Comparative transcriptional analysis identifies genes associated with the attenuation of Theileria parva infected cells after long-term in vitro culture.

Autologous administration of attenuated Theileria parva-infected cells induces immunity to T. parva in cattle. The mechanism of attenuation, however, is largely unknown. Here, we used RNA sequencing of pathogenic and attenuated T. parva-infected T-cells to elucidate the transcriptional changes underpinning attenuation. We observed differential expression of several host genes, including TRAIL, PD-1, TGF-ß and granzymes that are known to regulate inflammation and proliferation of infected cells. Importantly, many genes linked with the attenuation of the related T. annulata-infected cells were not dysregulated in this study. Furthermore, known T. parva antigens were not dysregulated in attenuated relative to pathogenic cells, indicating that attenuation is not due to enhanced immunogenicity. Overall this study suggests that attenuation is driven by a decrease in proliferation and restoration of the inflammatory profile of T. parva-infected cells. Additionally, it provides a foundation for future mechanistic studies of the attenuation phenotype in Theileria-infected cells.

Large scale transcriptional analysis of MHC class I haplotype diversity in sheep.

Domestic sheep (Ovis aries) have been an important component of livestock agricultural production for thousands of years. Preserving genetic diversity within livestock populations maintains a capacity to respond to changing environments and rapidly evolving pathogens. MHC genetic diversity can influence immune functionality at individual and population levels. Here, we focus on defining functional MHC class I haplotype diversity in a large cohort of Scottish Blackface sheep pre-selected for high levels of MHC class II DRB1 diversity. Using high-throughput amplicon sequencing with three independent sets of barcoded primers we identified 134 MHC class I transcripts within 38 haplotypes. Haplotypes were identified with between two and six MHC class I genes, plus variable numbers of conserved sequences with very low read frequencies. One or two highly transcribed transcripts dominate each haplotype indicative of two highly polymorphic, classical MHC class I genes. Additional clusters of medium, low, and very low expressed transcripts are described, indicative of lower transcribed classical, non-classical and genes whose function remains to be determined.

Association between blood miR-26a levels following artificial insemination, and pregnancy outcome in dairy cattle.

Early pregnancy diagnosis is key to maximise productivity of dairy herds. We previously showed that an increase in the levels of miR-26 could be detected as soon as day 8 of pregnancy in heifers. The aims of this study were to determine whether 1) plasma miR-26 levels would be distinctly elevated, retrospectively, early after artificial insemination in lactating cows with successful compared to failed pregnancies, 2) the early increase in miRNA levels in cows with successful pregnancy could be accounted for by changes in miRNA expression in white blood cells (WBCs), presumably induced by the effects of embryo-derived interferon tau (IFNt), and 3) plasma miRNA levels may provide a reliable early predictor of pregnancy that could be used at a herd level. Blood samples were taken from a total of 34 dairy cows (lactation number 1 to 4) before (D0) and 9 and 18 days after artificial insemination at oestrus, followed by confirmation of pregnancy status by ultrasound on D32. In addition, WBCs collected from non-pregnant cows (n = 4) were stimulated in vitro with recombinant ovine IFNt (0-100 pg/ml). Levels of miRNAs and ISG15, a known IFNt-induced gene, were quantified by qPCR. Relative to D0, a larger increase in plasma miR-26a (P = 0.04) occurred on D9 in cows later confirmed to be pregnant (n = 12) than in cows with a failed pregnancy (n = 22). Expression of miR-26a in WBCs was not affected (P>0.1) by pregnancy status or IFNt stimulation in vitro, in contrast to ISG15 expression which increased markedly (P<0.0001) both in WBC samples collected on D18 from animals later confirmed to be pregnant, and in WBCs after stimulation with IFNt in vitro. Finally, ROC analyses revealed that miR-26a on D9 or D18 could predict pregnancy outcome with much lower accuracy than WBC ISG15 on D18 (Likelihood ratio, 2.3 vs 15.4). In summary, a modest increase in plasma miR-26a levels occurs during early pregnancy in mature dairy cows which may not accounted for by changes in miRNA levels in WBCs or the effects of IFNt. Moreover, compared to ISG15, changes in miR-26a levels may not provide an accurate test for early diagnosis of pregnancy in cows.

