Biomarkers for Detecting Resilience against Mycobacterial Disease in Animals

Towards a microRNA-based Johne's disease diagnostic predictive system: Preliminary results

BACKGROUND

Johne's disease, caused by Mycobacterium avium subspecies paratuberculosis (MAP), is a chronic enteritis that adversely affects welfare and productivity in cattle. Screening and subsequent removal of affected animals is a common approach for disease management, but efforts are hindered by low diagnostic sensitivity. Expression levels of small non-coding RNA molecules involved in gene regulation (microRNAs), which may be altered during mycobacterial infection, may present an alternative diagnostic method.

METHODS

The expression levels of 24 microRNAs affected by mycobacterial infection were measured in sera from MAP-positive (n = 66) and MAP-negative cattle (n = 65). They were then used within a machine learning approach to build an optimal classifier for MAP diagnosis.

RESULTS

The method provided 72% accuracy, 73% sensitivity and 71% specificity on average, with an area under the curve of 78%.

LIMITATIONS

Although control samples were collected from farms nominally MAP-free, the low sensitivity of current diagnostics means some animals may have been misclassified.

CONCLUSION

MicroRNA profiling combined with advanced predictive modelling enables rapid and accurate diagnosis of Johne's disease in cattle.

In silico design of Mycobacterium tuberculosis multi-epitope adhesin protein vaccines

Mycobacterium tuberculosis (Mtb) adhesin proteins are promising candidates for subunit vaccine design. Multi-epitope Mtb vaccine and diagnostic candidates were designed using immunoinformatic tools. The antigenic potential of 26 adhesin proteins were determined using VaxiJen 2.0. The truncated heat shock protein 70 (tnHSP70), 19 kDa antigen lipoprotein (lpqH), Mtb curli pili (MTP), and Phosphate transport protein S1 (PstS1) were selected based on the number of known epitopes on the Immune Epitope Database (IEDB). B- and T-cell epitopes were identified using BepiPred2.0, ABCpred, SVMTriP, and IEDB, respectively. Population coverage was analysed using prominent South African specific alleles on the IEDB. The allergenicity, physicochemical characteristics and tertiary structure of the tri-fusion proteins were determined. The in silico immune simulation was performed using C-ImmSim. Three truncated sequences, with predicted B and T cell epitopes, and without allergenicity or signal peptides were linked by three glycine-serine residues, resulting in the stable, hydrophilic molecules, tnlpqH-tnPstS1-tnHSP70 (64,86 kDa) and tnMTP-tnPstS1-tnHSP70 (63,96 kDa). Restriction endonuclease recognition sequences incorporated at the N- and C-terminal ends of each construct, facilitated virtual cloning using Snapgene, into pGEX6P-1, resulting in novel, highly immunogenic vaccine candidates (0,912-0,985). Future studies will involve the cloning, recombinant protein expression and purification of these constructs for downstream applications.

Proteomic Serum Profiling of Holstein Friesian Cows with Different Pathological Forms of Bovine Paratuberculosis Reveals Changes in the Acute-Phase Response and Lipid Metabolism

The lack of sensitive diagnostic methods to detect Mycobacterium avium subsp. paratuberculosis (Map) subclinical infections has hindered the control of paratuberculosis (PTB). The serum proteomic profiles of naturally infected cows presenting focal and diffuse pathological forms of PTB and negative controls (n = 4 per group) were analyzed using TMT-6plex quantitative proteomics. Focal and diffuse are the most frequent pathological forms in subclinical and clinical stages of PTB, respectively. One (focal versus (vs.) control), eight (diffuse vs. control), and four (focal vs. diffuse) differentially abundant (DA) proteins (q-value < 0.05) were identified. Ingenuity pathway analysis of the DA proteins revealed changes in the acute-phase response and lipid metabolism. Six candidate biomarkers were selected for further validation by specific ELISA using serum from animals with focal, multifocal, and diffuse PTB-associated lesions (n = 108) and controls (n = 56). Overall, the trends of the serum expression levels of the selected proteins were consistent with the proteomic results. Alpha-1-acid glycoprotein (ORM1)-based ELISA, insulin-like growth factor-binding protein 2 (IGFBP2)-based ELISA, and the anti-Map ELISA had the best diagnostic performance for detection of animals with focal, multifocal, and diffuse lesions, respectively. Our findings identify potential biomarkers that improve diagnostic sensitivity of PTB and help to elucidate the mechanisms involved in PTB pathogenesis.

