Bovine paratuberculosis (PTB), caused by Mycobacterium avium subsp. paratuberculosis (MAP), is a chronic granulomatous intestinal disease that leads to substantial economic losses in the global dairy industry. Current diagnostic tests have limited sensitivity, as they can reliably detect only animals that have advanced stages of disease characterized by diffuse lesions and with the presence of clinical signs, but fail to identify those in earlier or subclinical stages, with focal or multifocal lesions in gut tissues. Previous studies have suggested that multifocal granulomas prevent lesions progression, but the molecular mechanisms involved in the establishment and maintenance of a chronic MAP infection are not fully understood. This study aimed to compare the whole transcriptomic profiles of peripheral blood (PB) samples from Holstein cattle with multifocal lesions and those without lesions in gut tissues. Total RNA was extracted from samples from PB samples collected from 11 cows with multifocal lesions and no clinical signs of PTB, and from 4 control cows without lesions that tested negative in several PTB diagnostic assays. RNA libraries were prepared using 250 ng of RNA with the Illumina NEBNext Ultra Directional RNA library preparation kit and sequenced on an Illumina NextSeq sequencer. On average, 34.08 million raw reads were sequenced from PB samples. In cows with multifocal lesions compared with control cows, 1,272 differentially expressed genes (DEGs) were identified in PB. Protein-to-protein interaction analysis revealed that several DEGs were highly interconnected and associated with molecular processes related to splicing and translation inhibition, as well as with the activation of a robust innate immune response in PB. Overall, this study provides new insights into MAP pathogenesis and identifies potential biomarkers and therapeutic targets.

The Iberian lynx (Lynx pardinus) is one of the most endangered feline species in the world, and different infectious diseases, such as feline leukaemia virus, Aujeszky's disease or sarcoptic mange, have long posed a significant threat to its survival. Severe clinical disease caused by Sarcoptes scabiei have been reported in the Iberian lynx, however, the extent of S. scabiei infestations/infections in this species is unknown. In this context, we aimed (1) to assess S. scabiei exposure in Iberian lynx populations, and (2) to identify potential risk factors associated with parasite exposure. Between 2010 and 2023, 615 Iberian lynxes from captive (n = 270) and free-ranging (n = 345) populations were sampled across the Iberian Peninsula. Antibodies against S. scabiei were found in 15.4 % (95/615; 95 %CI: 12.8-18.5) of the Iberian lynxes using an in-house indirect enzyme-linked immunosorbent assay (ELISA) based on the immunodominant recombinant antigen Ssλ20ΔB3. Seropositive individuals were found in the three major free-range areas under study, such as the Central, Southern and Southwestern Iberian Peninsula. A significantly higher seroprevalence was detected in free-ranging (18.0 %) than in captive (12.2 %) lynxes. Logistic regression analysis identified "age" and "free-range sampling area" as potential risk factors for parasite exposure. Anti-S. scabiei antibodies were detected in lynxes sampled in each year of the study period, except for 2023, including five free-ranging yearlings sampled in 2012, 2019, 2020 and 2022. Our results confirm that both free-ranging and captive populations are naturally exposed to the parasite. The detected seroprevalence indicates moderate S. scabiei exposure of the Iberian lynx and provides evidence of endemic, widespread, and heterogeneous circulation of the parasite in lynx populations over the last two decades, which could be of animal health and even conservation concern. Additional studies are needed to assess the impact of S. scabiei in this vulnerable felid species.