High-Resolution Genotyping of Expressed Equine MHC Reveals a Highly Complex MHC Structure.

The Major Histocompatibility Complex (MHC) genes play a key role in a number of biological processes, most notably in immunological responses. The MHCI and MHCII genes incorporate a complex set of highly polymorphic and polygenic series of genes, which, due to the technical limitations of previously available technologies, have only been partially characterized in non-model but economically important species such as the horse. The advent of high-throughput sequencing platforms has provided new opportunities to develop methods to generate high-resolution sequencing data on a large scale and apply them to the analysis of complex gene sets such as the MHC. In this study, we developed and applied a MiSeq-based approach for the combined analysis of the expressed MHCI and MHCII repertoires in cohorts of Thoroughbred, Icelandic, and Norwegian Fjord Horses. The approach enabled us to generate comprehensive MHCI/II data for all of the individuals (n = 168) included in the study, identifying 152 and 117 novel MHCI and MHCII sequences, respectively. There was limited overlap in MHCI and MHCII haplotypes between the Thoroughbred and the Icelandic/Norwegian Fjord horses, showcasing the variation in MHC repertoire between genetically divergent breeds, and it can be inferred that there is much more MHC diversity in the global horse population. This study provided novel insights into the structure of the expressed equine MHC repertoire and highlighted unique features of the MHC in horses.

High throughput analysis of MHC class I and class II diversity of Zambian indigenous cattle populations.

The classical MHC class I and class II molecules play key roles in determining the antigenic-specificity of CD8+ and CD4+ T-cell responses-as such characterisation of the repertoire of MHCI and MHCII allelic diversity is fundamental to our ability to understand, and potentially, exploit how genetic diversity influences the outcome of immune responses. Cattle remain one of the most economically livestock species, with particular importance to many small-holder farmers in low-and-middle income countries (LMICs). However, our knowledge of MHC (BoLA) diversity in the indigenous breeds that form the mainstay of cattle populations in many LMICs remains very limited. In this study we develop a MiSeq-based platform to enable the rapid analysis of BoLA-DQA and BoLA-DQB, and combine this with similar platforms to analyse BoLA-I and BoLA-DRB repertoires, to study a large cohort of cattle (~800 animals) representing the 3 major indigenous breeds (Angoni, Barotse, Tonga) in Zambia. The data presented confirms the capacity of this high-throughput and high-resolution approach to provide a full characterisation of the MHCI-MHCII genotypes of cattle for which little previous MHC sequence data has been obtained. The cattle in Zambia were found to express a diverse range of MHCI, MHCII and extended MHCI-MHCII haplotypes. The combined MHCI-MHCII genotyping now possible opens new opportunities to rapidly expand our knowledge of MHC diversity in cattle that could find applications in a related translational disciplines such as vaccine development.

High throughput analysis of MHC-I and MHC-DR diversity of Brazilian cattle populations.

The major histocompatibility complex (MHC) contains many genes that play key roles in initiating and regulating immune responses. This includes the polymorphic MHCI and MHCII genes that present epitopes to CD8+ and CD4+ T-cells, respectively. Consequently, the characterisation of the repertoire of MHC genes is an important component of improving our understanding of the genetic variation that determines the outcomes of immune responses. In cattle, MHC (BoLA) research has predominantly focused on Holstein-Friesian animals (as the most economically important breed globally), although the development of high-throughput approaches has allowed the BoLA-DRB3 repertoire to be studied in a greater variety of breeds. In a previous study we reported on the development of a MiSeq-based method to enable high-throughput and high-resolution analysis of bovine MHCI repertoires. Herein, we report on the expansion of this methodology to incorporate analysis of the BoLA-DRB3 and its application to analyse MHC diversity in a large cohort of cattle from Brazil (>500 animals), including representatives from the three major Bos indicus breeds present in Brazil - Guzerat, Gir and Nelore. This large-scale description of paired MHCI-DRB3 repertoires in Bos indicus cattle has identified a small number of novel DRB3 alleles, a large number of novel MHCI alleles and haplotypes, and provided novel insights into MHCI-MHCII association - further expanding our knowledge of bovine MHC diversity.

