Identifying host pathogenic pathways in bovine digital dermatitis by RNA-Seq analysis

Proinflammatory CD14highCD16low monocytes/macrophages prevail in Treponema phagedenis-associated bovine digital dermatitis

Digital dermatitis (DD) is a skin disease in cattle characterized by painful inflammatory ulcerative lesions in the feet, mostly associated with local colonization by Treponema spp., including Treponema phagedenis. The reason why most DD lesions remain actively inflamed and progress to chronic conditions despite antibiotic treatment remains unknown. Herein, we show an abundant infiltration of proinflammatory (CD14highCD16low) monocytes/macrophages in active DD lesions, a skin response that was not mitigated by topical treatment with oxytetracycline. The associated bacterium, T. phagedenis, isolated from DD lesions in cattle, when injected subcutaneously into mice, induced abscesses with a local recruitment of Ly6G+ neutrophils and proinflammatory (Ly6ChighCCR2+) monocytes/macrophages, which appeared at infection onset (4 days post challenge) and persisted for at least 7 days post challenge. When exploring the ability of macrophages to regulate inflammation, we showed that bovine blood-derived macrophages challenged with live T. phagedenis or its structural components secreted IL-1β via a mechanism dependent on the NLRP3 inflammasome. This study shows that proinflammatory characteristics of monocytes/macrophages and neutrophils dominate active non-healing ulcerative lesions in active DD, thus likely impeding wound healing after antibiotic treatment.

Local and Systemic Inflammation in Finnish Dairy Cows with Digital Dermatitis

Digital dermatitis is a disease of the digital skin and causes lameness and welfare problems in dairy cattle. This study assessed the local and systemic inflammatory responses of cows with different digital dermatitis lesions and compared macroscopical and histological findings. Cow feet (n = 104) were evaluated macroscopically and skin biopsies histologically. Serum samples were analyzed for acute phase proteins (serum amyloid A and haptoglobin) and pro-inflammatory cytokines (interleukin-1 beta, interleukin-6, and tumor necrosis factor-alpha). Cows with macroscopically graded active lesions (p = 0.028) and non-active lesions (p = 0.008) had higher interleukin-1 beta levels in their serum compared to healthy cows. Interleukin-1 beta serum concentrations were also higher (p = 0.042) when comparing lesions with necrosis to lesions without necrosis. There was no difference when other cytokine or acute phase protein concentrations in healthy cows were compared to those in cows with different digital dermatitis lesions. A novel histopathological grading was developed based on the chronicity of the lesions and presence of necrosis and ulceration. The presence and number of spirochetes were graded separately. In the most severe chronic lesions, there was marked epidermal hyperplasia and hyperkeratosis with necrosis, deep ulceration, and suppurative inflammation. Spirochetes were found only in samples from necrotic lesions. This study established that digital dermatitis activates proinflammatory cytokines. However, this did not initiate the release of acute phase proteins from the liver. A histopathological grading that takes into account the age and severity of the lesions and presence of spirochetes was developed to better understand the progression of the disease. It is proposed that necrosis of the skin is a result of ischemic necrosis following reduced blood flow in the dermal papillae due to pressure and shear stress caused by thickened epidermis, and that the spirochetes are secondary invaders following tissue necrosis.

Natural Mycoplasma Infection Reduces Expression of Pro-Inflammatory Cytokines in Response to Ovine Footrot Pathogens

Ovine footrot is a complex multifactorial infectious disease, causing lameness in sheep with major welfare and economic consequences. Dichelobacter nodosus is the main causative bacterium; however, footrot is a polymicrobial disease with Fusobacterium necrophorum, Mycoplasma fermentans and Porphyromonas asaccharolytica also associated. There is limited understanding of the host response involved. The proinflammatory mediators, interleukin (IL)-1β and C-X-C Motif Chemokine Ligand 8 (CXCL8), have been shown to play a role in the early response to D. nodosus in dermal fibroblasts and interdigital skin explant models. To further understand the response of ovine skin to bacterial stimulation, and to build an understanding of the role of the cytokines and chemokines identified, primary ovine interdigital fibroblasts and keratinocytes were isolated, cultured and stimulated. The expression of mRNA and protein release of CXCL8 and IL-1β were measured after stimulation with LPS, D. nodosus or F. necrophorum, which resulted in increased transcript levels of IL-1β and CXCL8 in the M. fermentans-free cells. However, only an increase in the CXCL8 protein release was observed. No IL-1β protein release was detected, despite increases in IL-1β mRNA, suggesting the signal for intracellular pre-IL-1β processing may be lacking when culturing primary cells in isolation. The keratinocytes and fibroblasts naturally infected with M. fermentans showed little response to the LPS, a range of D. nodosus preparations or heat-inactivated F. necrophorum. Primary single cell culture models complement ex vivo organ culture models to study different aspects of the host response to D. nodosus. The ovine keratinocytes and fibroblasts infected with M. fermentans had a reduced response to the experimental bacterial stimulation. However, in the case of footrot where Mycoplasma spp. are associated with diseased feet, this natural infection gives important insights into the impact of multiple pathogens on the host response.