Paratuberculosis (PTB) is a chronic enteritis caused by Mycobacterium avium subsp. paratuberculosis (Map). Genome-wide association studies revealed a significant enrichment of the keratinization pathway in cattle with multifocal lesions, suggesting a potential role of cytokeratins (CKs) in PTB resilience mechanisms. To confirm this, the amount of CK-expressing cells was analyzed in granulomas from the distal jejunum (DJE) and jejunal lymph nodes (DJELN) of animals with focal, multifocal, and diffuse lesions, and in control animals without lesions. Quantitative double-immunohistochemical (D-IHC) analysis [using Iba1 (ionized calcium-binding adapter molecule-1) and CK, as specific markers of macrophages and epithelial cells, respectively] showed that animals with multifocal lesions had the highest numbers of double-Iba1/CK positive cells [epithelioid macrophages (EMs)]. Significant differences were observed with the focal (p < 0.001), diffuse (p = 0.038), and control groups (p < 0.001) in JELN. Similarly, these animals showed higher numbers of single-CK expressing cells in JELN and DJE. Two EM distribution patterns were observed. In Pattern 1, mostly observed in animals with multifocal lesions (low Map load, no clinical signs), EMs form a barrier-like arrangement around the granuloma, while in Pattern 2, mainly found in animals with diffuse lesions (high Map load, clinical signs), EMs have a diffuse arrangement throughout the granuloma. These findings suggest that animals with multifocal lesions might represent a resilient phenotype that controls Map infection and disease progression. This is achieved through the formation of ordered granulomas that prevent Map dissemination and maintain tissue integrity, which are characteristic features of resilient animals. CK could be considered a potential biomarker of PTB resilience.

In 2010, rabbit hemorrhagic disease virus (RHDV) GI.2 emerged, and unlike RHDV GI.1, it caused mortality in young rabbits, while existing vaccines were not fully protective. The GI.2-specific monoclonal antibody (mAb) 2D9 has been used as a tool to discriminate between these viruses in diagnostic tests. In this study, we mapped the binding epitope for 2D9 on the GI.2 The VP60 capsid protein demonstrated the neutralizing capacity of this mAb, which was able to prevent GI.2 infections in an experimental challenge. Our results suggest that external loops (1, 4 and 5) in the P2 subdomain of VP60 contribute to the discontinuous neutralizing epitope recognized by mAb 2D9. Moreover, analysis of naturally occurring RHDV GI.2 isolates revealed key residues involved in mAb 2D9 binding that are under selective pressure. The findings described in this work provide valuable information regarding our understanding of virus neutralization and immune escape, which may help in the development of novel antiviral compounds.

European badgers (Meles meles) are reservoirs for animal tuberculosis (TB) in some European countries, complicating TB control in cattle. Badger vaccination and a deeper understanding of the subsequent protection mechanisms are necessary for effective TB control. In a previous study, two of eight badgers immunized with the heat-inactivated Mycobacterium bovis (HIMB) vaccine exhibited an unusual immune response (divergent), developing exacerbated lesions. The present study aimed to describe the local immune response in divergent badgers (those with severe disease progression), with respect to that observed in standard (where the vaccine showed efficacy) and control badgers. Immunohistochemistry was performed to evaluate immune cells (macrophages, T and B lymphocytes, plasma cells), and proteins (TGF-β, IL-10, Fox-P3) within TB granulomas in the lung and bronchial lymph node (LN), after TB challenge. Lung lesion volume, bacterial load and immunological response were also evaluated. The divergent immune response was characterized by elevated IL-10 and Fox-P3, few macrophages and high B lymphocytes (mainly in lungs), suggesting a Th1/Th2 imbalance with reduced Th1 cellular immunity leading to severe TB. In contrast, vaccinated badgers with a standard immune response showed a balanced response, with significantly lower bacterial loads (85.5% LN and 99.9% lung) than control group. This study provides new insights into the immune mechanisms in HIMB-vaccinated badgers, to improve TB control strategies.