Farmer and Veterinary Practices and Opinions Related to Fertility Testing and Pregnancy Diagnosis of UK Dairy Cows.

Dairy cow farming plays an important role in the UK and worldwide economies. Significant challenges are currently being faced regarding sustainability of the dairy industry. Dairy cow subfertility remains an important issue limiting herd productivity, resulting in annual losses of hundreds of millions of pounds in the UK alone. To address this, accurate monitoring of reproductive status and early detection of fertility issues in individual cows is essential. The aim of this study was to gather farmer and veterinarian opinions on current practices and perceived gaps related to diagnosis of fertility issues and pregnancy testing in UK dairy farms. Using online questionnaires, data were collected and analyzed from a total of 40 farmers and 59 veterinarians. The results showed that non-seen bulling checks and ultrasound were the most frequent tools to detect fertility issues, and that most farmers tested post-calving, and often again before or during mating. Most farmers believed that current tests did not meet their expectations, with half of those being willing to pay more than they were currently paying for fertility testing. In regard to pregnancy testing, ultrasound was most commonly used, at 30-50 days post-insemination either in individual or groups of cows. Again, most farmers believed that current tests did not meet their expectations, and a majority would consider paying a higher cost for a test that was better than those currently available. In addition, a majority of farmers would consider using a test that could detect pregnancy within 2 weeks post-insemination, if such test existed, because they believed it would help improve their herds' reproductive performance. Overall, the opinions of farmers and veterinarians indicate that there is significant scope for improving dairy herd fertility monitoring practices in the UK, through development of improved assays that can diagnose pregnancy and infertility earlier, are less disruptive to farm operations and are more cost effective than available tools. They also provide useful information to guide the future development and implementation of better diagnostics for improving reproductive performance of dairy cattle.

Analysis of Genetic Variation in the Bovine SLC11A1 Gene, Its Influence on the Expression of NRAMP1 and Potential Association With Resistance to Bovine Tuberculosis.

Bovine tuberculosis (bTB), caused by Mycobacterium bovis, is a chronic zoonotic disease where host genetics is thought to contribute to susceptibility or resistance. One of the genes implicated is the SLC11A1 gene, that encodes for the natural resistance-associated macrophage protein 1 (NRAMP1). The aim of this study was to identify SLC11A1 polymorphisms and to investigate any resulting functional differences in NRAMP1 expression that might be correlated with resistance/susceptibility to M. bovis infection. Sequencing of the SLC11A1 gene in cDNA isolated from Brown Swiss, Holstein Friesian, and Sahiwal cattle identified five single nucleotide polymorphisms (SNPs) in the coding region, but only one of these (SNP4, c.1066C>G, rs109453173) was present in all three cattle breeds and therefore warranted further investigation. Additionally, variations of 10, 11, and 12 GT repeats were identified in a microsatellite (MS1) in the SLC11A1 3'UTR. Measurement of NRAMP1 expression in bovine macrophages by ELISA showed no differences between cells generated from the different breeds. Furthermore, variations in the length of the MS1 microsatellite did not impact on NRAMP1 protein expression as analyzed by luciferase reporter assay. However, further analysis of the ELISA data identified that the presence of the alternative G allele at SNP4 was associated with increased expression of NRAMP1 in bovine macrophages. Since NRAMP1 has been shown to influence the survival of intracellular pathogens such as M. bovis through the sequestering of iron, it is possible that cattle expressing the alternative G allele might have an increased resistance to bTB through increased NRAMP1 expression in their macrophages.

Characterisation of serum IgG(T) responses to potential diagnostic antigens for equine cyathostominosis.

