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

Bayesian latent class modelling of true prevalence in animal subgroups with application to bovine paratuberculosis infection

The prevalence of an infectious disease of animals living in separate groups (e.g. herds) is naturally analyzed using a Bayesian hierarchical latent class model. We propose an extension to this methodology by including subgroup level prevalence measures within the groups of animals. As an application illustrating the merits of our methodology, we reassessed the prevalence of bovine paratuberculosis (PTBC) infection in Hungarian commercial dairy farms. Our aim was to consolidate previous findings using a large amount of recent data and priors based on historical data. To model the subgroup level infection prevalence within animal groups, we considered correlated prevalences following beta distributions derived from independent normally distributed random herd effects. In the application, infection status of herds was handled as latent classes, multiparous and primiparous cows as within-herd subgroups. The novel methodology allows us to estimate both the mean and median conditional within-herd true prevalence (CWHP) related to each animal subgroup as well as other measures characterizing the interrelation of subgroups. The results of the application aligned with the findings of the former PTBC study, while the more recent and considerably larger dataset and the use of historical priors increased the reliability of the results. The STAN and JAGS codes of the application are available in Supplementary material.

An observational study of ear-tagged calf mortality (1 to 100 days) on Irish dairy farms and associations between biosecurity practices and calf mortality on farms participating in a Johne's disease control program

Postnatal mortality among replacement stock has a detrimental effect on the social, economic, and environmental sustainability of dairy production. Calf mortality rates vary between countries and show differences in temporal trends; most, however, are characterized by high levels of between-farm variability. Explaining this variation can be difficult because herd-level information on management practices relevant to calf health is often not available. The Irish Johne's Control Programme (IJCP) contains a substantial on-farm monitoring program called the Veterinary Risk Assessment and Management Plan (VRAMP). Although this risk assessment is largely focused on factors relevant to the transmission of paratuberculosis, many of its principles are good practice biocontainment policies that are also advocated for the protection of calf health. The objectives of this study were (1) to quantify mortality in ear-tagged Irish dairy calves between 2016 and 2020 using both survival and risk approaches, (2) to determine risk factors for 100-d cumulative mortality hazard in ear-tagged Irish dairy calves between 2016 and 2020, (3) to determine whether 100-d cumulative mortality hazard was higher in ear-tagged calves within herds registered in the IJCP versus those that were not registered in the IJCP and whether there were differences between these cohorts over time, and (4) within IJCP herds, to determine whether VRAMP score or changes in VRAMP score were associated with 100-d cumulative mortality hazard. Excluding perinatal mortality, the overall 100-d cumulative mortality hazard was 4.1%. Calf mortality was consistently underestimated using risk approaches that did not account for calf censoring. Cox proportional hazards models showed that cumulative mortality hazard was greater in male calves; particularly, calves born to Jersey breed dams and those with a beef breed sire. Mortality hazard increased with increasing herd size, was highest in calves born in herds that contract-reared heifers, and lowest in those born in mixed dairy-beef enterprises. Mortality hazard decreased over time with the mortality hazard in 2020 being 0.83 times that of 2016. Mortality hazard was higher in IJCP-registered herds than nonregistered herds (hazard ratio 1.06, 95% CI 1.01-1.12), likely reflecting differences in herds that enrolled in the national program. However, we detected a significant interaction between IJCP status (enrolled vs. not enrolled) and year (hazard ratio 0.96, 95% CI 0.92-1.00), indicating that the decrease in mortality hazard between 2016 and 2020 was greater in IJCP herds versus non-IJCP herds. Finally, increasing VRAMP scores (indicating higher risk for paratuberculosis transmission) were positively associated with increased calf mortality hazard. Postnatal calf mortality rates in Irish dairy herds declined between 2016 and 2020. Our study suggests that implementation of recommended biocontainment practices to control paratuberculosis in IJCP herds was associated with a reduction in calf mortality hazard.

Bayesian diagnostic test evaluation and true prevalence estimation of mycoplasma bovis in dairy herds

The true prevalence of dairy cattle herds with M. bovis infections in the Netherlands is unknown. Previous attempts to estimate prevalences were hampered by the absence of a diagnostic serological test that was validated under field conditions. This study estimated sensitivity and specificity of two commercial serum ELISAs and the true M. bovis herd prevalence using different Bayesian latent class models. A total of 7305 serum samples from 415 randomly chosen dairy herds were collected in fall/winter 2019 and investigated for presence of antibodies against M. bovis using the BIO-K-260 ELISA from Bio-X. Serum samples from 100 of these herds were also tested with a second ELISA, from IDvet. A Bayesian latent class model using the paired test results estimated a sensitivity of 14.1% (95% Bayesian probability interval (BPI): 11.6-16.7%) for the Bio-X ELISA and a specificity of 97.2% (95% BPI: 95.9-98.4%). Sensitivity and specificity for the IDvet ELISA were estimated at 92.5% (95% BPI: 88.3-96.5%) and 99.3% (95% BPI: 98.7-99.8%), respectively. Also, Bio-X ELISA sensitivity was considerably higher with data from calves only and with data from a selection of herds with a clinical outbreak, whereas the IDvet ELISA sensitivity was fairly constant under these conditions. These differences in test sensitivity is expected to be related to an effect of time since infection. A second Bayesian model, applied on test results of all 415 herds, estimated a true herd prevalence of 69.9% (95% BPI: 62.7-77.6%), suggesting M. bovis in endemic amongst dairy cattle herds in the Netherlands. To what extent seropositive herds have experienced a clinical outbreak needs further investigation.