Progress in Paratuberculosis Control Programmes for Dairy Herds

While paratuberculosis control has been studied for over a century, knowledge gaps still exist regarding the uptake and efficacy of control programmes. This narrative review aims to summarise studies on control programmes presented at the IDF ParaTB Fora in 2021 and 2022 and the International Colloquium on Paratuberculosis in 2022. Studies were grouped by topic as follows: successful control, field studies, education and extension, voluntary and compulsory control programmes, and surveillance. Various Map control programmes resulted in a decreasing animal and herd level Map prevalence. Long-term stakeholder commitment, stable funding, involvement of herd veterinarians and incentives for farmers to participate were shown to be pivotal for long-term success. Control measures focused on vertical and calf-to-calf transmission may improve Map control in infected herds. Easy-to-capture visualisation of surveillance test results to inform participants on the progress of Map control in their herds was developed. The probability of freedom from disease and estimated within-herd prevalence were identified as good candidates for categorisation of herds to support low-risk trade of cattle. Results of the surveillance schemes may inform genetic selection for resistance to Map infection. In conclusion, successful paratuberculosis control is feasible at both the herd and country level provided that crucial prerequisites are met.

Zebrafish tsc1 and cxcl12a increase susceptibility to mycobacterial infection

Regulation of host miRNA expression is a contested node that controls the host immune response to mycobacterial infection. The host must counter subversive efforts of pathogenic mycobacteria to launch a protective immune response. Here, we examine the role of miR-126 in the zebrafish-Mycobacterium marinum infection model and identify a protective role for infection-induced miR-126 through multiple effector pathways. We identified a putative link between miR-126 and the tsc1a and cxcl12a/ccl2/ccr2 signalling axes resulting in the suppression of non-tnfa expressing macrophage accumulation at early M. marinum granulomas. Mechanistically, we found a detrimental effect of tsc1a expression that renders zebrafish embryos susceptible to higher bacterial burden and increased cell death via mTOR inhibition. We found that macrophage recruitment driven by the cxcl12a/ccl2/ccr2 signalling axis was at the expense of the recruitment of classically activated tnfa-expressing macrophages and increased cell death around granulomas. Together, our results delineate putative pathways by which infection-induced miR-126 may shape an effective immune response to M. marinum infection in zebrafish embryos.

miRNAs as Biomolecular Markers for Food Safety, Quality, and Traceability in Poultry Meat-A Preliminary Study

In this study, the expression and abundance of two candidate chicken (Gallus gallus; gga) microRNAs (miRNAs, miR), gga-miR-21-5p (miR-21) and gga-miR-126-5p (miR-126), have been analyzed in order to identify biomarkers for the traceability and quality of poultry meat. Two breeds of broiler chickens were tested: the most common Ross308 (fast-growing) and the high-quality Ranger Gold (slow-growing). A preliminary analysis of the two miRNAs expressions was conducted across various tissues (liver, lung, spleen, skeletal muscle, and kidney), and the three tissues (lung, spleen, and muscle) with a higher expression were chosen for further analysis. Using quantitative reverse transcription polymerase chain reaction (RT-qPCR), the expression of miRNAs in the three tissues of a total of thirteen animals was determined. The results indicate that miR-126 could be a promising biomarker for the lung tissue in the Ranger Gold (RG) breed (p < 0.01), thus suggesting a potential applicability for tracing hybrids. RG exhibits a significantly higher miR-126 expression in the lung tissue compared to the Ross308 broilers (R308), an indication of greater respiratory capacity and, consequently, a higher oxidative metabolism of the fast-growing hybrid. During sampling, two R308 broilers presented some anomalies, including airsacculitis, hepatic steatosis, and enlarged spleen. The expression of miR-126 and miR-21 was compared in healthy animals and in those presenting anomalies. Chickens with airsacculitis and hepatic steatosis showed an up-regulation of miR-21 and miR-126 in the most commercially valuable tissue, the skeletal muscle or breast (p < 0.05).

