Genotypic analysis of a localised hotspot of Pestivirus A (BVDV-1) infections in Northern Ireland.

BACKGROUND: Bovine viral diarrhoea (BVD) is caused by Pestivirus A and Pestivirus B. Northern Ireland (NI) embarked on a compulsory BVD eradication scheme in 2016, which continues to this day, so an understanding of the composition of the pestivirus genotypes in the cattle population of NI is required. METHODS: This molecular epidemiology study employed 5' untranslated region (5'UTR) genetic sequencing to examine the pestivirus genotypes circulating in samples taken from a hotspot of BVD outbreaks in the Enniskillen area in 2019. RESULTS: Bovine viral diarrhoea virus (BVDV)-1e (Pestivirus A) was detected for the first time in Northern Ireland, and at a high frequency, in an infection hotspot in Enniskillen in 2019. There was no evidence of infection with BVDV-2 (Pestivirus B), Border disease virus (pestivirus D) or HoBi-like virus/BVDV-3 (pestivirus H). LIMITATIONS: Only 5'UTR sequencing was used, so supplementary sequencing, along with phylogenetic trees that include all BVDV-1 genotype reference strains, would improve accuracy. Examination of farm locations and animal movement/trade is also required. CONCLUSIONS: Genotype BVDV-1e was found for the first time in Northern Ireland, indicating an increase in the genetic diversity of BVDV-1, which could have implications for vaccine design and highlights the need for continued pestivirus genotypic surveillance.

Behavioural Factors Influencing the Intention to Adopt Sheep Scab Control Measures in Northern Ireland.

Sheep scab, caused by infestation with the ectoparasitic mite Psoroptes ovis, is an endemic disease in the Northern Ireland (NI) sheep flock and constitutes significant economic and welfare burdens for the NI farming industry. Despite its endemic nature, historically, little research has been undertaken to support the control of the disease in NI. This study offers the first attempt to analyse the psychological and behavioural factors influencing farmers' intentions to implement effective sheep scab control measures in NI. To achieve our objective, quantitative data from a sample of 126 sheep farmers were statistically analysed using an extended theory of planned behaviour approach in an ordered logistic regression modelling framework. Our analyses showed that sheep scab remains an issue of concern in Northern Ireland. The attitudes of the farmers, as well as perceived behavioural control, emotional effect, membership of Business Development Groups (BDGs), and higher education qualifications, were found to be statistically significant factors influencing farmers' intentions to adopt sheep scab control measures. This study provides a solid foundation for how to promote behavioural changes among sheep farmers to improve their ability to implement effective disease control measures, helping to tackle this challenging disease in a more sustainable way in the future.

Quantification of the effect of in-utero events on lifetime resilience in dairy cows.

Currently, the dairy industry is facing many challenges that could affect its sustainability, including climate change and public perception of the industry. As a result, interest is increasing in the concept of identifying resilient animals, those with a long productive lifespan, good reproductive performance and milk yield. There is much evidence that events in utero, i.e., the Developmental Origins of Health and Disease (DOHaD), alter life-course health of offspring and we hypothesized that these could alter resilience in calves, where resilience is identified using lifetime data. The aim of this study was to quantify lifetime resilience scores (LRS) using an existing scoring system based on longevity with secondary corrections for age at first calving and calving interval and to quantify the effects of in-utero events on the LRS using 2 data sets. The first was a large data set of cattle in 83 farms in Great Britain born from 2006 to 2015 and the second was a smaller, more granular data set of cattle born between 2003 and 2015 in the Langhill research herd at Scotland's Rural College. Events during dam's pregnancy included health events (lameness, mastitis, use of an antibiotic or anti-inflammatory medication), the impact of heat stress as measured by temperature-humidity index and perturbations in milk yield and quality (somatic cell count, percentage fat, percentage protein and fat:protein ratio). Daughters born to dams that experienced higher temperature-humidity indexes while they were in-utero during the first and third trimesters of pregnancy had lower LRS. Daughter LRS scores were also lower where milk yields or median fat percentages in the first trimester were low, and when milk yields were high in the third trimester. Dam LRS was positively associated with LRS of their offspring, however, as parity of the dam increased, LRS of their calves decreased. Similarly, in the Langhill herd, dams of a higher parity produced calves with lower LRS. Additionally, dams which recorded a high max locomotion score in the third trimester of pregnancy were negatively associated with lower calf LRS in the Langhill herd. Our results suggest that events that occur during pregnancy have lifelong consequences for the calf's lifetime performance. However, experience of higher temperature-humidity indexes, higher dam LRS scores and mothers in higher parities explained a relatively small proportion of variation in offspring LRS, which suggests that other factors play a substantial role in determining calf LRS scores. While 'big data' can contain a considerable amount of noise, similar findings between the 2 data sets indicate it is likely these findings are real.