Evaluation of Single Nucleotide Polymorphisms (SNPs) Associated with Genetic Resistance to Bovine Paratuberculosis in Marchigiana Beef Cattle, an Italian Native Breed

Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of paratuberculosis (PTB), a widespread chronic enteritis of ruminants. The progression of the infection depends on the containment action of innate and cell-mediated immunity (CMI), and it is related to environmental and genetic factors. In particular, PTB susceptibility seems to be associated with specific genes coding for immune regulators involved in the cell-mediated response during the infection. The aim of this preliminary study was to verify, in Italian beef cattle, an association between MAP infectious status and the presence of single nucleotide polymorphisms (SNPs) in candidate genes. To the best of our knowledge, this is the first investigation conducted on a native beef cattle breed, known as Marchigiana, reared in Central Italy. The present research, based on a longitudinal study, aimed to identify and correlate phenotypic and genetic profiles characteristic of the subjects potentially able to contrast or contain PTB. In a MAP-infected herd, ELISA, IFN-γ tests, qPCR, and cultures were performed at a follow-up, occurring within a period ranging from three to six years, to evaluate the individual state of infection. Animals testing positive for at least one test were considered infected. DNA samples of 112 bovines, with known MAP statuses, were analyzed to verify an association with SNPs in the genes encoding gamma-interferon (BoIFNG), interleukin receptor 10 (IL10RA), interleukin receptor 12 (IL12RB2), and toll-like receptors (TLR1, TLR2, TLR4). Regarding statistical analysis, the differences among target genes and pairs of alleles in the analyzed groups of animals, were evaluated at a significance level of p < 0.05. For IL10RA and for IL12RB2 genes, relevant differences in genotypic frequencies among the considered cattle groups were observed. For all candidate genes studied in this investigation, SNP genotypes already associated with PTB resistance were found more frequently in our population, suggesting potential resistance traits in the Marchigiana breed.

Association between the severity of histopathological lesions and Mycobacterium avium subspecies paratuberculosis (MAP) molecular diversity in cattle in southern Chile

The objective was to evaluate the association between the severity of histopathological lesions caused by Mycobacterium avium subspecies paratuberculosis (MAP) infection and the molecular diversity of this pathogen. Blood, ileum, and mesenteric lymph node samples were collected at slaughter, from 1,352 adult cattle [source population 1 (SP1)]. In addition, 42 dairy herds (n = 4,963 cows) were followed for 2 years, and samples from compatible paratuberculosis clinical cases [source population 2 (SP2)] were collected. MAP infection was confirmed using an ELISA test, liquid media culture, and PCR. Isolates were genotyped using five MIRU-VNTR markers. Tissues from confirmed samples were subjected to a histopathological examination. A histopathological severity score (HSS) system was developed and used to grade (0 to 5) the magnitude of lesions caused by MAP. In general, the HSS system assesses the number of foci and degree of macrophage infiltration, together with the presence of multinucleated giant cells (MGCs) and acid-fast bacilli (AFB), in addition to the fusion of the intestinal villi and hyperplasia of the crypts. Despite the large sampling effort, only 79 MAP isolates were successfully genotyped, where 19 different haplotypes were described. A mixed-effect Poisson regression model was used to assess the relationship between haplotypes and HSS values. The model was controlled by animal age, and the farm was used as a random effect. Haplotypes were grouped based on their relative frequency: the most frequent haplotype (group i, 49.4%), the second most frequent haplotype (group ii, 12.7%), and all other haplotypes (group iii, 37.9%). Model outputs indicated that group i had significantly higher HSS values than group iii. In addition, group i was also associated with higher optical density (OD) values of the ELISA test. These results support the existence of differences in pathogenicity between MAP haplotypes. However, results were based on a relatively small sample size; thus, these should be taken with caution. Despite this, study findings suggest that haplotypes would be associated with differences in disease progression, where the dominant haplotype tends to generate more severe lesions, which could be linked to a greater shed of MAP cells than non-dominant haplotypes, increasing their chances of transmission.

Prevalence of respiratory disease in Irish preweaned dairy calves using hierarchical Bayesian latent class analysis

Introduction

Bovine respiratory disease (BRD) has a significant impact on the health and welfare of dairy calves. It can result in increased antimicrobial usage, decreased growth rate and reduced future productivity. There is no gold standard antemortem diagnostic test for BRD in calves and no estimates of the prevalence of respiratory disease in seasonal calving dairy herds.

Methods

To estimate BRD prevalence in seasonal calving dairy herds in Ireland, 40 dairy farms were recruited and each farm was visited once during one of two calving seasons (spring 2020 & spring 2021). At that visit the prevalence of BRD in 20 calves between 4 and 6 weeks of age was determined using thoracic ultrasound score (≥3) and the Wisconsin respiratory scoring system (≥5). Hierarchical Bayesian latent class analysis was used to estimate the calf-level true prevalence of BRD, and the within-herd prevalence distribution, accounting for the imperfect nature of both diagnostic tests.

Results

In total, 787 calves were examined, of which 58 (7.4%) had BRD as defined by a Wisconsin respiratory score ≥5 only, 37 (4.7%) had BRD as defined by a thoracic ultrasound score of ≥3 only and 14 (1.8%) calves had BRD based on both thoracic ultrasound and clinical scoring. The primary model assumed both tests were independent and used informed priors for test characteristics. Using this model the true prevalence of BRD was estimated as 4%, 95% Bayesian credible interval (BCI) (1%, 8%). This prevalence estimate is lower or similar to those found in other dairy production systems. Median within herd prevalence varied from 0 to 22%. The prevalence estimate was not sensitive to whether the model was constructed with the tests considered conditionally dependent or independent. When the case definition for thoracic ultrasound was changed to a score ≥2, the prevalence estimate increased to 15% (95% BCI: 6%, 27%).

Discussion

The prevalence of calf respiratory disease, however defined, was low, but highly variable, in these seasonal calving dairy herds.