Continuous activation of the IL-17F driven inflammatory pathway in acute and chronic digital dermatitis lesions in dairy cattle

Objectives of the present study were to get a deeper insight into the course of the inflammatory pathways of digital dermatitis lesions in dairy cattle by investigating the gene expression patterns throughout the different clinical stages (M0 to M4.1) of the disease. Normal skin samples (M0) were used as a reference for comparing the gene expression levels in the other M-stages through RNA Seq-technology. Principal component analysis revealed a distinct gene expression pattern associated with digital dermatitis lesions in comparison to healthy skin with a further clustering of the acute M1, M2 and M4.1 stages versus the chronic M3 and M4 stages. The majority of the up-and downregulated genes in the acute and chronic stages can be placed into a common 'core' set of genes involved in inflammation, such as A2ML1, PI3, CCL11 and elafin-like protein, whereas the most downregulated genes included keratins and anti-inflammatory molecules such as SCGB1D and MGC151921. Pathway analysis indicated the activation of the pro-inflammatory IL-17 signaling pathway in all the M stages through the upregulation of IL-17F. These results indicate that digital dermatitis is associated with an excessive inflammatory immune response concomitant with a disrupted skin barrier and impaired wound repair mechanism. Importantly, despite their macroscopically healed appearance, a significant inflammatory response (Padj < 0.05) was still measurable in the M3 and M4 lesions, potentially explaining the frequent re-activation of such lesions.

Functional Variants Associated With CMPK2 and in ASB16 Influence Bovine Digital Dermatitis

Bovine digital dermatitis (BDD) is an infectious disease of the hoof in cattle with multifactorial etiology and a polygenic influence on susceptibility. With our study, we identified genomic regions with the impact on occurrence and development of BDD. We used 5,040 genotyped animals with phenotype information based on the M-stage system for genome-wide association. Significant associations for single-nucleotide polymorphisms were found near genes CMPK2 (chromosome 11) and ASB16 (chromosome 19) both being implicated in immunological processes. A sequence analysis of the chromosomal regions revealed rs208894039 and rs109521151 polymorphisms as having significant influence on susceptibility to the disease. Specific genotypes were significantly more likely to be affected by BDD and developed chronic lesions. Our study provides an insight into the genomic background for a genetic predisposition related to the pathogenesis of BDD. Results might be implemented in cattle-breeding programs and could pave the way for the establishment of a BDD prescreening test.

Acute phase response of sole ulcer, white line disease and digital dermatitis in dairy cows

•

Serum amyloid A, a marker of inflammation, was still elevated two weeks after treatment of sole ulcers.

•

Body temperature and concentration of cytokine interleukin-6 declined from day 0 to day 7 in sole ulcer group.

•

Sole ulcer is a chronic hoof disorder that heals slowly and therefore early detection, good management, and proper pain medication of cows with sole ulcers is important.

Hoof disorders cause lameness and welfare problems for dairy cattle. Acute phase proteins, including serum amyloid A and haptoglobin, with increased rectal temperature and interleukin-6 concentrations, are markers of acute phase response. This study assessed the inflammatory response of cows with either sole ulcer, white line disease or digital dermatitis compared to healthy cows. Another aim was to monitor the inflammatory response changes over time after diagnosis (at hoof trimming, seven and 14 days later) in cows with different hoof disorders.

Serum amyloid A concentration in cows with sole ulcer was significantly higher compared with the control group (cows with no hoof lesions) within the two-week study period. Interleukin-6 and rectal temperature declined from day zero to day seven in the sole ulcer group. These results suggest that sole ulcers initiate a long lasting systemic inflammatory response in dairy cows.