Analysis of the Veterinary Risk Assessment and Management Plan questionnaire responses for dairy herds enrolled in the Northern Ireland Johne's disease control programme.

Background: Animal Health and Welfare Northern Ireland has been enrolling dairy herds across Northern Ireland (NI) in a voluntary Johne's disease (JD) control programme since October 2020. A Veterinary Risk Assessment and Management Plan (VRAMP) questionnaire was completed for each herd enrolled and recommendations for improved farm management practices were provided to farmers. Herd JD testing was recommended but was not mandatory. Methods: This study analysed VRAMP responses for 1569 dairy herds that had enrolled in the JD control programme up to October 2022. Univariate and multivariate regression models were applied to the data as appropriate. Results: Overall, 21.4% of the dairy herds had completed herd JD screening, with 13.7% of herds reporting a confirmed case of JD. A further 31.5% of herds reported suspected case(s) of JD. Eighty-nine percent of farms had introduced animals from outside the herd. Herds that utilise a mixed calving pen and hospital pen, and herds that do not separate JD-positive or sick animals within the calving pen, were significantly (p > 0.001) more likely to be a high-probability JD herd. Accidental mixing of neighbouring herds significantly (p = 0.01) increased the risk of a suspected or confirmed case of JD. Herds that utilise rented land (70%) were significantly (p > 0.001) more likely to be at a high risk for JD. Conclusions: The VRAMP analysis identified areas of JD control that should be focused on in NI dairy herds, such as calving pen management and hygiene. The results highlight the importance of common JD recommendations in the management of on-farm disease risk.

Pestivirus apparent prevalence in sheep and goats in Northern Ireland: A serological survey.

BACKGROUND: Bovine viral diarrhoea virus (BVDV) and border disease virus (BDV) can cause significant health problems in ruminants and economic impacts for farmers. The aim of this study was to evaluate pestivirus exposure in Northern Ireland sheep and goat flocks, and to compare findings with a previous study from the region. METHODS: Up to 20 animals were sampled from 188 sheep and 9 goat flocks (n = 3,418 animals; 3,372 sheep and 46 goats) for pestivirus antibodies. Differentiation of the causative agent in positive samples was inferred using serum neutralisation. Abortion samples from 177 ovine cases were tested by BVDV reverse-transcription polymerase chain reaction and antigen ELISA. RESULTS: Apparent animal and flock (one antibody positive animal within a flock) prevalence was 1.7% and 17.3%, respectively, a statistically significant drop in apparent prevalence since a survey in 1999. 52.6% of samples testing positive had higher antibody titres to BVDV than to BDV. Of the ovine abortion samples, only one positive foetal fluid sample was detected by ELISA. CONCLUSION: The present study found that, since 1999, there has been a decrease in apparent animal and flock prevalence of 3.7 and 12.8 percentage points respectively, suggesting pestivirus prevalence has decreased across Northern Ireland between 1999 and 2018.

The Northern Ireland Control Programmes for Infectious Cattle Diseases Not Regulated by the EU.