Modelling transmission of Mycobacterium avium subspecies paratuberculosis between Irish dairy cattle herds

Bovine paratuberculosis is an endemic disease caused by Mycobacterium avium subspecies paratuberculosis (Map). Map is mainly transmitted between herds through movement of infected but undetected animals. Our objective was to investigate the effect of observed herd characteristics on Map spread on a national scale in Ireland. Herd characteristics included herd size, number of breeding bulls introduced, number of animals purchased and sold, and number of herds the focal herd purchases from and sells to. We used these characteristics to classify herds in accordance with their probability of becoming infected and of spreading infection to other herds. A stochastic individual-based model was used to represent herd demography and Map infection dynamics of each dairy cattle herd in Ireland. Data on herd size and composition, as well as birth, death, and culling events were used to characterize herd demography. Herds were connected with each other through observed animal trade movements. Data consisted of 13 353 herds, with 4 494 768 dairy female animals, and 72 991 breeding bulls. We showed that the probability of an infected animal being introduced into the herd increases both with an increasing number of animals that enter a herd via trade and number of herds from which animals are sourced. Herds that both buy and sell a lot of animals pose the highest infection risk to other herds and could therefore play an important role in Map spread between herds.

Mycobacterium avium subspecies paratuberculosis infection in cattle - a review in the context of seasonal pasture-based dairy herds

Johne’s disease is an infectious disease affecting cattle, other ruminants and non-ruminant wildlife worldwide, caused by Mycobacterium avium subspecies paratuberculosis (MAP). This review provides an up-to-date concise overview of the pathogenesis of MAP, the significance of Johne’s disease in cattle and the use of diagnostic testing at both animal and herd level in the context of seasonal pasture-based herds. While MAP can only replicate intracellularly, the bacterium is sufficiently robust to survive for months in the environment. Transmission of MAP is mostly via the faecal-oral route, however in-utero transmission in also possible. The bacteria evade the immune system by persisting in macrophages in the small intestine submucosa, with this latent stage of infection lasting, in most cases, for at least two years before bacterial shedding and clinical signs begin. The slowly progressive nature of MAP infection, poor performance of diagnostic tests and management systems that expose susceptible calves to infection make control of Johne’s disease challenging, particularly in seasonal calving herds. Testing of individual animals provides little assurance for farmers and vets due to the poor sensitivity and, in the case of ELISA, imperfect specificity of the available tests. Repeated herd-level testing is utilised by the IJCP to detect infected herds, identify high risk animals, and provide increasing confidence that test-negative herds are free of infection. The IJCP aims to control the spread of Johne’s disease in cattle in Ireland, in order to protect non-infected herds, limit the economic and animal health impact of the disease, improve calf health and reassure markets of Johne’s disease control in Ireland.

Bayesian estimation of prevalence of Johne's disease in dairy herds in Southern Italy

Johne's disease (JD) is a chronic granulomatous disease caused by Mycobacterium avium subsp. paratuberculosis (MAP) causing important losses on dairy farms. In Italy, voluntary programs to control MAP infection in dairy cattle are implemented in the Northern part of the country, where several studies have been carried out. Conversely, the disease status has not been fully investigated in the Southern regions. The aims of this study were to (i) determine the herd-level true prevalence (HTP) and (ii) the conditional within herd animal-level prevalence (CWHP) of JD in selected dairy cattle herds in Southern Italy. Serum samples were taken from 27 farms and analysed using a commercial ELISA test. A Bayesian model was fitted to the data. The estimated posterior mean of HPT was 0.46 (89 % CI 0.25-0.67), while the mean CWHP was 0.03 (89 % CI: 0.012-0.045). The results presented in this study call for designing and implementing an effective JD control program at national level.

Longitudinal Prevalence of Antibodies to Endemic Pathogens in Bulk Tank Milk Samples From Dairy Herds Engaged or Not in Contract Heifer Rearing

Since the abolition of EU milk production quotas in 2015, Europe's dairy industries have undergone a period of rapid expansion with possible resultant increased inter-herd transmission of endemic pathogens. The aims of this study were (1) to establish the post-2015 prevalence of antibodies to selected endemic infectious diseases and (2) to determine if prevalences differed between herds where heifers were reared at home and those where heifers were sent out for contract-rearing. Three bulk tank milk (BTM) samples were collected annually between May and August of 2018-20 inclusively from 120 Irish dairy herds. Additionally, herd vaccination status was collected by questionnaire. Milk samples were tested using commercially available ELISAs for eight pathogens: bovine viral diarrhea virus (BVDV), bovine herpesvirus 1 (BoHv-1), bovine respiratory syncytial virus (BRSV), Mycoplasma bovis, Mycobacterium avium subspecies paratuberculosis (MAP), Salmonella Dublin (S. Dublin), Leptospira Hardjo (L. Hardjo), and Neospora caninum (N. caninum). The true prevalence of each pathogen was calculated using a Rogan-Gladen estimator. The true prevalences (95% CI) of BTM antibodies in unvaccinated herds across the 3 years were as follows (i) BVDV: 57, 86, and 73% (95% CI: 40.7-65.9, 74-94, and 58-85) (n = 56, 56, and 48), (ii) BoHv-1: 47, 49, and 19% (95% CI: 26.3-69.7, 25-75, and 1-56) (n = 21, 20, and 11), (iii) L. Hardjo: 34, 59, and 73% (95% CI: 12.5-63, 33-82, and 33-99) (n = 15, 21, and 10), (iv) S. Dublin 32, 57, and 11% (95% CI: 12.21-68.1, 30.2-90.1, and 0) (n = 19, 22, and 13), (v) BRSV: 100% (95% CI: 99.5-100, 100, and 100) (n = 120, 109, and 91), (vi) MAP: 0% (95% CI: 0, 0, and 0) (n = 120, 109, and 91) (vii) N. caninum 0% (95% CI: 0, 0, and 0) (n = 120, 109, and 91) and (viii) M. bovis (ELISA) 53, 0.42, and 30% (95% CI: 3.95-6.84, 0, and 21-41) (n = 120, 109, and 91). M. bovis was detected by PCR in 0, 1, and 0% of herds in 2018, 2019, and 2020, respectively. This study showed that expanding Irish dairy herds are endemically infected with several of the studied pathogens. No differences in herd prevalence of infectious agents were observed between farms with different heifer rearing strategies (contract-rearing vs. traditional rearing).