Behavioral patterns as indicators of resilience after parturition in dairy cows

During the transition phase, dairy cows are susceptible to develop postpartum diseases. Cows that stay healthy or recover rapidly can be considered to be more resilient in comparison to those that develop postpartum diseases. An indication of loss of resilience will allow for early intervention with preventive and supportive measures before the onset of disease. We investigated which quantitative behavioral characteristics during the dry period could be used as indicators of reduced resilience after calving, using noninvasive Smart Tag neck and Smart Tag leg sensors in dairy cows (Nedap N.V.). We followed 180 cows during 2 wk before until 6 wk after parturition at 4 farms in the Netherlands. Serving as proxy for loss of resilience, as defined by the duration and severity of disease, a clinical assessment was performed twice weekly and blood samples were taken in the first and fifth week after parturition. For each cow, clinical and serum value deviations were aggregated into a total deficit score (TDS total). We also calculated TDS values relating to inflammation, locomotion, or metabolic problems, which were further divided into macro-mineral and liver-related deviations. Smart Tag neck and leg sensors provided continuous behavioral activity signals of which we calculated the average, variance, and autocorrelation during the dry period. Diurnal patterns in the behavioral activity signals were derived by fast Fourier transformation and the calculation of the nonperiodicity. To select significant predictors of resilience, we first performed a univariate analysis with TDS as dependent variable and the behavioral characteristics that were measured during the dry period, as potential predictors with cow as experimental unit. We included parity group as fixed effect and farm as random effect. Next, we performed multivariable analysis with only significant predictors, followed by a variable selection procedure to obtain a final linear mixed model with an optimal subset of predictors with parity group as fixed effect and farm as random effect. The TDS total was best predicted by average inactive time, nonperiodicity ruminating, nonperiodicity of bouts standing up and fast Fourier transformation stand still. Average inactive time was negatively correlated with average eating time, and these 2 predictors could be exchanged with only little difference in model performance. Our best performing model predicted TDS total at a cutoff level of 60 points, with a sensitivity of 79.5% and a specificity of 73.2% with a positive predicted value of 0.69 and a negative predicted value of 0.83. The models to predict the other TDS categories showed a lower predictive performance as compared with the TDS total model, which could be related to the limited sample size and therefore, low occurrence of problems within a specific TDS category. Furthermore, more resilient dairy cows are characterized by high averages of eating time with high regularity in rumination and low averages of inactive time. They reveal high regularity in standing time and transitions from lying to standing, in the dry period. These behaviors can be used as indicators of resilience and allow for preventive intervention during the dry period in vulnerable dairy cattle. However, further examination is still required to find clues for adequate intervention strategies.

Comparative Characterization of Immune Response in Sheep with Caseous Lymphadenitis through Analysis of the Whole Blood Transcriptome

Caseous lymphadenitis (CL) is a chronic contagious disease that affects small ruminants and is characterized by the formation of pyogranulomas in lymph nodes and other organs. However, the pathogenesis of this disease and the response of the host genome to infection are not yet fully understood. This study aimed to investigate the whole blood transcriptome and evaluate differential gene expression during the later stages of CL in naturally infected ewes. The study included diseased, serologically positive (EP), exposed, serologically negative (EN) ewes from the same infected flock and healthy ewes (CN) from a different flock. RNA sequencing was performed using the Illumina NextSeq system, and differential gene expression was estimated using DESeq2 and Edge R approaches. The analysis identified 191 annotated differentially expressed genes (DEGs) in the EP group (102 upregulated and 89 downregulated) and 256 DEGs in the EN group (106 upregulated and 150 downregulated) compared to the CN group. Numerous immunoregulatory interactions between lymphoid and nonlymphoid cells were influenced in both EP and EN ewes. Immune DEGs were preferentially assigned to antigen presentation through the MHC complex, T lymphocyte-mediated immunity, and extracellular matrix interactions. Furthermore, the EP group showed altered regulation of cytokine and chemokine signaling and activation and recombination of B-cell receptors. Conversely, NF-kappa B signaling, apoptosis, and stress response were the main processes influenced in the EN group. In addition, statistically significant enrichment of the essential immune pathways of binding and uptake of ligands by scavenger receptors in EP and p53 signaling in the EN group was found. In conclusion, this study provides new insights into the disease course and host-pathogen interaction in naturally CL-infected sheep by investigating the blood transcriptome.