The disease control programmes for Bovine Viral Diarrhoea (BVD), Infectious Bovine Rhinotracheitis (IBR), Johne's Disease (JD), Leptospirosis and Neosporosis are described including the approved diagnostic tools, diagnostic quality systems, and the role of vaccination (where appropriate). This paper describes the control programmes within NI, the challenges relating them, as well as assessing their impact and effectiveness, taking into consideration the quality of data available and number of herds participating. With the NI agricultural industry experiencing increasing financial pressures and post Brexit changes, the necessity of working to maximise the performance of bovine disease control programmes at the individual farm level as well as at the regional level is increasingly important. The programmes described fall into two categories with two distinct aims. Two managed by Animal Health & Welfare NI (AHWNI), the BVD eradication and JD Dairy Control programmes seek to eradicate or control infection at the regional level. A further 5 programmes, covering BVD, JD, IBR, Leptospirosis and Neosporosis, are managed by the Agri-Food and Biosciences Institute (AFBI) and focus on facilitating eradication or control at the individual herd level. These latter programmes conform to the Cattle Health Certification Standards (UK) (CHeCS) which is a UK self-regulatory body set up to ensure consistency between different disease control schemes across herds. The largest of all the programmes described is the AHWNI BVD Eradication Programme which has led to significant reductions in infection incidence. Compliance with it has been high with more than 97% of all cattle alive at the end of 2020 having a BVD test status. The rolling annual incidence of BVD virus positive calves has fallen by 56% since the start of the compulsory programme in 2016. This decrease has occurred largely through industry initiatives to deal with BVD positives, including the voluntary culling of persistently infected (PI) animals by herd owners, a voluntary abattoir ban on the slaughter of BVD virus (BVDv) positive animals, and the inclusion of retention of a BVDv positive animal as a non-conformance in the industry-run Farm Quality Assurance Scheme.

An Overview of Current Approaches and Challenges to the Control of Endemic Infectious Cattle Diseases in Albania.

Agriculture is an important production sector in Albania that makes a significant contribution to the gross domestic product (GDP) and employment. The livestock sector contributes more than half of the agricultural GDP. The Albanian cattle population represents 50% of the total livestock units and accounts for 85% of the national milk production, the rest being supplied by small ruminants. Cattle productivity, health and welfare are hindered by infectious diseases, some of which are also transmissible to humans (zoonosis). The aim of this manuscript is to provide an overview of the control of selected regulated and non-EU regulated cattle diseases in Albania and to highlight specific challenges for the Albanian cattle industry. The most important infectious cattle diseases in Albania for which national control and eradication strategies are in place are bovine brucellosis, bovine tuberculosis, and anthrax, which are all zoonotic. Additionally, lumpy skin disease recently emerged in the Balkan region and is currently subject to controls. Most of the available funds and European Union support are allocated to the control of EU regulated zoonotic diseases. For control of non-EU regulated cattle diseases, no funds are available resulting in the lack of national control programmes (CPs). Based on research, clinical investigations and laboratory results, several non-EU regulated cattle infectious diseases appear endemic in Albanian dairy farms. While no national CPs exist for any of them, regional initiatives are available on a voluntary basis to control infectious bovine rhinotracheitis and bovine viral diarrhea. In the voluntary CPs, there is no monitored requirement to prove disease freedom of purchased animals and to re-evaluate the herd's free status after the introduction of animals into a herd. Data on animal movements that are routinely collected could potentially be used to control the risk of purchase, but quality needs to be further improved to increase its usefulness in disease CPs. This overview aims to collate existing information on the CPs implemented in Albania and to evaluate these to highlight gaps and threats in disease control, as well as opportunities and strengths through a SWOT (Strengths, Weaknesses, Opportunities, and Threats) analysis, with the goal of providing a framework for the future implementation of animal disease control measures in Albania.

Existence and Quality of Data on Control Programs for EU Non-regulated Cattle Diseases: Consequences for Estimation and Comparison of the Probability of Freedom From Infection.