Summary-data-based Mendelian randomization (SMR) analysis identified a novel cis-expression quantitative loci (cis-eQTL) associated with the upregulation of the expression of the early growth response factor 4 (EGR4) gene in animals with paratuberculosis (PTB)-associated multifocal lesions, which has been suggested to be modulating the NF-kβ-induced proinflammatory immune response to Mycobacterium avium subsp. paratuberculosis (Map) infection. To confirm these findings and to study the role of EGR4 expression in PTB resilience, the number of EGR4-expressing cells were analysed in paraffin-fixed gut tissues and regional lymph nodes of naturally Map-infected Holstein Friesian cows with focal, multifocal (subclinical and clinical), and diffuse lesions (intermediate and multibacillary), and in controls without lesions by quantitative anti-EGR4 immunohistochemistry. Subclinical animals with multifocal lesions showed a significantly higher number of EGR4-positive cells and were sacrificed at a significantly older average age than the remaining groups (p < 0.001 in all cases). We hypothesize that EGR4 could be mitigating the negative impact of Map infection on host clinical status through its involvement in three molecular mechanisms that promote resilience: (i) limiting NF-kβ-mediated proinflammatory responses, (ii) controlling tissue damage, acting as a brake on T-cell proliferation and cytokine production, and (iii) favouring tissue repair through interaction with epidermal growth factor receptor (EGFR).

A recent genome-wide association study identified 92 genetic variants in cattle with paratuberculosis (PTB)-associated multifocal lesions. Pathway analysis with the identified candidate genes revealed a significant enrichment of the keratinization (KRT) pathway in those animals. To confirm, at the protein level, this enrichment the number and distribution pattern of cytokeratin (CK)-expressing cells in granulomas of distal jejunum (DJE) and jejunal lymph nodes (JELN) of animals with different PTB-associated lesions (focal, multifocal and diffuse) and in control animals without lesions was determined by quantitative double-immunohistochemical analysis using Iba1 (ionized calcium-binding adapter molecule-1) and CK as specific markers of macrophages and epithelial cells, respectively. Animals with multifocal lesions showed the highest numbers of double-Iba1/CK positive cells (epithelioid macrophages (EMs)) showing significant differences with focal, diffuse and control animals in JELN and higher numbers of single-CK expressing cells in JELN and DJE. Two distribution patterns of the EMs in the granulomas were observed. In focal and multifocal animals EMs were surrounding the granuloma forming a barrier crucial to control Map infection while in animals with diffuse lesions (with significantly higher infection scores) EMs were throughout all the extension of the granuloma. Multifocal animals might be resilient to the disease as they control the shift from subclinical to the clinical through formation of ordered granulomas where EMs have a relevant role preventing Map dissemination and maintaining tissue integrity. Since CK expression was enriched in cattle with multifocal lesions, it could be considered as a potential biomarker of PTB resilience.

In this study we determined occurrence of mange in breeding rabbits on 1368 commercial farms in Portugal and Spain during 1996-2022. We obtained our information by carrying out 11 737 visits to 1334 doe farms, 11 farms only with growers, and 23 artificial insemination (AI) centres. The median size of the visited doe farms was 450 does (minimum to maximum: 100–2500 does) and 1175 does (ranging from100 to 6000 does) in 1996 and 2022, respectively. AI was used on 9% of the farms visited in 1996 and 95% in 2022. For our diagnoses we used (1) clinical observations on all visited farms to detect sarcoptic mange; (2) examination of the outer ear of breeding rabbits on a subset of farms to assess the prevalence of otodectic clinical mange (OCM); and (3) the examination of breeding rabbits and youngstock does (2.5 to 5.5 mo old) on a subset of 72 farms during 2018 to estimate prevalence of body mange compatible with cheyletiellosis. They were mainly clinical diagnoses, supported sometimes by a laboratorial confirmation. Over the course of the 27-yr clinical study, the cumulative incidence of sarcoptic mange was low; we recorded a total of 13 affected doe farms. The percentage of farms affected by OCM dropped from 55% in 1996 to 28% in 2022. OCM mean prevalence for the period 1996-2022 and 95% binomial confidence interval (CI) were 3.2% (95% CI [3.1-3.3%]), and 3.9% (95% CI [3.7-4.1%]) in does and bucks, respectively. We observed an improvement over time; the OCM yearly mean prevalence decreased from 7% in 1996 to 2.3% in 2022 in females and from 7.2% to 2.2% in males, respectively. This progress was compatible with the use of semen coming from AI centres; biosecurity measures and medical management also contributed. Genetic type was predisposing risk factor for OCM. Enabling risk factors were year and season (more affected in summer). Hair and skin disorders along the back, compatible with cheyletiellosis, were also assessed during 2018; we detected 50% of positive farms with various prevalence results in females, males or young does. In this study, we describe protocols observed in the control of benign and severe cases of mange in rabbitries, which included the use of ivermectin and synthetic acaricides. Ivermectin was used on 36% of doe farms visited during 2018-2022; we suggest that it should be used less often to lower its negative impact on the environment.