Estimation of the true prevalence of inaccurate artificial inseminations in Irish milk recording dairy cows using a Bayesian latent class analysis

Inaccurate artificial insemination (IAI) refers to an artificial insemination (AI) that is performed when a cow is not in oestrus. IAIs have economic impacts on the dairy industry through of semen wastage or iatrogenic pregnancy loss. However, few studies have quantified the prevalence of IAIs in a population. The primary objective of this prospective study was to estimate the cow-level true prevalence of IAIs in Irish milk recording dairy herds using a latent class model with a Bayesian framework. Milk samples were collected at a milk recording laboratory from 576 dairy cows in 125 herds who had received an AI on the same day they were sampled for routine milk constituent analysis. Milk progesterone (MP4) analysis was conducted on these samples using radioimmunoassay to determine the progesterone concentration. Fertility data (i.e., subsequent calving date) was retrospectively obtained from the Irish National Cattle Breeding Federation for milk sampled cows and an apparent conception (AC) to the sample AI was determined based on an estimated gestational range of 270-290 days. Both tests (MP4 and AC) were used in a latent class model to estimate the true prevalence of IAI. For the MP4 test, a concentration of ≥ 5 ng/mL in whole milk was deemed to be test positive while for the AC test, a cow that did not conceive to the sampled AI was deemed test positive. Prior information for prevalence of IAI was obtained from a literature review while MP4 sensitivity (Se) and specificity (Sp) were obtained from expert opinion. Non-informative priors were used for the Se and Sp of the AC test. Posterior inferences (median and 95 % Bayesian probability intervals; BPI) were obtained using the 'rjags' package in the R statistical software. In the final model, median cow-level true prevalence of IAI was 4.4 % (BPI; 1.7-9.0 %). Median Se and Sp estimates for MP4, were 83.0 % (BPI; 65.0-96.2 %) and were 97.4 % (BPI; 94.6-99.6 %), respectively. Median Se and Sp estimates for AC, were 64.8 % (BPI; 44.5-88.6 %) and 49.8 % (BPI; 45.3-54.1 %), respectively. The present study estimates that the overall cow-level true prevalence of IAI in Irish dairy cows is relatively low. This is the first study to report the cow-level true prevalence of IAI using a Bayesian latent class model.

The Irish Johne's Control Programme

The Irish Johne's Control Programme (IJCP) provides a long-term approach to the voluntary control of Johne's disease (JD) in Ireland, strongly supported by Irish cattle industry leadership. It leverages the establishment of Animal Health Ireland for control of animal diseases not regulated by the European Union. The IJCP has four objectives: facilitate protection against spread of JD to uninfected farms; reduce the level of infection when present; assure markets of JD control in Ireland; and improve calf health and farm biosecurity. Key IJCP elements are an annual veterinary risk assessment and management plan (VRAMP), annual whole herd test (WHT) by ELISA on blood or milk samples with ancillary faecal PCR testing of ELISA reactors, and Targeted Advisory Service on Animal Health (TASAH) investigations of infected herds. There are pathways for assurance of herds with continuing negative tests and for management of test-positive herds. Herdowners are responsible for on-farm activities, and specifically-trained (approved) veterinary practitioners have a pivotal role as technical advisors and service providers. The programme is supported by training of veterinarians, performance of testing in designated laboratories, documentation of policies and procedures, innovative data management for herd and test activities and for programme administration, training, and broad communication and awareness activities. Tools and systems are refined to address emerging issues and enhance the value of the programme. An Implementation Group comprising industry, government and technical leaders sets strategic direction and policy, advised by a Technical Working Group. Shared funding responsibilities are agreed by key stakeholders until 2022 to support herds in the programme to complete requirements. Herd registrations have increased steadily to exceed 1,800. National bulk tank milk surveillance is also being deployed to identify and recruit test-positive herds with the expectation that they have a relatively high proportion of seropositive animals. The programme will continue to innovate and improve to meet farmer and industry needs.

A Bayesian inference approach to quantify average pathogen loads in farmyard manure and slurry using open-source Irish datasets

Farm-to-fork quantitative microbial risk assessments (QMRA) typically start with a preliminary estimate of initial concentration (C_initial) of microorganism loading at farm level, consisting of an initial estimate of prevalence (P) and the resulting pathogen levels in animal faeces. An average estimation of the initial concentration of pathogens can be achieved by combining P estimates in animal populations and the levels of pathogens in colonised animals' faeces and resulting cumulative levels in herd farmyard manure and slurry (FYM&S). In the present study, 14 years of data were collated and assessed using a Bayesian inference loop to assess the likely P of pathogens. In this regard, historical and current survey data exists on P estimates for a number of pathogens, including Cryptosporidium parvum, Mycobacterium avium subspecies paratuberculosis (MAP), Salmonella spp., Clostridium spp., Campylobacter spp., pathogenic E. coli, and Listeria monocytogenes in several species (cattle, pigs, and sheep) in Ireland. The results revealed that Cryptosporidium spp. has potentially the highest mean P (P_mean) (25.93%), followed by MAP (15.68%) and Campylobacter spp. (8.80%) for cattle. The P_mean of E. coli is highest (7.42%) in pigs, while the P_mean of Clostridium spp. in sheep was estimated to be 7.94%. C_initial for Cryptosporidium spp., MAP., Salmonella spp., Clostridium spp., and Campylobacter spp. in cattle faeces were derived with an average of 2.69, 4.38, 4.24, 3.46, and 3.84 log₁₀ MPN g ^-1, respectively. Average C_initial of Cryptosporidium spp., Salmonella spp., Clostridium spp., and E. coli in pig slurry was estimated as 1.27, 3.12, 3.02, and 4.48 log₁₀ MPN g ^-1, respectively. It was only possible to calculate the average C_initial of Listeria monocytogenes in sheep manure as 1.86 log₁₀ MPN g ^-1. This study creates a basis for future farm-to-fork risk assessment models to base initial pathogen loading values for animal faeces and enhance risk assessment efforts.