Cyathostomins are ubiquitous parasitic nematodes of horses. These worms spend substantial periods as intestinal wall stage encysted larvae, which can comprise up to 90% of the total burden. Several million larvae have been reported in individuals. Emergence of these larvae from the gut wall can lead to life-threatening colitis. Faecal egg count tests, increasingly used by horse owners to inform anthelmintic treatments, do not correlate with the intra-host burden of cyathostomins; this represents a key gap in the diagnostic toolbox. Previously, a cyathostomin Gut Associated Larval Antigen was identified as a promising marker for the intra-host stages of infection. Here, cyathostomin Gut Associated Larval Antigen and an additional protein, Cyathostomin Immuno-diagnostic antigen, were investigated to examine their value in providing information on cyathostomin burden. ELISA analyses examined serum IgG(T) responses to recombinant proteins derived from individual cyathostomin species. Receiver Operator Characteristic curve analysis was performed on the ELISA data; proteins with the highest Area Under the Curve values were selected to test protein combinations to investigate which were the most informative in identifying the infection status of individuals. Three cocktail combinations were tested, comprising: (a) Cy-GALA proteins from two species and a Cy-CID protein from a third species (CT3), (b) Cy-GALA proteins from five species (CT5), and (c) all CT5 components, plus a Cy-CID protein from an additional species (CT6). The best predictive values for infection were obtained using CT3 and CT6, with similar values achieved for both. Proteins in CT3 are derived from the most commonly reported species, Cyathostomum catinatum, Cylicocyclus nassatus and Cylicostephanus longibursatus. This combination was selected for future development since it represents a more commercially viable format for a diagnostic test.

A survey of the level of horse owner uptake of evidence-based anthelmintic treatment protocols for equine helminth control in the UK.

Interval treatment control programmes used widely in equine helminth control have favoured the development of anthelmintic resistance worldwide. Best practice guidelines have been designed to address resistance and include the requirement for improved pasture hygiene to break helminth transmission cycles, along with anthelmintic application informed by the results of diagnostic tests to reduce selection pressure for resistance. Using an online questionnaire, this study examined uptake of measures recommended in these guidelines by UK horse owners. The survey comprised 58 questions spanning grazing management, anthelmintic use and use of faecal egg count (FEC) testing to inform treatment decisions. Analysis was carried out using a combination of Chi-square and Mann-Whitney tests. In total, 705 owners responded and, following specific exclusion criteria, the responses of 652 individuals were analysed. The majority of the respondents owned <20 horses on private premises or livery yards in England. The main outputs of the survey were as follows. Overall, 60.9% of respondents used FEC tests to inform the requirement to administer anthelmintics, with macrocyclic lactones the most frequently-used anthelmintics. Of the respondents, 38% obtained advice on anthelmintic choice from their veterinarians; however, many respondents (43.8%) purchased anthelmintics via the internet. Encouragingly, 74.4% of respondents stated that they practiced good pasture hygiene by removing dung from pasture. Generally, there were differences between the responses of participants who based anthelmintic treatments on FEC testing (targeted treatments; TT) and those who practiced calendar-based anthelmintic treatments (interval treatments; IT). Briefly, the "key" findings from the Chi-square analysis included higher levels of satisfaction with the level of knowledge about equine parasites/parasitic diseases and higher levels of concern about anthelmintic resistance from TT-respondents compared to IT-participants. Confusion on the interpretation of quarantine recommendations was identified in this study group and there was poor uptake of testing for anthelmintic effectiveness. Overall, compared to previous reports, this study indicated improved engagement of UK horse owners with some helminth control practices recommended to reduce the spread of anthelmintic resistance. However, a proportion of respondents did not utilise these practices and there were still important gaps in the use of appropriate quarantine and efficacy testing. These identified gaps must be taken into consideration in knowledge dissemination activities in the future.

Conservation of a microRNA cluster in parasitic nematodes and profiling of miRNAs in excretory-secretory products and microvesicles of Haemonchus contortus.

microRNAs are small non-coding RNAs that are important regulators of gene expression in a range of animals, including nematodes. We have analysed a cluster of four miRNAs from the pathogenic nematode species Haemonchus contortus that are closely linked in the genome. We find that the cluster is conserved only in clade V parasitic nematodes and in some ascarids, but not in other clade III species nor in clade V free-living nematodes. Members of the cluster are present in parasite excretory-secretory products and can be detected in the abomasum and draining lymph nodes of infected sheep, indicating their release in vitro and in vivo. As observed for other parasitic nematodes, H. contortus adult worms release extracellular vesicles (EV). Small RNA libraries were prepared from vesicle-enriched and vesicle-depleted supernatants from both adult worms and L4 stage larvae. Comparison of the miRNA species in the different fractions indicated that specific miRNAs are packaged within vesicles, while others are more abundant in vesicle-depleted supernatant. Hierarchical clustering analysis indicated that the gut is the likely source of vesicle-associated miRNAs in the L4 stage, but not in the adult worm. These findings add to the growing body of work demonstrating that miRNAs released from parasitic helminths may play an important role in host-parasite interactions.