Alternatives to antibiotics in veterinary medicine: considerations for the management of Johne's disease

Antibiotic resistance has become a major health concern globally, with current predictions expecting deaths related to resistant infections to surpass those of cancer by 2050. Major efforts are being undertaken to develop derivative and novel alternatives to current antibiotic therapies in human medicine. What appears to be lacking however, are similar efforts into researching the application of those alternatives, such as (bacterio)phage therapy, in veterinary contexts. Agriculture is still undoubtedly the most prominent consumer of antibiotics, with up to 70% of annual antibiotic usage attributed to this sector, despite policies to reduce their use in food animals. This not only increases the risk of resistant infections spreading from farm to community but also the risk that animals may acquire species-specific infections that subvert treatment. While these diseases may not directly affect human welfare, they greatly affect the profit margin of industries reliant on livestock due to the cost of treatments and (more frequently) the losses associated with animal death. This means actively combatting animal infection not only benefits animal welfare but also global economies. In particular, targeting recurring or chronic conditions associated with certain livestock has the potential to greatly reduce financial losses. This can be achieved by developing novel diagnostics to quickly identify ill animals alongside the design of novel therapies. To explore this concept further, this review employs Johne's disease, a chronic gastroenteritis condition that affects ruminants, as a case study to exemplify the benefits of rapid diagnostics and effective treatment of chronic disease, with particular regard to the diagnostic and therapeutic potential of phage.

Protein Levels of Pro-Inflammatory Cytokines and Chemokines as Biomarkers of Mycobacterium bovis Infection and BCG Vaccination in Cattle

Bovine tuberculosis (bTB), caused by Mycobacterium bovis, is a globally prevalent infectious disease with significant animal welfare and economic impact. Difficulties in implementing test-and-slaughter measures in low- and middle-income countries (LMICs) and the underperformance of the current diagnostics establish a clear need to develop improved diagnostics. Adaptive immunity biomarkers other than IFNγ could be useful as suggested by various gene expression studies; however, a comprehensive assessment at the protein level is lacking. Here, we screened a range of chemokines and cytokines for their potential as biomarkers in samples from M. bovis experimentally challenged or naive animals. Although serum concentrations for most proteins were low, the pro-inflammatory markers, IL-2, CXCL-9, IP-10 and CCL4, in addition to IFNγ, were found to be significantly elevated in bovine tuberculin (PPDb)-stimulated whole blood supernatants. Further assessment of these molecules in BCG-vaccinated with or without subsequent M. bovis challenge or naive animals revealed that PPDb-specific IL-2 and IP-10, in addition to IFNγ, could discriminate naive and BCG-vaccinated from M. bovis challenged animals. Moreover, these proteins, along with CCL4, showed DIVA potential, i.e., enabling differentiation of M. bovis-infected animals from BCG-vaccinated animals. Combined analysis of cytokines and chemokines could also accurately identify M. bovis infection with strong correlations observed between PPDb-specific IFNγ, IL-2 and IP-10 levels. This provides proof of concept for utilizing multiple biomarker signatures for discrimination of animals with respect to M. bovis infection or BCG vaccination status.

Mycobacterium avium subsp. paratuberculosis exploits miRNA expression to modulate lipid metabolism and macrophage polarisation pathways during infection

Pathogenic mycobacteria including Mycobacterium avium subsp. paratuberculosis (MAP), the causative agent of Johne's disease, manipulate host macrophages to persist and cause disease. In mycobacterial infection, highly plastic macrophages, shift between inflammatory M1 and permissive M2 phenotypes which alter the disease outcome and allow bacteria to survive intracellularly. Here we examine the impact of MAP infection on polarised macrophages and how increased lipid availability alters macrophage phenotype and bacterial persistence. Further, we assess if host microRNA (miRNA) are sensitive to macrophage polarisation state and how MAP can drive their expression to overcome innate responses. Using in vitro MAP infection, we find that increasing lipid availability through supplementing culture media with exogenous lipid increases cellular nitric oxide production. Lipid-associated miRs -19a, -129, -24, and -24-3p are differentially expressed following macrophage polarisation and lipid supplementation and are further regulated during MAP infection. Collectively, our results highlight the importance of host lipid metabolism in MAP infection and demonstrate control of miRNA expression by MAP to favour intracellular persistence.

