 100 oeufs par gramme). La mortalité était plus élevée suivant la vaccination à j0 (RC=8.3) et lorsque la fièvre était élevée (RC=41.6). Il y a eu une perte de croissance de 10.3 lb (4.6 kg) suivant la vaccination à j0, une perte de 24.1 lb (11 kg) lorsque la fièvre était modérée (103­103.9°F), une perte de 16 lb (7.3 kg) lorsque la fièvre était élevée et une perte de 17.5 lb (8 kg) pour chaque traitement additionnel contre le CRB reçu par un veau. La vermifugation n'a pas eu d'effet bénéfique ou néfaste sur tous les facteurs reliés à la santé ou à la performance. La santé et la croissance des veaux d'élevage peuvent être affectées négativement par la vaccination à l'arrivée, par un COF initialement élevé et par la fièvre à l'arrivée.

A Systems Biology Approach Using Transcriptomic Data Reveals Genes and Pathways in Porcine Skeletal Muscle Affected by Dietary Lysine.

Nine crossbred finishing barrows (body weight 94.4 ± 6.7 kg) randomly assigned to three dietary treatments were used to investigate the effects of dietary lysine on muscle growth related metabolic and signaling pathways. Muscle samples were collected from the longissimus dorsi of individual pigs after feeding the lysine-deficient (4.30 g/kg), lysine-adequate (7.10 g/kg), or lysine-excess (9.80 g/kg) diet for five weeks, and the total RNA was extracted afterwards. Affymetrix Porcine Gene 1.0 ST Array was used to quantify the expression levels of 19,211 genes. Statistical ANOVA analysis of the microarray data showed that 674 transcripts were differentially expressed (at p ≤ 0.05 level); 60 out of 131 transcripts (at p ≤ 0.01 level) were annotated in the NetAffx database. Ingenuity pathway analysis showed that dietary lysine deficiency may lead to: (1) increased muscle protein degradation via the ubiquitination pathway as indicated by the up-regulated DNAJA1, HSP90AB1 and UBE2B mRNA; (2) reduced muscle protein synthesis via the up-regulated RND3 and ZIC1 mRNA; (3) increased serine and glycine synthesis via the up-regulated PHGDH and PSPH mRNA; and (4) increased lipid accumulation via the up-regulated ME1, SCD, and CIDEC mRNA. Dietary lysine excess may lead to: (1) decreased muscle protein degradation via the down-regulated DNAJA1, HSP90AA1, HSPH1, and UBE2D3 mRNA; and (2) reduced lipid biosynthesis via the down-regulated CFD and ME1 mRNA. Collectively, dietary lysine may function as a signaling molecule to regulate protein turnover and lipid metabolism in the skeletal muscle of finishing pigs.