Little is known about the role of alternative splicing (AS) in regulating gene expression in Mycobacteria-infected individuals in distinct stages of infection. Pre-mRNA AS consists of the removal of introns and the assembly of exons contained in eukaryotic genes. AS events can influence transcript stability or structure with important physiological consequences. Using RNA-Seq data from peripheral blood (PB) and ileocecal valve (ICV) samples collected from Holstein cattle with focal and diffuse paratuberculosis (PTB)-associated histopathological lesions in gut tissues and without lesions (controls), we detected differential AS profiles between the infected and control groups. Four of the identified AS events were experimentally validated by reverse transcription-digital droplet PCR (RT-ddPCR). AS events in several genes correlated with changes in gene expression. In the ICV of animals with diffuse lesions, for instance, alternatively spliced genes correlated with changes in the expression of genes involved in endocytosis, antigen processing and presentation, complement activation, and several inflammatory and autoimmune diseases in humans. Taken together, our results identified common mechanisms of AS involvement in the pathogenesis of PTB and human diseases and shed light on novel diagnostic and therapeutic interventions to control these diseases.

MicroRNAs (miRNAs) regulate the post-transcriptional expression of genes by binding to their target mRNAs. In this study, whole miRNA sequencing was used to compare the expression of miRNAs in ileocecal valve (ICV) and peripheral blood (PB) samples of cows with focal or diffuse paratuberculosis (PTB)-associated lesions in gut tissues versus (vs) control cows without lesions. Among the eight miRNAs differentially expressed in the PB samples from cows with diffuse lesions vs controls, three (miR-19a, miR-144, miR32) were also down-regulated in cows with diffuse vs focal lesions. In the ICV samples, we identified a total of 4, 5, and 18 miRNAs differentially expressed in cows with focal lesions vs controls, diffuse lesions vs controls, and diffuse vs focal lesions, respectively. The differential expression of five microRNAs (miR-19a, miR-144, miR-2425-3p, miR-139, miR-101) was confirmed by RT-qPCR. Next, mRNA target prediction was performed for each differentially expressed miRNA. A functional analysis using the predicted gene targets revealed a significant enrichment of the RNA polymerase and MAPK signaling pathways in the comparison of cows with focal vs no lesions and with diffuse vs focal lesions, respectively. The identified miRNAs could be used for the development of novel diagnostic and therapeutical tools for PTB control.

Although mortality caused by Sarcoptes scabiei has been reported in European wild rabbit (Oryctolagus cuniculus) and Iberian hare (Lepus granatensis), there is a lack of detailed information regarding the exposure of wild lagomorph species to this parasite. Here, we aimed to determine the seroprevalence and potential risk factors associated with S. scabiei exposure in European wild rabbits and Iberian hares in Mediterranean ecosystems of southern Spain. Between 2018/2019 and 2021/2022 hunting seasons, serum samples from 464 wild rabbits and 132 Iberian hares were collected from 100 hunting grounds in Andalusia (southern Spain). Sera were tested using an in-house indirect ELISA to detect specific anti-S. scabiei antibodies based on the immunodominant protein Ssλ20ΔB3. The overall apparent individual seroprevalence was 15.9% (95/596; 95%CI: 13.0-18.9). Antibodies against S. scabiei were detected in 11.6% (54/464; 95%CI: 8.7-14.5) of the European wild rabbits and 31.1% (41/132; 95%CI: 23.2-39.0) of the Iberian hares. Species (Iberian hare), age (adults) and geographical area (western Andalusia) were identified as risk factors potentially associated with S. scabiei exposure using generalized estimating equation analysis. By applying spatial analysis, two significant cluster of high seropositivity were detected in western and central Andalusia, respectively. The seroprevalence values obtained provide evidence of endemic, widespread and heterogeneous exposure to S. scabiei among wild lagomorph populations in Spanish Mediterranean ecosystems. Our findings underscore the importance of implementing integrated surveillance programs for sarcoptic mange in wild lagomorphs as well as in other sympatric species.