Some European countries have successfully implemented country-specific control programs (CPs) for infectious cattle diseases that are not regulated or are regulated only to a limited extent at the European Union (EU) level. Examples of such diseases include bovine viral diarrhea (BVD), infectious bovine rhinotracheitis (IBR), and Johne's disease (JD). The CPs vary between countries in the design and quality of collected data as well as methods used to detect infection and estimate prevalence or probability of freedom from infection. Differences in disease status between countries and non-standardized approaches to assess freedom from infection pose a risk for countries with CPs for non-regulated diseases as infected animals may influence the progress of the disease control or eradication program. The implementation of output-based standards allows estimation and comparison of the probability of freedom for non-regulated cattle diseases in European countries. The aim of the current study was to assess the existence and quality of data that could be used for estimating freedom from infection in European countries. The online data collection tool was sent to 32 countries participating in the SOUND control COST Action and was completed by 24 countries. Data on cattle demographics and data from CPs of IBR and BVD exist in more than 50% of the response countries. However, data describing risk factors and CP of JD was reported as existing in <25% of the countries. The overall quality of data in the sections on demographics and CPs of IBR and BVD were evaluated as "good", but risk factors and JD data were mostly evaluated as "fair." Data quality was considered less good mainly due to two quality criteria: accessibility and accuracy. The results of this study show that the quantity and quality of data about cattle populations and CPs are relatively similar in many surveyed countries. The outcome of this work provides an overview of the current situation in the European countries regarding data on EU non-regulated cattle diseases and will further assist in the development and implementation of output-based standards.

The Impact of Paratuberculosis on Milk Production, Fertility, and Culling in Large Commercial Hungarian Dairy Herds.

Paratuberculosis (PTBC) is a chronic disease caused by Mycobacterium avium subsp. paratuberculosis (MAP), which is common in dairy herds worldwide, although the scale of its impact on herd productivity is unclear. The aim of our study was to determine the differences between MAP ELISA positive vs. negative cows in terms of milk production and quality, reproductive parameters, and culling. The data of five large dairy herds that participated in the voluntary PTBC testing program in Hungary were analyzed. Cows were tested by ELISA (IDEXX Paratuberculosis Screening Ab Test, IDEXX Laboratories, Inc., Westbrook, ME, USA) using milk samples collected during official performance testing. The outcome of the initial screening test involving all milking cows in the herds was used for the classification of the cows. The 305-day milk production, reproduction and culling data of 4,341 dairy cows, and their monthly performance testing results (n = 87,818) were analyzed. Multivariate linear and logistic models, and right censored tobit model were used for the statistical analysis. Test-day and 305-day milk production of ELISA positive cows decreased by 4.6 kg [95% CI: 3.5-5.6 kg, P < 0.0001 (-13.2%)] and 1,030 kg [95% CI: 708-1,352 kg, P < 0.0001 (-9.4%)], compared to their ELISA negative herdmates, respectively. Milk ELISA positive cows had 35.8% higher [95% CI: 17.9-56.4%, P < 0.0001] somatic cell count, on average. Test positive cows conceived 23.2 days later [95% CI: 9.2-37.3 days, P = 0.0012 (+16.5%)] and their calving interval was 33.8 days longer [95% CI: 13.2-54.4 days, P = 0.0013, (+9.7%)], compared to the negative cows, on average. Milk ELISA positive cows were less likely to conceive to first insemination (odds ratio: 0.49, 95% CI: 0.31-0.75, P = 0.0013), and required 0.42 more inseminations to conceive [95% CI: 0.07-0.77, P = 0.0192 (+13.7%)], on average. Milk ELISA positive cows were culled 160.5 days earlier after testing compared to their ELISA negative herdmates (95% CI: 117.5-203.5 days, P < 0.0001). Our results suggest that MAP ELISA positive cows experience decreased milk production, milk quality, fertility, and longevity, which supports the need to control the prevalence of PTBC in dairy herds.

Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes project.

Background: Most publicly available genomes of Salmonella enterica are from human disease in the US and the UK, or from domesticated animals in the US. Methods: Here we describe a historical collection of 10,000 strains isolated between 1891-2010 in 73 different countries. They encompass a broad range of sources, ranging from rivers through reptiles to the diversity of all S. enterica isolated on the island of Ireland between 2000 and 2005. Genomic DNA was isolated, and sequenced by Illumina short read sequencing. Results: The short reads are publicly available in the Short Reads Archive. They were also uploaded to EnteroBase, which assembled and annotated draft genomes. 9769 draft genomes which passed quality control were genotyped with multiple levels of multilocus sequence typing, and used to predict serovars. Genomes were assigned to hierarchical clusters on the basis of numbers of pair-wise allelic differences in core genes, which were mapped to genetic Lineages within phylogenetic trees. Conclusions: The University of Warwick/University College Cork (UoWUCC) project greatly extends the geographic sources, dates and core genomic diversity of publicly available S. enterica genomes. We illustrate these features by an overview of core genomic Lineages within 33,000 publicly available Salmonella genomes whose strains were isolated before 2011. We also present detailed examinations of HC400, HC900 and HC2000 hierarchical clusters within exemplar Lineages, including serovars Typhimurium, Enteritidis and Mbandaka. These analyses confirm the polyphyletic nature of multiple serovars while showing that discrete clusters with geographical specificity can be reliably recognized by hierarchical clustering approaches. The results also demonstrate that the genomes sequenced here provide an important counterbalance to the sampling bias which is so dominant in current genomic sequencing.

Trends in Salmonella serovars and antimicrobial resistance in pigs and poultry in Northern Ireland between 1997 and 2016.

BACKGROUND: In the EU, salmonellosis is the second most commonly reported zoonosis. This pattern is reflected in Northern Ireland. Historically, foodborne salmonellosis has largely been attributed to the consumption of poultry products, and as such a number of legislative measures have been introduced by the EC. These policies focus mainly on five target Salmonella serovars. METHODS: Here the authors present a descriptive analysis of 20 years of data from the Northern Ireland National Reference Laboratory for Salmonella. RESULTS: The study's results show, for poultry submissions, a large decrease in the detection of four of the five targeted Salmonella serovars over the study period, with the fifth serovar undetected throughout the study. Additionally, there was an increase in the detection of a number of other non-regulated serovars. In pigs, S Typhimurium, which is among the most common causes of human salmonellosis, was the most commonly isolated serovar. When comparing levels of antimicrobial resistance in S Typhimurium between livestock groups, the authors found a decrease over time in poultry, but an increase in pigs, highlighting the potential significance of pigs in addressing public health concerns. CONCLUSION: The authors conclude that continued surveillance is important in the assessment of control measures at a national and transnational scale.

Is There a Relationship Between Bovine Tuberculosis (bTB) Herd Breakdown Risk and Mycobacterium avium subsp. paratuberculosis Status? An Investigation in bTB Chronically and Non-chronically Infected Herds.