Challenge of Bovine Foot Skin Fibroblasts With Digital Dermatitis Treponemes Identifies Distinct Pathogenic Mechanisms

Bovine digital dermatitis (BDD) is a common infectious disease of digital skin in cattle and an important cause of lameness worldwide, with limited treatment options. It is of increasing global concern for both animal welfare and food security, imposing a large economic burden on cattle farming industries each year. A polytreponemal etiology has been consistently identified, with three key phylogroups implicated globally: Treponema medium, Treponema phagedenis, and Treponema pedis. Pathogenic mechanisms which might enable targeted treatment/therapeutic development are poorly defined. This study used RNA sequencing to determine global differential mRNA expression in primary bovine foot skin fibroblasts following challenge with three representative BDD treponemes and a commensal treponeme, Treponema ruminis. A pro-inflammatory response was elicited by the BDD treponemes, mediated through IL-8/IL-17 signaling. Unexpectedly, the three BDD treponemes elicited distinct mechanisms of pathogenesis. T. phagedenis and T. pedis increased abundance of mRNA transcripts associated with apoptosis, while T. medium and T. pedis increased transcripts involved in actin rearrangement and loss of cell adhesion, likely promoting tissue invasion. The upregulation of antimicrobial peptide precursor, DEFB123, by T. phagedenis spirochaetes may present a microbial ecological advantage to all treponemes within BDD infected tissue, explaining their dominance within lesions. A commensal, T. ruminis, significantly dysregulated over three times the number of host mRNA transcripts compared to BDD treponemes, implying BDD treponemes, akin to the syphilis pathogen (Treponema pallidum), have evolved as "stealth pathogens" which avoid triggering substantial host immune/inflammatory responses to enable persistence and tissue invasion. Immunohistochemistry demonstrated increased IL-6, IL-8, RND1, and CFB protein expression in BDD lesions, confirming in vitro fibroblast observations and highlighting the system's value in modeling BDD pathogenesis. Several unique shared gene targets were identified, particularly RGS16, GRO1, MAFF, and ZC3H12A. The three key BDD Treponema phylogroups elicited both distinct and shared pathogenic mechanisms in bovine foot skin; upregulating inflammation whilst simultaneously suppressing adaptive immunity. The novel gene targets identified here should enable future vaccine/therapeutic approaches.

Genome-Wide Association Studies Reveal Susceptibility Loci for Digital Dermatitis in Holstein Cattle

Digital dermatitis (DD) causes lameness in dairy cattle. To detect the quantitative trait loci (QTL) associated with DD, genome-wide association studies (GWAS) were performed using high-density single nucleotide polymorphism (SNP) genotypes and binary case/control, quantitative (average number of FW per hoof trimming record) and recurrent (cases with ≥2 DD episodes vs. controls) phenotypes from cows across four dairies (controls n = 129 vs. FW n = 85). Linear mixed model (LMM) and random forest (RF) approaches identified the top SNPs, which were used as predictors in Bayesian regression models to assess the SNP predictive value. The LMM and RF analyses identified QTL regions containing candidate genes on Bos taurus autosome (BTA) 2 for the binary and recurrent phenotypes and BTA7 and 20 for the quantitative phenotype that related to epidermal integrity, immune function, and wound healing. Although larger sample sizes are necessary to reaffirm these small effect loci amidst a strong environmental effect, the sample cohort used in this study was sufficient for estimating SNP effects with a high predictive value.

Identification of candidate genes for milk production traits by RNA sequencing on bovine liver at different lactation stages

Background

RNA-sequencing was performed to explore the bovine liver transcriptomes of Holstein cows to detect potential functional genes related to lactation and milk composition traits in dairy cattle. The bovine transcriptomes of the nine liver samples from three Holstein cows during dry period (50-d prepartum), early lactation (10-d postpartum), and peak of lactation (60-d postpartum) were sequenced using the Illumina HiSeq 2500 platform.

Results

A total of 204, 147 and 81 differentially expressed genes (DEGs, p < 0.05, false discovery rate q < 0.05) were detected in early lactation vs. dry period, peak of lactation vs. dry period, and peak of lactation vs. early lactation comparison groups, respectively. Gene ontology and KEGG pathway analysis showed that these DEGs were significantly enriched in specific biological processes related to metabolic and biosynthetic and signaling pathways of PPAR, AMPK and p53 (p < 0.05). Ten genes were identified as promising candidates affecting milk yield, milk protein and fat traits in dairy cattle by using an integrated analysis of differential gene expression, previously reported quantitative trait loci (QTL), data from genome-wide association studies (GWAS), and biological function information. These genes were APOC2, PPP1R3B, PKLR, ODC1, DUSP1, LMNA, GALE, ANGPTL4, LPIN1 and CDKN1A.