Sarcoptic mange caused by Sarcoptes scabiei can have catastrophic consequences for wildlife. We inspected 122 Andean foxes (Lycalopex culpaeus), collected by active (n=66) or passive (n=56) surveillance, and 28 South American gray foxes (Lycalopex griseus; all from passive surveillance) for mange in Chile (2015-19). In Andean foxes, gross lesions of mange were diagnosed in 24% of passively and 9% of actively collected foxes, although observed prevalences might be underestimated. Seroprevalence was 37 and 18%, respectively, indicating that some individuals recovered from infection or were developing the disease. No differences were found between age and sex groups. Comparing data from passive surveillance, occurrence of gross lesions was lower in gray foxes (5%). Body condition was significantly better in Andean foxes without lesions than in diseased foxes, which had significantly lower albumin concentrations than healthy individuals. Among the 12 foxes with gross lesions, four, six and two individuals were categorized as having type I, type II, and type III lesions, respectively, based on clinical severity. Histologic severity correlated with gross lesions and included irregular epidermal hyperplasia with hyperkeratosis, which was marked in type II and III infections. Conventional PCR targeting of the cox1 gene fragment revealed four nucleotide sequence types, showing 99-100% identity among them and between 99% and 100% identity with previously published sequences of S. scabiei. A significant association between the occurrence of mange in foxes and distance to the nearest house was found. We speculate that diseased foxes tended to approach human settlements, perhaps in search of food. Visual inspection of 211 rural dogs from the study area did not reveal gross mange lesions in any animal. Sarcoptic mange is enzootic in the Andean fox in the study area and should be considered in the management of the species.

Tuberculosis BCG vaccination induced non-specific protective effects in humans led to postulate the concept of trained immunity (TRAIM) as an innate type of immune mechanism that triggered by a pathogen, protects against others. Killed vaccines have been considered not to be effective. However, field efficacy of a commercial vaccine against paratuberculosis, as well as of a recently developed M. bovis heat-inactivated vaccine (HIMB) prompted to test whether it could also induce TRAIM. To this, we used a sarcoptic mange rabbit model. Twenty-four weaned rabbits were treated orally or subcutaneously with a suspension of either HIMB (10 7 UFC) or placebo. Eighty-four days later the animals were challenged with approximately 5000 S. scabiei mites on the left hind limb. Skin lesion extension was measured every 2 weeks until 92 days post-infection (dpi). Two animals were killed at 77 dpi because of extensive skin damage. The rest were euthanized and necropsied and the lesion area and the mite burden per squared cm were estimated. Specific humoral immune responses to S. scabiei and to M. bovis were investigated with the corresponding specific ELISA tests. Subcutaneously and orally HIMB vaccinated animals compared with placebo showed reduced lesion scores (up to 74% and 62%, respectively) and mite counts (−170% and 39%, respectively). This, together with a significant positive correlation (r = 0.6276, p = 0.0031) between tuberculosis-specific antibodies and mite count at 92 dpi supported the hypothesis of non-specific effects of killed mycobacterial vaccination. Further research is needed to better understand this mechanism to maximize cross protection.