MAP, Johne's disease and the microbiome; current knowledge and future considerations

Mycobacterium avium subsp. paratuberculosis is the causative agent of Johne's disease in ruminants. As an infectious disease that causes reduced milk yields, effects fertility and, eventually, the loss of the animal, it is a huge financial burden for associated industries. Efforts to control MAP infection and Johne's disease are complicated due to difficulties of diagnosis in the early stages of infection and challenges relating to the specificity and sensitivity of current testing methods. The methods that are available contribute to widely used test and cull strategies, vaccination programmes also in place in some countries. Next generation sequencing technologies have opened up new avenues for the discovery of novel biomarkers for disease prediction within MAP genomes and within ruminant microbiomes. Controlling Johne's disease in herds can lead to improved animal health and welfare, in turn leading to increased productivity. With current climate change bills, such as the European Green Deal, targeting livestock production systems for more sustainable practices, managing animal health is now more important than ever before. This review provides an overview of the current knowledge on genomics and detection of MAP as it pertains to Johne's disease.

Evaluation using latent class models of the diagnostic performances of three ELISA tests commercialized for the serological diagnosis of Coxiella burnetii infection in domestic ruminants

ELISA methods are the diagnostic tools recommended for the serological diagnosis of Coxiella burnetii infection in ruminants but their respective diagnostic performances are difficult to assess because of the absence of a gold standard. This study focused on three commercial ELISA tests with the following objectives (1) assess their sensitivity and specificity in sheep, goats and cattle, (2) assess the between- and within-herd seroprevalence distribution in these species, accounting for diagnostic errors, and (3) estimate optimal sample sizes considering sensitivity and specificity at herd level. We comparatively tested 1413 cattle, 1474 goat and 1432 sheep serum samples collected in France. We analyzed the cross-classified test results with a hierarchical zero-inflated beta-binomial latent class model considering each herd as a population and conditional dependence as a fixed effect. Potential biases and coverage probabilities of the model were assessed by simulation. Conditional dependence for truly seropositive animals was high in all species for two of the three ELISA methods. Specificity estimates were high, ranging from 94.8% [92.1; 97.8] to 99.2% [98.5; 99.7], whereas sensitivity estimates were generally low, ranging from 39.3 [30.7; 47.0] to 90.5% [83.3; 93.8]. Between- and within-herd seroprevalence estimates varied greatly among geographic areas and herds. Overall, goats showed higher within-herd seroprevalence levels than sheep and cattle. The optimal sample size maximizing both herd sensitivity and herd specificity varied from 3 to at least 20 animals depending on the test and ruminant species. This study provides better interpretation of three widely used commercial ELISA tests and will make it possible to optimize their implementation in future studies. The methodology developed may likewise be applied to other human or animal diseases.

Phagomagnetic separation-quantitative PCR: A rapid, sensitive and specific surveillance tool for viable Mycobacterium avium ssp. paratuberculosis in bulk tank and individual cow milk samples

Bulk tank milk samples from 392 Northern Ireland dairy farms and individual milk from animals (n = 293) on 4 of these farms were tested by a novel phagomagnetic separation (PhMS)-quantitative (q)PCR assay able to detect and quantify viable Mycobacterium avium ssp. paratuberculosis (MAP), to demonstrate its potential utility as a milk surveillance tool. Viable MAP were detected in 26.5% of the bulk tank milks, with MAP contamination levels ranging from 1 to 8,432 MAP/50 mL of milk; less than 2% of farms had MAP contamination levels >100 MAP/50 mL in their bulk tank milk. Follow-up PhMS-qPCR testing of milk from individual animals on 4 farms that had the highest numbers of MAP in their bulk tank milks indicated that 17 to 24% of animals in each herd were shedding viable MAP in their milk. Mean MAP numbers detected ranged between 6.7 and 42.1 MAP/50 mL of milk. No significant correlation was observed between the detection of viable MAP in bulk or individual milks by PhMS-qPCR and parallel milk ELISA results, or between PhMS-qPCR results and any other milk recording results (somatic cell count, total bacterial count, % butterfat, or % protein). Viable MAP was detected by IS900 qPCR in 52 (85.2%) Pozzato broth cultures of 61 PhMS-qPCR-positive individual milks after 12 wk of incubation, suggesting few PhMS-qPCR results were false positives. The mean sensitivities of the PhMS-qPCR assay and milk ELISA applied to individual milks were estimated by Bayesian latent class analysis to be 0.7096 and 0.2665, respectively, and mean specificities were similar (0.9626 and 0.9509). Our findings clearly demonstrate that the novel PhMS-qPCR assay could be a useful milk surveillance tool for dairy processors, or a milk monitoring tool for Johne's disease control or milk quality assurance programs.