Conclusion

This study explored the complexity of the liver transcriptome across three lactation periods in dairy cattle by performing RNA sequencing. Integrated analysis of DEGs and reported QTL and GWAS data allowed us to find ten key candidate genes influencing milk production traits.

Missing pieces of the puzzle to effectively control digital dermatitis

Since the first report of bovine digital dermatitis (DD) in 1974, there is a large body of the literature published; however, effective prevention and control of the disease remain elusive. Although many aspects of the pathogenesis of DD have been investigated, even some of the most basic questions such as the aetiology of this disease remain under debate. Treponema spp. have been strongly associated with DD lesions and occur in abundance in advanced lesions; however, efforts to induce disease with pure cultures of these organisms have been largely underwhelming and inconsistent. Furthermore, although the disease has been presented for several decades, there is limited scientific evidence regarding effective treatment of DD. Apparent discrepancies between effectiveness in vitro and in vivo have challenged the scientific community to identify new potential treatment options. With no treatment resulting in a 100% cure rate, the current expectation is manageable control, but prospects for the eradication of the disease are unlikely using current approaches. In order to develop more effective approaches to control DD on-farm, there is a critical need for a deeper understanding regarding the causation, ecology, transmission and treatment of this disease. In this article, we attempt to provide insights into specific research needs related to DD in order to assist the industry, researchers, pharmaceutical companies and research sponsors with decision-making and identified research gaps.

A distinct bacterial dysbiosis associated skin inflammation in ovine footrot

Ovine footrot is a highly prevalent bacterial disease caused by Dichelobacter nodosus and characterised by the separation of the hoof horn from the underlying skin. The role of innate immune molecules and other bacterial communities in the development of footrot lesions remains unclear. This study shows a significant association between the high expression of IL1β and high D. nodosus load in footrot samples. Investigation of the microbial population identified distinct bacterial populations in the different disease stages and also depending on the level of inflammation. Treponema (34%), Mycoplasma (29%) and Porphyromonas (15%) were the most abundant genera associated with high levels of inflammation in footrot. In contrast, Acinetobacter (25%), Corynebacteria (17%) and Flavobacterium (17%) were the most abundant genera associated with high levels of inflammation in healthy feet. This demonstrates for the first time there is a distinct microbial community associated with footrot and high cytokine expression.

Digital Dermatitis in Cattle: Current Bacterial and Immunological Findings

Globally; digital dermatitis is a leading form of lameness observed in production dairy cattle. While the precise etiology remains to be determined; the disease is clearly associated with infection by numerous species of treponemes; in addition to other anaerobic bacteria. The goal of this review article is to provide an overview of the current literature; focusing on discussion of the polybacterial nature of the digital dermatitis disease complex and host immune response. Several phylotypes of treponemes have been identified; some of which correlate with location in the lesion and some with stages of lesion development. Local innate immune responses may contribute to the proliferative, inflammatory conditions that perpetuate digital dermatitis lesions. While serum antibody is produced to bacterial antigens in the lesions, little is known about cellular-based immunity. Studies are still required to delineate the pathogenic traits of treponemes associated with digital dermatitis; and other host factors that mediate pathology and protection of digital dermatitis lesions.

Bovine digital dermatitis: Current concepts from laboratory to farm

Bovine digital dermatitis (DD) is a severe infectious disease causing lameness in dairy cattle worldwide and is an important ruminant welfare problem that has considerable economic issues. Bovine DD is endemic in many regions worldwide and it is important to understand this major disease so that effective control strategies can be identified. There is substantial evidence that specific treponeme phylotypes play an important causative role in bovine DD. This review considers current research, including DD Treponema spp. investigations, associated DD pathobiology, and current and potential treatment and control options. Epidemiological data, alongside new microbiological data, help delineate important transmission routes and reservoirs of infection that allow effective interventions to be identified. Better on-farm housing hygiene, pasture access, routine footbathing and claw trimming with disinfected equipment need to be implemented to significantly reduce the incidence of DD. There is a paucity of peer reviewed research into both commonly used and novel treatments. In vitro antimicrobial susceptibility studies of DD treponemes and effective treatment of human treponematoses clearly indicate that antibiotics frequently selected for DD treatments are not the most efficacious. Whilst there are understandable concerns over milk withdrawal times in dairy cattle, more needs to be done to identify, license and implement more appropriate antibiotic treatments, since continued overuse of less efficacious antibiotics, applied incorrectly, will lead to increased disease recurrence and transmission. More research is needed into methods of preventing DD that circumvent the use of antibiotics, including vaccination and transmission blocking studies, to reduce or hopefully eradicate DD in the future.