Mycobacterium avium subsp. paratuberculosis (MAP) causes bovine paratuberculosis (PTB). PTB is responsible for significant economic losses in dairy herds around the word. PTB control programs that rely on testing and culling of test-positive cows have been developed. Current diagnostics, such as ELISA for detecting MAP antibodies in serum samples and PCR detecting MAP DNA in feces, have inadequate sensitivity for detecting subclinical animals. Innovative “omics” technologies such as next-generation sequencing (NGS) technology-based RNA-sequencing (RNA-Seq), proteomics and metabolomics can be used to find host biomarkers. The discovered biomarkers (RNA, microRNAs, proteins, metabolites) can then be used to develop new and more sensitive approaches for PTB diagnosis. Traditional approaches for measuring host antibodies and biomarkers, such as ELISAs, northern blotting, quantitative reverse-transcriptase polymerase chain reaction (RT-qPCR), cDNA microarrays, and mass spectrometry are time-consuming, expensive, and sometimes exhibit poor sensitivity. With the rapid development of nanotechnology, low-cost monitoring devices for measuring antibodies against MAP proteins in point-of-care (POC) settings have been developed. Lateral flow assays (LFAs), in particular, are thought to be appropriate for the on-site detection of antibodies to MAP antigens and/or host biomarkers. This review aims to summarize LFAs that have recently been developed to accurately detect antibodies against MAP antigens, as well as the benefits that host biomarkers linked with MAP infection give to PTB diagnosis. The identification of these novel biomarkers could be the basis for the development of new LFAs. The dairy industry and producers are likely to benefit from reliable and rapid technologies capable of detecting MAP infection in situ to establish a quick and sensitive PTB diagnosis.

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.

Badgers (Meles meles) are a major tuberculosis (TB) reservoir in Europe, with the potential to transmit infection to cattle. Here we assessed whether a recently described oral tuberculosis vaccine based on heat-inactivated Mycobacterium bovis (HIMB), delivered as edible baits, can protect badgers from infection. Eight badgers were given individually five baits, each one consisting of a ball of peanut butter, natural peanut and oat flakes including a dose of the vaccine containing 5 × 107 colony-forming units. In parallel, a control group of seven badgers did not receive the vaccine. One month and a half later a second dose of the vaccine was offered to the vaccinated group. Ninety-four days after the second dose, all badgers were challenged with M. bovis (103 colony-forming units per animal) delivered endobronchially to the right middle lung lobe. Clinical, immunological, pathological and bacteriological variables were measured throughout the whole study to assess the efficacy of the vaccine. Two vaccinated animals showed high bacterial load of M. bovis and worsening of pathological lesions of TB. Conversely, the other six vaccinated animals showed slight improvement in bacterial load and pathology with respect to the control group. These results suggest that delivering the TB vaccine via food bait can partially protect wild badger populations, although vaccination can lead to either protection or tolerization, likely depending on the animal's immune status and general condition at the time of vaccination. Further optimization of the vaccination trial/strategy is needed to reduce the rate of tolerization, such as altering vaccine dose, number of doses, type of bait, use of adjuvants or route of administration.

Genome-wide association studies (GWAS) have identified host genetic variants associated with paratuberculosis (PTB) susceptibility. Most of the GWAS-identified SNPs are in non-coding regions. Connecting these non-coding variants and downstream affected genes is a challenge and, up to date, only a few functional mutations or expression quantitative loci (cis-eQTLs) associated with PTB susceptibility have been identified. In the current study, the associations between imputed whole-genome sequence genotypes and whole RNA-Sequencing data from peripheral blood (PB) and ileocecal valve (ICV) samples of Spanish Holstein cows (N = 16) were analyzed with TensorQTL. This approach allowed the identification of 88 and 37 cis-eQTLs regulating the expression levels of 90 and 37 genes in PB and ICV samples, respectively (False discorey rate, FDR ≤ 0.05). Next, we applied summary-based data Mendelian randomization (SMR) to integrate the cis-eQTL dataset with GWAS data obtained from a cohort of 813 culled cattle that were classified according to the presence or absence of PTB-associated histopathological lesions in gut tissues. After multiple testing corrections (FDR ≤ 0.05), we identified two novel cis-eQTLs affecting the expression of the early growth response factor 4 (EGR4) and the bovine neuroblastoma breakpoint family member 6-like protein isoform 2 (MGC134040) that showed pleiotropic associations with the presence of multifocal and diffuse lesions in gut tissues; P = 0.002 and P = 0.017, respectively. While EGR4 acts as a brake on T-cell proliferation and cytokine production through interaction with the nuclear factor Kappa β (NF-κß), MGC134040 is a target gene of NF-κß. Our findings provide a better understanding of the genetic factors influencing PTB outcomes, confirm that the multifocal lesions are localized/confined lesions that have different underlying host genetics than the diffuse lesions, and highlight regulatory SNPs and regulated-gene targets to design future functional studies.