Early Detection of Mycobacterium avium subsp. paratuberculosis Infected Cattle: Use of Experimental Johnins and Innovative Interferon-Gamma Test Interpretative Criteria

Paratuberculosis (PTB), also known as Johne's disease, is a chronic proliferative enteritis of ruminants caused by Mycobacterium avium subsp.paratuberculosis (MAP). To date, PTB diagnosis, based on serology, fecal culture, and real-time polymerase chain reaction, has identified animals in advanced stages of infection. To detect MAP infection in animals earlier, the interferon-gamma (IFN-γ) test may be applied. This assay detects cytokines produced by T-lymphocytes of infected subjects after stimulation with purified protein derivatives (PPDs), extracted from Mycobacterium bovis (MB) and from M. avium (MA). The study involved three bovine herds: one PTB-infected herd, one PTB-free herd, and one with an outbreak of bovine tuberculosis. The IFN-γ test was performed on 235 animals, using bovine PPD (PPDB), avian PPD (PPDA), and three experimental PPD Johnins (PPDJs) extracted from a synthetic liquid medium culture of MAP (PPDJ A, B, and C), to assess early MAP detection and avoid false reactions to MB. Furthermore, IFN-γ results were evaluated using 12 interpretative criteria (ICs), based on the differences and ratio between PPD optical density (OD) and IFN-γ basal OD values after lymphocytic stimulation. IC accuracy was expressed as area under the receiver operating characteristic curve. Through a longitudinal study, PPDJs proved to be specific and sensitive in the detection of MAP-infected animals. Among the evaluated ICs, six showed the best performance in terms of accuracy (p < 0.0001), highlighting PTB subclinical infections. In particular, the two best criteria reached sensitivity values of 100% [confidence interval (CI) 95%, 94.1–100%] with a specificity of 91.8% (CI 95%, 81.9–97.3%) and sensitivity levels of 80.6% (CI 95%, 69.1–89.2%) with a specificity of 100% (CI 95%, 94.1–100%). Thus, the IFN-γ assay proved to be a useful diagnostic tool to identify early subclinical MAP-infected animals, in order to manage infected cattle or those exposed to MAP and to monitor younger calves within a herd. Furthermore, the IFN-γ test can be considered an additional test to avoid the introduction of MAP-infected animals, especially in herds where disease has already been eradicated and preservation of the health status is required to maintain the PTB certification level.

Developing smarter vaccines for paratuberculosis: From early biomarkers to vaccine design

Vaccines for paratuberculosis have been used for over a hundred years but the disease continues to affect ruminant health and livestock industries globally. Mycobacterium avium subspecies paratuberculosis which causes the disease also known as Johne's disease is a subversive pathogen able to undermine both innate and adaptive host defense mechanisms. This review focuses on early protective immune pathways that lead to some animals becoming resilient to infection to provide a road map for designing better vaccines and emphasizes the need for harnessing the potential of mucosal immunity.

Biomarkers as diagnostic tools for mycobacterial infections in cattle

Mycobacterial infections are widely distributed in animals and cause considerable economic losses, especially in livestock animals. Bovine paratuberculosis and bovine tuberculosis, which are representative mycobacterial infections in cattle, are difficult to diagnose using current-generation diagnostics due to their relatively long incubation periods. Thus, alternative diagnostic tools are needed for the detection of mycobacterial infections in cattle. A biomarker is an indicator present in biological fluids that reflects the biological state of an individual during the progression of a specific disease. Therefore, biomarkers are considered a potential diagnostic tool for various diseases. Recently, the number of studies investigating biomarkers as tools for diagnosing mycobacterial infections has increased. In human medicine, many diagnostic biomarkers have been developed and applied in clinical practice. In veterinary medicine, however, many such developments are still in the early stages. In this review, we summarize the current progress in biomarker research related to the development of diagnostic biomarkers for mycobacterial infections in cattle.

MicroRNAs as Biomarkers for Animal Health and Welfare in Livestock

MicroRNAs (miRNAs) are small and highly conserved non-coding RNA molecules that orchestrate a wide range of biological processes through the post-transcriptional regulation of gene expression. An intriguing aspect in identifying these molecules as biomarkers is derived from their role in cell-to-cell communication, their active secretion from cells into the extracellular environment, their high stability in body fluids, and their ease of collection. All these features confer on miRNAs the potential to become a non-invasive tool to score animal welfare. There is growing interest in the importance of miRNAs as biomarkers for assessing the welfare of livestock during metabolic, environmental, and management stress, particularly in ruminants, pigs, and poultry. This review provides an overview of the current knowledge regarding the potential use of tissue and/or circulating miRNAs as biomarkers for the assessment of the health and welfare status in these livestock species.