Digital Dermatitis in Dairy Cows: A Review of Risk Factors and Potential Sources of Between-Animal Variation in Susceptibility

Simple Summary

Dairy cow lameness is a major problem for the industry, causing reduced animal welfare and economic loss. Digital dermatitis (DD) is a bacterial disease causing painful lesions, generally on the heels of the rear feet, and is an important cause of lameness. There appears to be individual variation between animals in susceptibility to this disease. Particular physical, physiological and behavioural factors might influence individual susceptibility, but further work is required to clarify the influence of these factors and to determine how this information could be used to develop breeding and management strategies to reduce DD prevalence.

Abstract

Digital dermatitis (DD) is a bacterial disease that primarily affects the skin on the heels of cattle. It is a major cause of lameness in dairy cows and a significant problem for the dairy industry in many countries, causing reduced animal welfare and economic loss. A wide range of infection levels has been found on infected farms, prompting investigations into both farm level and animal level risk factors for DD occurrence. There also appears to be individual variation between animals in susceptibility to the disease. The identification of factors affecting individual variation in susceptibility to DD might allow changes in breeding policies or herd management which could be used to reduce DD prevalence. Factors mentioned in the literature as possibly influencing individual variation in susceptibility to DD include physical factors such as hoof conformation and properties of the skin, physiological factors such as the efficacy of the immune response, and behavioural factors such as standing half in cubicles. Further work is required to determine the influence of these factors, identify the genetic basis of variation, clarify the level of heritability of DD susceptibility and to determine how this is correlated with production and health traits currently used in breeding programmes.

The etiology of digital dermatitis in ruminants: recent perspectives

Digital dermatitis (DD) is a multifactorial polymicrobial infectious disease originally described in dairy cattle, but is increasingly recognized in beef cattle, sheep, and more recently, elk and goats. Clinical bovine lesions typically appear on the plantar surface of the hind foot from the interdigital space and heel bulb to the accessory digits, with a predilection for skin–horn junctions. Lesions present as a painful ulcerative acute or chronic inflammatory process with differing degrees of severity. This variability reflects disease progression and results in a number of different clinical descriptions with overlapping pathologies that ultimately have a related bacterial etiology. The goal of this review article is to provide a concise overview of our current understanding on digital dermatitis disease to facilitate clinical recognition, our current understanding on the causative agents, and recent advances in our understanding of disease transmission.

Analysis of RNAseq datasets from a comparative infectious disease zebrafish model using GeneTiles bioinformatics

We present a RNA deep sequencing (RNAseq) analysis of a comparison of the transcriptome responses to infection of zebrafish larvae with Staphylococcus epidermidis and Mycobacterium marinum bacteria. We show how our developed GeneTiles software can improve RNAseq analysis approaches by more confidently identifying a large set of markers upon infection with these bacteria. For analysis of RNAseq data currently, software programs such as Bowtie2 and Samtools are indispensable. However, these programs that are designed for a LINUX environment require some dedicated programming skills and have no options for visualisation of the resulting mapped sequence reads. Especially with large data sets, this makes the analysis time consuming and difficult for non-expert users. We have applied the GeneTiles software to the analysis of previously published and newly obtained RNAseq datasets of our zebrafish infection model, and we have shown the applicability of this approach also to published RNAseq datasets of other organisms by comparing our data with a published mammalian infection study. In addition, we have implemented the DEXSeq module in the GeneTiles software to identify genes, such as glucagon A, that are differentially spliced under infection conditions. In the analysis of our RNAseq data, this has led to the possibility to improve the size of data sets that could be efficiently compared without using problem-dedicated programs, leading to a quick identification of marker sets. Therefore, this approach will also be highly useful for transcriptome analyses of other organisms for which well-characterised genomes are available.

The sheep genome illuminates biology of the rumen and lipid metabolism

Sheep (Ovis aries) are a major source of meat, milk, and fiber in the form of wool and represent a distinct class of animals that have a specialized digestive organ, the rumen, that carries out the initial digestion of plant material. We have developed and analyzed a high-quality reference sheep genome and transcriptomes from 40 different tissues. We identified highly expressed genes encoding keratin cross-linking proteins associated with rumen evolution. We also identified genes involved in lipid metabolism that had been amplified and/or had altered tissue expression patterns. This may be in response to changes in the barrier lipids of the skin, an interaction between lipid metabolism and wool synthesis, and an increased role of volatile fatty acids in ruminants compared with nonruminant animals.