Modelling transmission and control of Mycobacterium avium subspecies paratuberculosis within Irish dairy herds with compact spring calving

Paratuberculosis is a chronic bacterial infection of the intestine in cattle caused by Mycobacterium avium subspecies paratuberculosis (Map). To better understand Map transmission in Irish dairy herds, we adapted the French stochastic individual-based epidemiological simulation model to account for seasonal herd demographics. We investigated the probability of Map persistence over time, the within-herd prevalence over time, and the relative importance of transmission pathways, and assessed the relative effectiveness of test-and-cull control strategies. We investigated the impact on model outputs of calf separation from cows (calves grazed on pasture adjacent to cows vs. were completely separated from cows) and test-and-cull. Test-and-cull scenarios consisted of highly test-positive cows culled within 13 or 4 weeks after detection, and calf born to highly test-positive cows kept vs removed. We simulated a typical Irish dairy herd with on average 82 lactating cows, 112 animals in total. Each scenario was iterated 1000 times to adjust variation caused by stochasticity. Map was introduced in the fully naive herd through the purchase of a moderately infectious primiparous cow. Infection was considered to persist when at least one infected animal remained in the herd or when Map was present in the environment. The probability of Map persistence 15 years after introduction ranged between 32.2-42.7 % when calves and cows had contact on pasture, and between 18.9-29.4 % when calves and cows were separated on pasture. The most effective control strategy was to cull highly test-positive cows within four weeks of detection (absolute 10 % lower persistence compared to scenarios without control). Removing the offspring of highly test-positive dams did not affect either Map persistence or within-herd prevalence of Map. Mean prevalence 15 years after Map introduction was highest (63.5 %) when calves and cows had contact on pasture. Mean prevalence was 15 % lower (absolute decrease) when cows were culled within 13 weeks of a high test-positive result, and 28 % lower when culled within 4 weeks. Around calving, the infection rate was high, with calves being infected in utero or via the general indoor environment (most important transmission routes). For the remainder of the year, the incidence rate was relatively low with most calves being infected on pasture when in contact with cows. Testing and culling was an effective control strategy when it was used prior to the calving period to minimize the number of highly infectious cows present when calves were born.

Stakeholder perceptions of non-regulatory bovine health issues in Ireland: past and future perspectives

Background

In recent years, there have been multiple (political, environmental, cultural) drivers of change in Irish agriculture, including the establishment of Animal Health Ireland (AHI) in 2009, to provide leadership of non-regulatory livestock health issues (diseases and conditions of livestock that are endemic in Ireland but which are not currently subject to international legislation). In this study, we describe the opinion of stakeholders (farmers, veterinary practitioners and agricultural industry professional service providers), elicited by means of a survey, on their perceptions of changes in selected non-regulatory bovine health issues over the last 10 years and priority issues relevant to non-regulatory bovine health to be tackled over the next 10 years.

Results

A total of 673 individuals participated in the online questionnaire. For the majority of the non-regulatory bovine health issues, most participants felt there had been improvements over the last 10 years. However, professional service providers were generally more conservative in their response to improvements on-farm compared to farmers. Several issues, particularly BVD and udder health/milk quality, were viewed more positively by all relevant respondents. There was reasonable agreement between responses from different respondent types and sectors regarding the top three priorities relevant to non-regulatory bovine animal health for the next 10 years in Ireland, which included antimicrobial resistance (highlighting measures to reduce both on-farm usage and resistance), anthelmintic resistance, greenhouse emissions and calf welfare.

Conclusions

The results are encouraging, demonstrating a perception of improvement in a number of non-regulatory bovine health issues in Ireland over the last ten years. With respect to the next 10 years, stakeholders prioritised antimicrobial and anthelmintic resistance, greenhouse gas emissions and calf welfare, which aligns closely with broader societal concerns. This information is useful to AHI, particularly with respect to future priorities. However, these concerns are broad in scope and will require further considerations, including collaborations, between AHI and partnering organisations. Given that there were differences between farmers and professional service providers in responses, it is useful to consider how the aims and the benefits of future AHI programmes are framed and communicated to all stakeholders.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13620-020-00178-8.

Estimation of the sensitivity and specificity of four serum ELISA and one fecal PCR for diagnosis of paratuberculosis in adult dairy cattle in New Zealand using Bayesian latent class analysis

In New Zealand, a new diagnostic approach for the control of paratuberculosis in mixed aged milking cows has been developed using a combination of ELISA and quantitative fecal PCR (f-qPCR). Our analysis was designed to evaluate performance of these individual tests in infected or infectious mixed aged cows across the prevalence of infection typically encountered on NZ dairy farms and calculate test accuracy when used as a screening test of serological ELISAs for four separate antigens read in parallel followed by a confirmatory quantitative f-qPCR test. Data from a cross-sectional study of 20 moderate prevalence herds was combined with existing data from 2 low and 20 high prevalence herds forming a dataset of 3845 paired serum and fecal samples. Incidence of clinical Johne's disease (JD) was used to classify herds into three prevalence categories. High (≥ 3% annual clinical JD for the last three years), moderate (<3 - 1%) and low (<1% incidence for at least the last five years). Positive tests were declared if> 50 ELISA units and f-qPCR at two cut-points (≥1 × 10⁴ genomes/mL or >1 × 10³ genomes/mL). Fixed Bayesian latent class models at both f-qPCR cut-points, accounted for conditional independence and paired conditional dependence. Mixed models at both f-qPCR cut-points, using a different mechanism to account for conditional dependencies between tests were also implemented. Models (24 in number) were constructed using OpenBUGS. The aim was to identify Mycobacterium avium subsp. paratuberculosis (MAP) infected cows that met at least one of two criteria: shedding sufficient MAP in feces to be detected by f-qPCR or mounting a detectable MAP antibody response. The best fit to the data was obtained by modelling pairwise dependencies between tests in a fixed model or by accounting for dependencies in a mixed model at a fecal cut-off of ≥1 × 10⁴ genomes/mL. Test performance differed with prevalence, but models were robust to prior assumptions. For the fixed model, at a prevalence of 0.29 (95 % probability interval (PI) = 0.25-0.33), as a screening plus confirmatory f-qPCR, post-test probability for disease in a positive animal was 0.84 (95 %PI = 0.80-0.88) and 0.16 (95 %PI = 0.15-0.18) for disease in a test negative animal. In low prevalence herds (0.01(95 %PI = 0.00-0.04)) the equivalent figures were 0.84 (95 %PI = 0.08-0.92) and 0.00 (95 %PI = 0.00-0.02). These results suggest this is a useful tool to control JD on dairy farms, particularly in herds with higher levels of infection, where the sampling and testing cost per animal is defrayed across more detected animals.