Bovine paratuberculosis (PTB) is an infectious disease that affects ruminants worldwide and is a burden on the dairy industry. PTB control measures include culling of Mycobacterium avium subsp. paratuberculosis (MAP)-infected animals from the herd and the enhancement of farm-biosecurity measures. Diagnostics tools for the direct detection of MAP are fecal real-time qPCR and bacteriological culture, the last one being considered the gold standard. However, both show limitations for detecting subclinical MAP-infected cattle with low bacterial load in feces and gut tissues. Droplet digital polymerase chain reaction (ddPCR) is a third-generation PCR method that shows high reproducibility for the quantification of low DNA copy numbers. The objective of this study was to design a ddPCR assay to detect and quantify a fragment of the F57 MAP-specific sequence in samples of naturally MAP-infected Holstein cattle. DNA was isolated from whole-blood and fecal samples from control cows with a negative ELISA and qPCR result (N = 75) and from cows with PTB-associated focal (N = 32), multifocal (N = 21), and diffuse lesions (N = 17) in gut tissues. After ddPCR, the DNA extracted from fecal samples of cows with diffuse lesions showed higher mean copies per microliter (13,791.2 copies/μl) than samples from cows with multifocal lesions (78.8 copies/μl), focal lesions (177.1 copies/μl) or control cows (4.8 copies/μl) (P ≤ 0.05). Significant differences in mean DNA copies/μl were also observed in the blood samples from cows with focal lesions (47.7 copies/μl) when compared with cows with multifocal and diffuse lesions; 18.1 and 12.4 copies/μl, respectively. Using a principal component analysis, the results of the fecal ddPCR clustered together with the results of a commercial ELISA for the specific detection of MAP antibodies, fecal and tissue qPCR, and bacteriological culture results. In contrast, blood ddPCR results clustered together with the results of an ELISA for the detection of a biomarker of subclinical PTB, the ABCA13 transporter. Blood ddPCR was the most sensitive tool (sensitivity 71%, specificity 100%) of all the quantitative methods used in the study for the detection of subclinical cows with focal lesions.

Bovine paratuberculosis (PTB) is a chronic granulomatous enteritis, caused by Mycobacterium avium subsp. paratuberculosis (Map). The progression of PTB from subclinical to the clinical stage of the disease is determined locally at the level of the granuloma, a host defence hallmark against mycobacterial infection. Therefore, in-depth characterization of distinct cell populations controlling granuloma formation is critical to understanding PTB progression. Confocal laser scanning microscopy (CLSM) has been extensively used to visualize two or more proteins of interest concomitantly within a variety of cellular structures. As such, it is an invaluable tool for the correct identification and characterization of different cell populations. In this study, a novel approach, CLSM of whole-mount small intestinal mucosa samples, is used to characterize three-dimensional (3-D) paratuberculosis granulomas and epithelioid macrophages. Detailed optimized procedures to perform CLSM in whole mount small intestinal mucosa samples and also in formalin fixed paraffin embedded (FFPE) intestinal tissue sections of Holstein Friesian cows presenting different types of PTB-associated histological lesions are described.