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Johne’s disease or paratuberculosis, caused by Mycobacterium avium subsp. paratuberculosis (MAP), occurs in domestic and wild animals worldwide, causing a significant economic loss to livestock industries. After a prolonged incubation time, infected cattle shed MAP bacilli into feces and spread the disease to an uninfected animal population. It is largely unknown how (or whether) the interplay between the pathogen and the host immunity determines timing of shedding after the long incubation time. Such information would provide an understanding of pathogenesis in individual animals and the epidemiology of MAP infection in animal populations. In this review, we summarize current knowledge of bovine Johne’s disease pathology, pathogenesis, immunology and genetics. We discuss knowledge gaps that direly need to be addressed to provide a science-based approach to diagnostics and (immuno)prophylaxis. These knowledge gaps are related to anatomical/clinical manifestation of MAP invasion, interaction of bacteria with phagocytes, granuloma formation, shedding, establishment and kinetics of adaptive immune responses in the pathogenesis of the disease. These topics are discussed at the molecular, cellular and tissue levels with special attention to the within host dynamics including the temporal and the spatial context relevant for the various host-pathogen interactions.

The widespread chronic enteritis known as Paratuberculosis (PTB) or Johne's disease (JD) is caused by Mycobacterium avium subspecies paratuberculosis (MAP), posing a significant threat to global public health. Given the challenges associated with PTB or JD, the development and application of vaccines are potentially important for disease control. The aim of this study was to design a multi-epitope vaccine against MAP. A total of 198 MAP genomes were analyzed using pan-genome and reverse vaccinology approaches. B-cell and T-cell epitope analysis was performed on the selected promising cross-protective antigens followed by selection of epitopes with high antigenicity, no allergenicity, and no toxicity for the design of the vaccine. The designed vaccine was evaluated through molecular dynamics simulations, molecular docking, and immunological simulations. The results revealed the identification of five promising cross-protective antigens. In total, 10 B-cell epitopes, 10 HTL epitopes, and 9 CTL epitopes were selected for the design of the vaccine. Both the vaccine candidate and the vaccine-TLR4 complex demonstrated considerable stability in molecular dynamics simulations. Molecular docking studies confirmed that the vaccine candidate successfully interacted with TLR4. Immunological simulations showed an increase in both B-cell and T-cell populations after vaccination. Additionally, the vaccine candidate exhibited a codon adaptability index of 1.0 and a GC content of 53.64%, indicating strong potential for successful expression in Escherichia coli . This research developed a multi-epitope vaccine targeting MAP through pan-genomes and reverse vaccinology methods, offering innovative strategies for creating effective vaccines against MAP.

Paratuberculosis (PTB) is a chronic granulomatous enteritis caused by Mycobacterium avium subsp. paratuberculosis (Map). Vaccination is one of the most cost-effective tools for PTB control, although alternative treatments like the probiotic Dietzia have been explored with promising results. Using a rabbit model, we investigated the association of immunological and microbiota profiles in Gut Associated Lymphoid Tissue (GALT) with the effects in protection induced by the administration of Dietzia spp., the commercial vaccine (Silirum ® ) and the combination of both. The treatment with the probiotic diminished inflammation, but failed to control Map burden, suggesting a detrimental effect. Rabbits treated with the probiotic presented the highest rates of tissue lesion extension, although the immunological profile was not suggestive of an inflammatory state. Map load in both vaccinated groups was similar indicating that both treatments are equally effective in eliminating the infection, suggesting the role of vaccination in eliminating the infection prevails over the immunomodulatory effects of the probiotic. There were slight variations in the presence of some taxonomic groups depending on the treatment, highlighting the complexity of microbial interactions and the need to optimise treatment combinations in the context of each disease and animal species.

Increasing evidence links a worldwide bacterial infection of cattle and other animal species by Mycobacterium avium ssp. paratuberculosis (MAP) to Crohn’s disease (CD). A large, FDA phase 2/3 controlled clinical trial of combination antimycobacterial antibiotic therapy for CD has been completed, and the report describing the trial is pending publication. The identification of MAP infection in CD patients will become increasingly important. Thus, it is desirable to develop MAP-based tests that accurately predict which CD patients have a MAP infection. A prospective, case-control laboratory test study of 199 subjects (61 CD patients and 138 non-CD controls) was performed using a panel of MAP antigens, including Hsp65, PknG, PtpA, CL1, and MAP IDEXX, which were measured under blind conditions in the plasma of the 199 subjects. Results showed that compared to any individual MAP antigen, combinations of antigens showed improved CD classification performance. For the Hsp65 antigen, the sensitivity (SEN), specificity (SPE), positive predictive value (PPV), negative predictive value (NPV), correct classification (CC), and area under the curve (AUC) were 59.02%, 58.70%, 38.71%, 76.42%, 59.3% and 0.606, respectively. For the best combination of MAP antibodies (Hsp65 and PknG), the SEN, SPE, PPV, NPV, CC, and AUC were 59.02%, 60.87%, 40.00%, 77.06%, 60.30%, and 0.631, respectively. Further improvement of the CD classification performance was achieved by combining IFN-γ, IL-8, and IL-17 cytokines with antibodies against MAP antigens, yielding SEN, SPE, PPV, NPV, CC, and AUC of 62.3%, 62.32%, 42.22%, 78.9%, 62.31% and 0.708, respectively. Thus, combinations of antibodies against MAP antigens and cytokine levels yield better CD diagnostic predictive performance than any individual antibodies against MAP antigens.