Background: Bovine tuberculosis (bTB; Mycobacterium bovis) remains a significant problem in a number of countries, and is often found where M. avium subsp. paratuberculosis (MAP) is also present. In the United Kingdom, bTB has been difficult to eradicate despite long-term efforts. Co-infection has been proposed as one partial mechanism thwarting eradication. Methods: A retrospective case-control study of 4,500 cattle herds in Northern Ireland, where serological testing of cattle for MAP, was undertaken (2004-2015). Blood samples were ELISA tested for MAP; infection of M. bovis was identified in herds by the comparative tuberculin test (CTT) and through post-mortem evidence of infection. Case-herds were those experiencing a confirmed bTB breakdown; control-herds were not experiencing a breakdown episode at the time of MAP testing. A second model included additional testing data of feces samples (culture and PCR results) to better inform herd MAP status. Multi-level hierarchical models were developed, controlling for selected confounders. A sensitivity analysis of the effect of MAP sample numbers per event and the prior timing of tuberculin-testing was undertaken. Results: 45.2% (n = 250) of case observations and 36.0% (3,480) of control observations were positive to MAP by ELISA (45.8% and 36.4% when including ancillary fecal testing, respectively). Controlling for known confounders, the adjusted odds ratio (aOR) for this association was 1.339 (95%CI:1.085-1.652; including ancillary data aOR:1.356;95%CI:1.099-1.673). The size-effect of the association increased with the increasing number of samples per event used to assign herd MAP status (aOR:1.883 at >2 samples, to aOR:3.863 at >10 samples), however the estimated CI increased as N decreased. 41.7% of observations from chronic herds were MAP serology-positive and 32.2% from bTB free herds were MAP positive (aOR: 1.170; 95%ci: 0.481-2.849). Discussion: Cattle herds experiencing a bTB breakdown were associated with increased risk of having a positive MAP status. Chronic herds tended to exhibit higher risk of a positive MAP status than bTB free herds, however there was less support for this association when controlling for repeated measures and confounding. MAP co-infection may be playing a role in the success of bTB eradiation schemes, however further studies are required to understand the mechanisms and to definitively establish causation.

Associations between paratuberculosis ELISA results and test-day records of cows enrolled in the Irish Johne's Disease Control Program.

The effect of the Mycobacterium avium ssp. paratuberculosis (MAP) ELISA status on test-day milk performance of cows from Irish herds enrolled in the pilot national voluntary Johne's disease control program during 2013 to 2015 was estimated. A data set comprising 92,854 cows and 592,623 complete test-day records distributed across 1,700 herds was used in this study. The resulting ELISA outcome (negative, inconclusive, and positive) of each cow within each year of the program was used to allocate the cow into different scenarios representing the MAP status. At MAPscenario1, all cows testing ELISA nonnegative (i.e., inconclusive and positive) were assigned a MAP-positive status; at MAPscenario2 only cows testing ELISA-positive were assigned a MAP-positive status; at MAPscenario3 only cows testing ELISA nonnegative (inconclusive or positive) and gathered exclusively from herds where at least 2 further ELISA nonnegative (inconclusive or positive) cows were found were assigned a MAP-positive status; at MAPscenario4 only cows testing ELISA-positive that were gathered exclusively from herds where at least 2 further ELISA-positive cows were found were assigned a MAP-positive status. Milk outputs based on test-day records were standardized for fat and protein contents (SMY) and the effect of MAP ELISA status on the SMY was estimated by a linear mixed effects model structure. The SMY mean difference recorded at test day between cows with a MAP-positive status and those with a MAP-negative status within MAPscenario1 was estimated at -0.182 kg/test day; the mean difference was -0.297 kg/test day for MAPscenario2; for MAPscenario3 mean difference between MAP-positive status and MAP test-negative cows was -0.209 kg/test day, and for MAPscenario4, the difference was -0.326 kg/test day.

Risk factors for failure to detect bovine tuberculosis in cattle from infected herds across Northern Ireland (2004-2010).