Strongyle egg reappearance period after moxidectin treatment and its relationship with management factors in UK equine populations.

Parasitic nematodes, particularly cyathostomins, are ubiquitous in grazing horses world-wide. Considerable burdens of cyathostomin larvae can encyst in the large intestinal wall. The most recommended treatment against these pathogenic stages is moxidectin. Information is required on how effective moxidectin is against cyathostomin populations in different regions. The objectives here were to determine the efficacy of moxidectin treatment and estimate the strongyle egg reappearance period (ERP) after treatment in several equine populations, to confirm the type of strongyle nematodes present and to identify other (i.e. management) factors associated with shortened ERP. Eight yards were recruited and moxidectin in combination with praziquantel administered to all horses (n=261). Faecal egg count (FEC) analysis was performed at weeks 0, 2, 6, 10 and 12 after treatment to determine efficacy and ERP. The ERP was estimated using two previously published methods. Morphological identification of cultured third stage larvae from the sample population was compared to a Strongylus vulgaris-specific end-point PCR to examine the presence of S. vulgaris in samples before and after treatment. Strongyle egg shedding patterns were also compared to worm management practices at each site. At 2 weeks post-treatment, moxidectin was highly effective (faecal egg count reduction range, 99.9-100%). The strongyle ERP ranged from 6 weeks to >12 weeks depending on the calculation method applied. Only cyathostomin larvae were detected by morphological identification. The results from the coprocultures and PCR showed that S. vulgaris was absent before and after treatment. Analysis revealed that regular faecal removal from pasture was associated with lower average FEC and lower prevalence of egg shedding.

Investigating interactions between UK horse owners and prescribers of anthelmintics.

Helminths are common pathogens of equids and anthelmintic resistance is a major issue in cyathostomin species and Parascaris equorum. At the heart of mitigating the impact of increasing anthelmintic resistance levels, is the responsible dissemination and use of these medicines following best practice principles. There is a paucity of information on interactions between horse owners and anthelmintic prescribers and how this shapes control. Here, a study was undertaken to determine opinions and experiences of horse owners as they relate to anthelmintics purchase and implementation of best practice control. An online survey was distributed via email and social media to explore owners' experiences of purchasing anthelmintics from United Kingdom prescribers, these being veterinarians, suitably qualified persons (SQPs) and pharmacists. Owner responses (n=494) were analysed statistically to compare answers of respondents grouped according to: (i) from whom they bought anthelmintics (Veterinarians n=60; SQPs n=256; Pharmacists n=42; More than one channel n=136), and (ii) by which route (Face-to-face n=234; Telephone n=31; Online n=226) they purchased. Owners who purchased from veterinarians predominantly did so face-to-face (81.3%), whilst those that bought from SQPs purchased via face-to-face (48.8%) and online (46.0%) interactions. Those who purchased from pharmacists predominantly bought anthelmintics online (76.2%). Participants who bought from veterinarians were more likely to view certain factors (i.e. time to talk to the supplier, supplier knowledge) as more important than those who purchased from other prescribers. Those who purchased from veterinarians were more likely to be recommended faecal egg count (FEC) test analysis; however, there was high uptake of FEC testing across all groups. There was a low uptake of anthelmintic efficacy testing; regardless of the prescriber type from whom anthelmintics were purchased. Those who purchased from veterinarians were more likely to agree that anthelmintics should be sold as veterinary prescription-only medicines. Those who purchased online (regardless of which type of prescriber they bought from) were less likely to consider prescriber advice or knowledge when deciding which product to buy and indicated that sellers were less likely to raise use of anthelmintics for targeting parasites. Across all groups, many owners stated that they were aware of or used non-chemical control measures such as dung removal and diagnostic FEC testing to target treatments. In summary, there were some differences in the type of advice provided at the point of purchase and this was dependent upon whom anthelmintics were purchased from and by which route they were bought.