•MVA85A boost did not improve the immune response induced by 6611 strain + IFA adjuvant.•Priming with 6611 + ISA201 and boosting with MVA85A elicited the highest immune response.•The protection provided by the 6611 + ISA201 vaccine is enhanced by the MVA85A boost. Vaccination is the best strategy to control Paratuberculosis (PTB), which is a significant disease in cattle and sheep. Previously we showed the humoral and cellular immune response induced by a novel vaccine candidate against PTB based on the Argentinian Mycobacterium avium subspecies paratuberculosis (Map) 6611 strain. To improve 6611 immunogenicity and efficacy, we evaluated this vaccine candidate in mice with two different adjuvants and a heterologous boost with a recombinant modified vaccinia Ankara virus (MVA) expressing the antigen 85A (MVA85A). We observed that boosting with MVA85A did not improve total IgG or specific isotypes in serum induced by one or two doses of 6611 formulated with incomplete Freund’s adjuvant (IFA). However, when 6611 was formulated with ISA201 adjuvant, MVA85A boost enhanced the production of IFNγ, Th1/Th17 cytokines (IL-2, TNF, IL-17A) and IL-6, IL-4 and IL-10. Also, this group showed the highest levels of IgG2b and IgG3 isotypes, both important for better protection against Map infection in the murine model. Finally, the heterologous scheme elicited the highest levels of protection after Map challenge (lowest CFU count and liver lesion score). In conclusion, our results encourage further evaluation of 6611 strain + ISA201 prime and MVA85A boost in bovines.

Mycobacterium avium subsp. paratuberculosis (MAP) primarily invades ruminants' small intestine via the Peyer's patches in the ileum and jejunum. Despite ongoing efforts to develop effective MAP vaccines, the effects of live-attenuated vaccines on mucosal immunity remain poorly understood. Previous studies indicate that the BacA oral vaccine confers localized protection against MAP in the ileum and ileocecal valve of calves, but not in the jejunum. This protection correlates with heightened levels of peripheral blood immune cells exhibiting pro-inflammatory and memory traits. This study aimed to evaluate immune responses induced by oral BacA vaccination in the ileum and jejunum Peyer's patches, comparing protection at both sites through mucosal immune cell profiling and RNA-seq transcriptome analyses. It represents the first exploration of mucosal immune responses in Peyer's patches following oral MAP vaccination. Oral BacA immunization increased CD4 + IFNγ+ and CD4 + TNFα+ cell frequencies, along with the T effector memory to T central memory cell ratio, in the ileum and jejunum of BacA-vaccinated animals challenged with wildtype MAP, compared to the infection control group challenged solely with wildtype MAP. Immune cells isolated from the ileum of vaccinated-challenged animals exhibited significant upregulation in IFNγ, IP-10, TNFα, IL-2, IL-15, and IL-17 expression upon restimulation compared to the uninfected control group, whereas minimal differences were observed in the jejunum under similar conditions. RNA-seq data further indicated a more robust host response in the ileum across all experimental groups. Gene ontology analyses revealed genes associated with increased phagocytic and apoptotic activities in the vaccinated-challenged group. Overall, the BacA oral vaccine's effectiveness appears to vary primarily due to differences in antigen-specific gene expression between the ileum and jejunum, with the ileum showing a more robust host response. Understanding these effects on young calves' mucosal immunity and how live vaccines modulate immune responses is crucial for advancing mucosal vaccine development against MAP.