Correctly identifying animals that are truly infected with a pathogen using ante-mortem tests is the cornerstone of any disease eradication programme. Failure to identify all infected animals will impede the progress towards controlling and eradicating disease and may also have unforeseen consequences when specific prevention measures are in place to avoid animal-to-animal transmission. In the case of bovine tuberculosis (bTB), the screening ante-mortem test, the Single Comparative Intradermal Tuberculin Test (SCITT), can exhibit moderate sensitivity which can result in a "hidden burden" of infection residing within the population. Using an animal-level dataset relating to the disclosure of infected cattle with Mycobacterium bovis, the causative agent of bTB within infected herds in Northern Ireland, we investigated what factors influenced the probability of an animal being a false-negative when truly infected (using post-mortem (PM) microbiological culture confirmation results to assess infection status). We found that different risk factors affected the probability of a test-negative outcome on infected animals depending on the ante-mortem test or their combination (SICTT and/or interferon gamma (IFN-É£) testing). Using multivariable models, SCITT disclosure performance varied significantly by age, location (region), and production type. The IFN-É£ tests were significantly affected by region or season, but these effects depended on the cut-off used during interpretation of the test which affected the tests characteristics. Parallel use of SCITT and IFN-É£ tests resulted in the least number of false-negatives, and their disclosure was affected by season and age-class. Understanding the factors that lead to the non-disclosure of infected animals is essential to optimise large-scale bTB disease eradication programmes.

Bayesian estimation of prevalence of paratuberculosis in dairy herds enrolled in a voluntary Johne's Disease Control Programme in Ireland.

Bovine paratuberculosis is a disease characterised by chronic granulomatous enteritis which manifests clinically as a protein-losing enteropathy causing diarrhoea, hypoproteinaemia, emaciation and, eventually death. Some evidence exists to suggest a possible zoonotic link and a national voluntary Johne's Disease Control Programme was initiated by Animal Health Ireland in 2013. The objective of this study was to estimate herd-level true prevalence (HTP) and animal-level true prevalence (ATP) of paratuberculosis in Irish herds enrolled in the national voluntary JD control programme during 2013-14. Two datasets were used in this study. The first dataset had been collected in Ireland during 2005 (5822 animals from 119 herds), and was used to construct model priors. Model priors were updated with a primary (2013-14) dataset which included test records from 99,101 animals in 1039 dairy herds and was generated as part of the national voluntary JD control programme. The posterior estimate of HTP from the final Bayesian model was 0.23-0.34 with a 95% probability. Across all herds, the median ATP was found to be 0.032 (0.009, 0.145). This study represents the first use of Bayesian methodology to estimate the prevalence of paratuberculosis in Irish dairy herds. The HTP estimate was higher than previous Irish estimates but still lower than estimates from other major dairy producing countries.

Novel Monoclonal Antibody and Peptide Binders for Mycobacterium avium subsp. paratuberculosis and Their Application for Magnetic Separation.

The generation of novel Mycobacterium avium subsp. paratuberculosis (MAP)-specific monoclonal antibodies and phage-display derived peptide binders, along with their application for the magnetic separation (MS) of MAP cells, is described. Our aim was to achieve even greater MAP capture capability than is possible with peptide-mediated magnetic separation (PMS) using a 50:50 mix of biotinylated-aMp3 and biotinylated-aMptD peptide-coated beads. Gamma-irradiated whole MAP cells and ethanol extracted antigens (EEA) from these cells were used to elicit an immune response and as phage-display biopanning targets. A range of novel binders was obtained and coated onto paramagnetic beads, both individually and in various combinations, for MS evaluation. IS900 PCR was employed after MS to provide quick results. Capture sensitivity was assessed using a range of MAP concentrations after which the most promising beads were tested for their specificity for MAP, by performing MS followed by culture using 10 other Mycobacterium species. Magnetic beads coated with the biotinylated EEA402 peptide demonstrated a greater level of MAP capture than the current PMS method, even when low numbers of MAP (<10 cfu/ml) were present; however these beads also captured a range of other mycobacteria and so lacked capture specificity. Magnetic beads coated with monoclonal antibodies 6G11 and 15D10 (used as a 50:50 mix or as dually coated beads) also demonstrated improved MAP capture relative to the current PMS method, but with little cross-reactivity to other Mycobacterium spp. Therefore, two new MS protocols are suggested, the application of which would be dependent upon the required endpoint. Biotinylated EEA402-coated beads could potentially be used with a MAP-specific PCR to ensure detection specificity, while beads coated with 6G11 and 15D10 monoclonal antibodies could be used with culture or the phage amplification assay.