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.

Bayesian estimation of the true prevalence of paratuberculosis in Hungarian dairy cattle herds

Paratuberculosis is a chronic incurable disease caused by Mycobacterium avium subsp. paratuberculosis (MAP), which leads to extensive economic losses on dairy farms, and may also pose serious public health risk to the consumers. The aim of our study was to estimate the true prevalence of paratuberculosis in commercial dairy cattle herds participating in a voluntary MAP testing programme that started in February 2018 in Hungary. Milk samples collected during official milk recording were used for MAP ELISA testing. A Bayesian two-stage hierarchical (herd and animal level) model was fitted to the data. Altogether, 26,437 cows from 51 herds were sampled, which represents 14.4 % of the Hungarian dairy cow population. The median herd size was 477 cows (interquartile range: 331-709). Each studied farm had at least one ELISA positive cow, resulting in a herd-level apparent prevalence of 100 %. The overall within herd apparent prevalence was 5.5 %. Herd-level true prevalence was estimated at 89.1 % [95 % credible interval (CrI): 80.3-95.6%]. Within the infected herds, the median animal-level true prevalence was 4.4 % (3.2-5.8%) for primiparous and 10.3 % (7.9-12.9%) for multiparous cows, respectively. The probability of having an animal-level true prevalence of at least 5% among primiparous cows, within infected herds, was 17.8 %. Similarly, the probability of having an animal-level true prevalence of at least 5% or 10 % among multiparous cows was 100 % and 56 %, respectively. Simulations assuming herd-level true prevalence varying from 50 to 100 % revealed high accuracy of our Bayesian model. Our study showed that a large percentage of the studied Hungarian dairy cattle herds was infected with MAP.

Johne's disease in Irish dairy herds: considerations for an effective national control programme

The Irish dairy industry has established a reputation for the production of safe and healthy dairy products and is seeking to further expand its export market for high value dairy products. To support its reputation, stakeholders aim to control Johne’s disease. To assist decision-makers determine the most appropriate design for an Irish programme, a narrative review of the scientific literature on the epidemiology of Johne’s disease, and selected control programmes throughout the world was undertaken. Two modelling studies specifically commissioned by Animal Health Ireland to assess testing methods used to demonstrate confidence of freedom in herds and to evaluate a range of possible surveillance strategies provided additional information. The majority of control programmes tend to be voluntary, because of the unique epidemiology of Johne’s disease and limited support for traditional regulatory approaches. While acknowledging that test performance and sub-clinical sero-negative shedders contributes to the spread of infection, a range of socio-political issues also exist that influence programme activities. The paper provides a rationale for the inclusion of a Veterinary Risk Assessment and Management Plan (VRAMP), including voluntary whole herd testing to identify infected herds and to support assurance-based trading through repeated rounds of negative testing, national surveillance for herd-level case-detection, and improved understanding of biosecurity management practices. Identification and promotion of drivers for industry and producer engagement in Ireland is likely to guide the future evolution of the Irish Johne’s Control Programme (IJCP) and further enhance its success. The provision of training, education and extension activities may encourage farmers to adopt relevant farm management practices and help them recognize that they are ultimately responsible for their herd’s health and biosecurity.

Individual and herd-level milk ELISA test status for Johne's disease in Ireland after correcting for non-disease-associated variables

Antibody-detecting tests for Mycobacterium avium ssp. paratuberculosis (MAP) have low sensitivity and imperfect specificity for detection of infection. Sensitivity increases as the disease progresses. Aside from infection status and stage of disease, several factors affect test performance. These factors have not yet been studied in dairy cows producing lower volumes of milk with higher solids concentration, such as those managed in low-input, pasture-based production systems. Furthermore, the effect of correcting for these associations on individual and herd test status is also unknown. The first objective of this study was to examine the relationship between MAP antibody response in milk and milk yield, somatic cell count (SCC), fat and protein contents, and stage of lactation in dairy cows enrolled in the national Johne's Disease Control Programme (JDCP) in Ireland. The second objective was to examine the effect of correcting the antibody response for these associations on the test status of individual cows and herds, given that individual tests are often used to define a herd's status. Data were extracted for herds in the JDCP from January 2014 to December 2015 inclusive, consisting of 42,657 milk recordings from 18,569 cows across 187 dairy herds. Two linear regression models were constructed to investigate the association between log-transformed MAP sample-to-positive ratio and milk recording data and in primi- and multiparous cows. Days in milk was modeled as a B-spline in each model, and cow and herd were included as random effects. Across both models, natural log-transformed MAP antibody response was negatively associated with milk yield, positively associated with protein and fat production, and had a curvilinear association with log-transformed SCC. The association between MAP antibody response and days in milk varied over the course of the lactation. However, when combined, these variables explained only 5.1% of the variation in the antibody response of the population. After correcting for these associations, 93 multiparous cows and 20 primiparous cows changed category (negative, suspect, or positive). When considered at the herd-test level, out of a total of 531 herd tests, 1 herd changed from negative to positive, and 5 herds changed from positive to negative. This study provides useful information to aid in the interpretation of antibody results for herds testing animals for the presence of MAP infection. At an overall population level, correction of the serological response for non-disease-associated factors has the potential to change the status of only a small number of cows. At the herd level, the proportion of herds changing status was minimal. However, depending on the implications of a herd-level serological diagnosis, consideration should be given to correcting for these non-disease-associated variables within the context of national JD control programs.