Current diagnostic methods for Johne’s disease in cattle allow reliable detection of infections with Mycobacterium avium ssp. paratuberculosis (MAP) not before animals are 2 years of age. Applying a flow cytometry-based approach (FCA) to quantify a MAP-specific interferon-gamma (IFN-γ) response in T cell subsets, the present study sought to monitor the kinetics of the cell-mediated immune response in experimentally infected calves. Six MAP-negative calves and six calves, orally inoculated with MAP at 10 days of age, were sampled every 4 weeks for 52 weeks post-inoculation (wpi). Peripheral blood mononuclear cells (PBMC) were stimulated with either purified protein derivatives (PPD) or whole cell sonicates derived from MAP (WCSj), M. avium ssp. avium or M. phlei for 6 days followed by labeling of intracellular IFN-γ in CD4 + and CD8 + T cells. No antigen-specific IFN-γ production was detectable in CD8 + cells throughout and the responses of CD4 + cells of MAP-infected and control calves were similar up to 12 wpi. However, the mean fluorescence intensity (MFI) for the detection of IFN-γ in CD4 + cells after WCSj antigen stimulation allowed for a differentiation of animal groups from 16 wpi onwards. This approach had a superior sensitivity (87.8%) and specificity (86.8%) to detect infected animals from 16 wpi onwards, i.e., in an early infection stage, as compared to the IFN-γ release assay (IGRA). Quantification of specific IFN-γ production at the level of individual CD4 + cells may serve, therefore, as a valuable tool to identify MAP-infected juvenile cattle.

Vaccination against paratuberculosis, before or after infection with Mycobacterium avium subsp. paratuberculosis (Map), could affect the progression of paratuberculosis, the development of lesions, the peripheral and local immune response, or the colonization of Map in tissues and its elimination through feces. An experimental study was conducted with thirty-five 1.5-month-old kids, which were separated into 6 experimental groups that include different intervention combinations (vaccinated, non-vaccinated, challenged and non-challenged) at different points and slaughtered at 120 and 330 days post-infection. The use of an inactivated vaccine against paratuberculosis could avoid clinical disease manifestation but does not prevent the tissue colonization, even when applied before Map exposure, achieving a reduction in the presence of viable bacteria in tissues and limiting the progression toward diffuse lesions. The therapeutic effect in vaccinated animals could not be confirmed. In this sense, vaccination not only modulates the immune response in terms of the production of IFN-γ and antibodies in peripheral blood and reduces tissue damage but also contributes to limiting the spread of infection through reduced bacterial shedding especially in goats vaccinated before Map infection.

RNA-Sequencing (RNA-Seq) studies using bovine samples from Mycobacterium avium subsp. paratuberculosis (MAP)-infected animals have identified a range of differentially expressed mRNAs with potential as biomarkers for MAP infection. As bioinformatic tools continue to develop, microRNAs (miRNAs) and alternative splicing (AS) have emerged as important contributors to host responses during infections. Although RNA-Seq enables AS analysis, most transcriptomic studies still emphasize gene-level expression due to the complexity of AS workflows, the need for deeper sequencing, and incomplete transcript annotations, even in humans. Nevertheless, interest in AS is growing, driven by its recognized role in tissue-specific functions and disease mechanisms. Recent findings have revealed distinct miRNAs and AS profiles in MAP-infected cattle compared to uninfected cows, indicating that post-transcriptional regulatory mechanisms are altered during MAP infection. In this comprehensive review, we examine critical aspects of post-transcriptional regulation in the context of MAP infection. We focus on recent studies investigating miRNAs and AS profiles, highlighting their roles in modulating immune responses and their potential as novel diagnostic biomarkers. Notably, overlapping mechanisms involving miRNAs and AS have been identified in paratuberculosis and in several human diseases, suggesting conserved pathways of host-pathogen interaction and immune regulation.

Recent evidence points at the role that human endogenous retroviruses (HERVs) may play through the activation of genes integrated across the human genome. Although a variety of genetic/epigenetic mechanisms maintain most HERVs silenced, independent environmental stimuli including infections may transactivate endogenous elements favoring pathogenic conditions. Several studies associated exposures to Mycobacterium avium subsp. paratuberculosis (MAP) with increased anti-MAP seroreactivity in T1D patients. Here, we assessed humoral responses against HERV envelope antigens (HERV-K and HERV-W ) and four MAP-derived peptides with human homologs in distinct populations: Sardinian children at T1D risk (rT1D) (n = 14), rT1D from mainland Italy (n = 54) and Polish youths with T1D (n = 74) or obesity unrelated to autoimmunity (OB) (n = 26). Unlike Sardinian rT1D, youths displayed increased anti-HERV-W Abs prevalence compared to age-matched OB or healthy controls (24.32 vs. 11.54%, p = 0.02 for Polish T1D/OB and 31.48 vs. 11.90%, p = 0.0025 for Italian rT1D). Anti-HERV-K responses showed variable trends across groups. A strong correlation between Abs levels against HERV-W and homologous peptides was mirrored by time-related Abs patterns. Elevated values registered for HERV-W overlaped with or preceded the detection of T1D diagnostic autoantibodies. These results support the hypothesis of MAP infection leading to HERV-W antigen expression and enhancing the production of autoantibodies in T1D.