Gastrointestinal parasite (GIP) infections pose significant challenges in pasture-based sheep farming, leading to economic losses and welfare concerns. This study aimed to uncover the genetic basis of resistance to Moniezia spp. infections in Central Anatolian Merino (CAM) sheep. Genome-Wide Association Analysis (GWAS) was conducted between Moniezia spp. egg burden and genomic data from 226 CAM lambs. Thirteen significant Single-Nucleotide Polymorphisms (SNPs) were identified, with five surpassing the genome-wide threshold and eight exceeding the chromosome-wide threshold. Functional annotation revealed associations with genes involved in immune function, notably CD79A and MAP3K7. CD79A, integral to B-cell activation and antibody production, plays a key role in the immune response against parasitic infections. Its interaction with helminth-derived proteins modulates B-cell function, highlighting its potential as a therapeutic target. MAP3K7, a central regulator of immune signaling pathways, modulates host responses to helminth infections by influencing NF-κB activity. Additionally, it regulates macrophage function in bacterial infections, showcasing its versatility in mediating immune responses against diverse pathogens. From a practical perspective, the findings of the current research underscore the potential of integrating genomic information into breeding programs to bolster disease resilience in livestock populations for sustainable production purposes. However, further research is needed to elucidate the functional significance of identified SNPs and associated genes. This study underscores the potential of genomic approaches in combating parasitic diseases and promoting sustainable agriculture in sheep production systems.

The bighorn sheep ( Ovis canadensis ), despite its close relation to domestic sheep, suffer higher morbidity and mortality from respiratory disease complexes, likely due to genetic differences in immune responses. Unraveling highly repetitive regions such as immune loci and genetic differences was problematic until now. We generated a bighorn sheep telomere-to-telomere assembly, adding 14.28% of novel sequence compared to the previous reference. This enabled the first complete immune loci annotation revealing the IGL and TR loci are significantly short in bighorn sheep. Importantly, a critical immune gene GBP5 and ZNF501 , involved in Golgi-mediated immune response, are lacking in bighorn but present in domestic sheep. Re-analysis of a Mycoplasma ovipneumoniae carriage study, using this assembly, identified the immune gene CAPN2 as a key genetic marker for disease carriage, not observable in the original study. This work provides a critical resource for identifying phenotype-linked genetic variation and exploring evolutionary adaptations of bighorn sheep.

Background: Flock-level prevalence and characterization of Mycoplasma ovipneumoniae is determined almost exclusively using nasal swabbing followed by molecular detection with either quantitative PCR or multi-locus sequence typing. However, the diagnostic performance and efficiency of swabbing the nasal passage compared to other anatomical locations has not been determined within sheep populations. The goal of this research was to assess the diagnostic capability of nasopharyngeal swabs in comparison to nasal swabs for the detection of Mycoplasma ovipneumoniae. Results: Nasal and nasopharyngeal swabs were collected during a controlled exposure study of domestic sheep with Mycoplasma ovipneumoniae. Both swab types were then analyzed via conventional and quantitative PCR. This dataset showed that the use of nasopharyngeal swabs in lieu of nasal swabs resulted in higher sensitivity, reduced inhibition during quantitative PCR, and higher bacterial copy numbers per swab. Moreover, it was demonstrated that diagnostic sensitivity could be further increased during quantitative PCR via ten-fold dilution of the extracted DNA. To confirm these observations in naturally infected animals, we conducted a field study employing a production flock of domestic sheep using both nasal and nasopharyngeal swabbing techniques. Extracted DNA was assessed using the same molecular techniques, where detection of Mycoplasma ovipneumoniae was confirmed by sequencing of either the rpoB or 16S rRNA gene. Similar improvements were observed for nasopharyngeal swabs and template treatment methods within the naturally infected flock. Conclusions: Results demonstrate increased diagnostic sensitivity and specificity when sampling with nasopharyngeal swabs as compared to nasal swabs. Therefore, alternate field-testing strategies employing nasopharyngeal swabs should be considered for diagnosis of the presence of M. ovipneumoniae. Importantly, sample treatment following acquisition was found to affect the sensitivity of quantitative PCR, where dilution of eluted DNA template doubled the calculated sensitivity. This demonstrates that, in addition to anatomical location, the presence of inhibitory components in swab extracts also strongly influences diagnostic performance.