Development of a recombinant protein-based ELISA for diagnosis of larval cyathostomin infection.

Cyathostomins are ubiquitous nematodes of horses. Once ingested, they can spend a substantial time as encysted larvae in the intestinal wall. The larvae can comprise up to 90% of the total burden, with up to several million worms reported in individuals. These stages can emerge in large numbers to cause life-threatening colitis. Direct methods for detection of encysted larval burdens in live horses do not exist. Previously, two antigen complexes were identified as promising markers for infection. A component of these, cyathostomin gut associated larval antigen-1 (Cy-GALA-1), was identified following immunoscreening of a complementary DNA library. Serum immunoglobulin G(T) (IgG(T)) responses to Cy-GALA-1 were shown to inform on larval infection. Sequence analysis of polymerase chain reaction products amplified from individual worms indicated that Cy-GALA-1 was derived from Cyathostomum pateratum. As cyathostomin infections always comprise multiple species, a diagnostic test must account for this. Here, segments of the Cy-gala gene were isolated from four common species, Cyathostomum catinatum, Cylicocyclus ashworthi, Cylicostephanus goldi and Cylicostephanus longibursatus, and the associated proteins expressed in recombinant form. The specificity and immunogenicity of each protein was confirmed. Each protein was assessed by enzyme linked immuno sorbent assay (ELISA) for its ability for informing on the presence of encysted larval infection and the level of burden.

A preliminary proteomic characterisation of extracellular vesicles released by the ovine parasitic nematode, Teladorsagia circumcincta.

Teladorsagia circumcincta is a major cause of ovine parasitic gastroenteritis in temperate climatic regions. The development of high levels of anthelmintic resistance in this nematode species challenges its future control. Recent research indicates that many parasite species release extracellular vesicles into their environment, many of which have been classified as endocytic in origin, termed exosomes. These vesicles are considered to play important roles in the intercellular communication between parasites and their hosts, and thus represent potentially useful targets for novel control strategies. Here, we demonstrate that exosome-like extracellular vesicles can be isolated from excretory-secretory (ES) products released by T. circumcincta fourth stage larvae (Tci-L4ES). Furthermore, we perform a comparative proteomic analysis of vesicle-enriched and vesicle-free Tci-L4ES. Approximately 73% of the proteins identified in the vesicle-enriched fraction were unique to this fraction, whilst the remaining 27% were present in both vesicle-enriched and vesicle-free fraction. These unique proteins included structural proteins, nuclear proteins, metabolic proteins, proteolytic enzymes and activation-associated secreted proteins. Finally, we demonstrate that molecules present within the vesicles-enriched material are targets of the IgA and IgG response in T. circumcincta infected sheep, and could potentially represent useful targets for future vaccine intervention studies.

Electrocardiographic indicators of excitability in horses for predicting recovery quality after general anaesthesia.

OBJECTIVE: To determine whether preoperative electrocardiographic measurements linked to sympathetic nervous activity could be used to predict recovery quality after general anaesthesia in horses. STUDY DESIGN: Prospective, clinical study. ANIMALS: Eighteen adult client-owned horses. METHODS: The electrocardiogram (ECG) was recorded presurgery in horses under three standard conditions: stabled unattended; with a groom whilst being led along a standard course; alone in the induction box. After surgery, each animal's recovery quality was scored by eight experienced anaesthetists or technicians using Donaldson's scoring system (2000). The digitized ECG recordings were analyzed for T-wave morphology, mean heart rate (HR), HR variability (HRV) and HRV derivatives including mean R-R interval, standard deviation of normal intervals (SDNN) and the root mean square of successive intervals (RMSSD), low (LF) and high frequency (HF) activity and the LF/HF ratio in both fast Fourier transformed and autoregressive spectra. Correlations between ECG variables and recovery score were examined using Spearman's rank correlation. RESULTS: There was no significant correlation between preanaesthetic ECG measurements and recovery quality. CONCLUSIONS: Predictions of recovery quality after general anaesthesia in horses cannot be based on preanaesthetic ECG variables. CLINICAL RELEVANCE: Measures other than those based on the ECG should be investigated as predictors of recovery quality.