Bighorn sheep (BHS) populations have been reported to experience high levels of morbidity and mortality following infection with Mycoplasma ovipneumoniae. This contrasts with the subclinical presentation in domestic sheep (DS). Understanding this difference requires baseline knowledge of pre- and post-infection immune responses of both species. The present study identifies differences in leukocyte phenotypes between adult BHS and DS before and after intranasal inoculation with 1 × 10⁸ Mycoplasma ovipneumoniae. Prior to inoculation, BHS were confirmed to have a higher abundance of leukocyte CD14 and serum concentrations of IL-36RA. In contrast, DS had a higher leukocyte abundance of CD16 in addition to previously observed integrin markers and CD172a, as well as greater serum TNF-α concentrations. Within 15 days of inoculation, BHS displayed signs of mild respiratory disease and M. ovipneumoniae DNA was detected on nasal swabs using a quantitative PCR; meanwhile, DS exhibited few to no clinical signs and had levels of M. ovipneumoniae DNA below the standard curve threshold. Immunologic markers remained relatively consistent pre- and post-inoculation in DS, while BHS demonstrated changes in the peripheral leukocyte expression of CD172a and CD14. Circulating serum IL-36RA decreased and CXCL10 increased within BHS. These findings highlight significant differences in cellular immunity between BHS and DS, raised and housed under similar conditions, prior to and following inoculation with M. ovipneumoniae.

Background: Coxiella burnetii is the causative agent of Q fever, a human disease that can be acquired from livestock. Diseases caused by this organism have caused great losses in livestock and human health. No vaccine is approved for use in the United States, and formalin-inactivated whole-cell vaccines pose a significant manufacturing risk for biocontainment. A subunit vaccine using recombinant peptides from C. burnetii would be safer and less resource-intensive to produce. This study used reverse vaccinology to expand our prediction sets of T-cell epitopes for the major histocompatibility complex (MHC) Class I and II alleles of cattle, sheep, and goats. Thereafter, the present results were compared with those from our previous prediction sets for mice and humans. Results: Small ruminant breed representation for the United States was ensured by querying whole genome sequences on the National Center for Biotechnology Information database. Consequently, twenty-two sheep MHC Class I, seventeen goat MHC Class I, and one goat MHC Class II alleles were added to the analyses, resulting in a total of fifty-six sheep MHC Class I, eighteen goat MHC Class II, and twenty-seven goat MHC Class II alleles. Predicted interactions of C. burnetii proteome-derived peptides with each MHC allele were categorized as strong, weak, or non-binding based on bioinformatic scores. Interspecies comparisons resulted in 256 peptides of interest for MHC Class II presentation and 766 peptides of interest for MHC Class I presentation. Of these, 51 peptides were predicted to bind with both classes of MHC alleles, of which 33 were newly identified. Conclusion: The high scoring T-cell epitope predictions identified in this study provide grounds for prioritizing subunit candidates to further develop a safe and perhaps broadly effective C. burnetii vaccine.

Domestic and bighorn sheep can both be infected by the bacterium Mycoplasma (Mesomycoplasma) ovipneumoniae. Disease presentation differs between these hosts, with bighorn sheep experiencing more severe outcomes; however, both species mount a humoral immune response following infection. This serological response has yet to be fully characterized; however, study of other species of Mycoplasma has demonstrated that disease severity can vary depending on the presence of antibodies, suggesting an important role of antibody production in disease manifestation. In the present study, a domestic sheep flock historically positive for M. ovipneumoniae was sampled to examine the relationship between the detection of the Mycoplasma in the nasal cavity and circulating antibodies. Our results revealed that animals harboring multiple M. ovipneumoniae strains exhibited more complex antigen banding patterns during immunocapillary reaction. Identification of candidate proteins driving the humoral response in domestic and bighorn sheep predominantly revealed adhesin and proteins containing domain of unknown function. These findings will enable future studies to elucidate the roles of these proteins in M. ovipneumoniae pathogenesis.