Bayesian latent class estimation of sensitivity and specificity parameters of the PMS-PCR test for the diagnosis of cattle sub-clinically infected with Mycobacterium avium subsp. paratuberculosis

The objective of this study was to estimate the performance of the peptide magnetic separation PCR test (PMS-PCR) for the diagnosis of Mycobacterium avium subsp. paratuberculosis (MAP) in sub-clinically infected dairy cattle. Twenty-one herds were randomly selected from a source population of 131 commercial dairy herds with a known history of MAP infection, located in the De Los Rios and De Los Lagos regions, in southern Chile. In the selected herds, all milking cows with ≥2 parities and without any clinical signs were sampled, collecting feces and blood-serum samples. The PMS-PCR test was used to analyze the fecal samples, while serum samples were analyzed using a commercial ELISA kit. A Bayesian latent class model was used to estimate the sensitivity (Se) and specificity (Sp) of the diagnostic tests. A total of 1381 animals were sampled in the 21 selected dairy herds, with an average sample size of 65 animals per herd (range 10-721). The PMS-PCR test had a greater Se than the ELISA test, with a median of 85.5 % (posterior probability interval (PPI) 95 %: 79.3-91.0%), while the ELISA test presented a median of 21.7 % (95 % PPI: 18.3-25.4%). On the other hand, the ELISA test had a better Sp than the PMS-PCR test, with a median of 97.7 % (95 % PPI: 96.6-98.5%), whereas PMS-PCR presented a median of 90.8 % (95 % PPI: 88.3-93.9%). Model results showed that PMS-PCR has a better Se than all available tests for MAP diagnosis in subclinical animals. However, this test should be used with care in herds with high infection rates, where a high MAP environmental load is expected, potentially increasing the frequency of false positive cases due to the pass-through phenomenon.

A pilot study using environmental screening to determine the prevalence of Mycobacterium avium subspecies paratuberculosis (MAP) and antimicrobial resistance (AMR) in Irish cattle herds

Background

Dairy and beef cattle can be reservoirs of many pathogens, including Salmonella and Mycobacterium avium subsp. paratuberculosis (MAP), the causative agent of Johne’s disease (JD). Farm environments may provide potential entry points for the transmission of infectious agents into the food chain. Antibiotics are used to treat a wide variety of infections on farms, and administration of antimicrobial agents to cattle is considered to be a driving factor for antimicrobial resistance (AMR). Control of JD and AMR are priority for animal health initiatives in Ireland. A national JD pilot programme was introduced by Animal Health Ireland in 2014, while the national action plan launched by Department of Health and Department of Agriculture, Food and Marine introduced in 2017 aims to improve the surveillance of AMR. The current investigation was undertaken as a pilot study to determine the proportion of herds positive for MAP, Salmonella species (Salmonella spp), commensal Escherichia coli (E. coli), Extended-spectrum beta-lactamase (ESBL) AmpC β-lactamase and carbapenemase-producing E. coli from 157 environmental faecal samples in Irish farms.

Results

MAP was detected in 10.2% of samples collected; on culture in 4 (4.9%) of the dairy herds and from 1 (1.3%) of the beef/suckler herds, and by PCR in 10 (12.3%) and 6 (7.9%) of these herds respectively. All culture positive herds were also positive by PCR. An additional 11 herds were positive by PCR only. Salmonella was not detected, while commensal E. coli were isolated from 70.7% of the samples (111/157) with 101 of these isolates shown to be fully susceptible to all antimicrobials tested. Of the 27 presumptive ESBL AmpC β-lactamase producing E. coli detected, one isolate was resistant to ten antimicrobials, nine isolates were resistant to nine antimicrobials, and four isolates were resistant to eight antimicrobials. Carbapenemase-producing E. coli were not isolated.

Conclusions

The results highlight the importance of monitoring farm environments for Johne’s disease. This disease is a growing concern for dairy and beef producers in Ireland, and sampling the farm environment may offer a useful means to rapidly screen for the presence of MAP. Non-pathogenic common enteric commensal and multiple-drug-resistant E. coli may contribute to AMR acting as a reservoir and transferring resistance to other species/pathogens in the environment.

Estimating the herd and cow level prevalence of bovine digital dermatitis on New Zealand dairy farms: A Bayesian superpopulation approach

A cross-sectional study of 127 dairy herds distributed across four regions of New Zealand (NZ) was conducted to estimate the regional herd-level prevalence of bovine digital dermatitis (BDD) and the prevalence of cows with BDD lesions within affected herds. Each herd was visited once during the 2016-2017 lactating season and the rear feet of all cows in the milking herd were examined to detect the presence of BDD lesions. Of the 127 herds examined, 63 had at least one cow with a detected BDD lesion. Of the 59 849 cows observed, 646 cows were observed with BDD lesions. All of the herds in which BBD was detected were located in three of the four regions (Waikato, Manawatu and South Canterbury). No convincing lesions were observed on the West Coast. The probability of BDD freedom on the West Coast was predicted to be 99.97% using a Bayesian latent class model. For the three regions where BDD lesions were observed, the true herd level and cow level prevalences were estimated using a Bayesian superpopulation approach which accounted for the imperfect diagnostic method. Based on priors obtained from previous research in another region of NZ (Taranaki), the true herd level prevalences in Waikato, Manawatu and South Canterbury were estimated to be 59.2% (95% probability interval [PI]: 44.3%-73.9%), 43.3% (95%PI: 29%-59%) and 65.9% (95%PI: 49.5%-79.9%), respectively, while the true median within-herd prevalences were estimated as 3.2% (95%PI: 2%-5%), 1.7% (95%PI: 0.9%-3.1%) and 3.7% (95%PI: 2.4%-5.5%), respectively. All of these estimates except for the true herd level prevalence in Manawatu were fairly robust to changes in the priors. For Manawatu region, changing from the prior obtained in Taranaki (the best estimate of the herd level prevalence = 60%, 95% sure > 40%) to one where the mode was 50% (95% sure < 80%) reduced the posterior from 43.3% to 35.2% (95%PI: 20.1%-53.5%). The marked variation in BDD prevalence between regions and between farms highlights the need for further exploration into risk factors for disease.

A review of paratuberculosis in dairy herds - Part 1: Epidemiology

Bovine paratuberculosis is a chronic infectious disease of cattle caused by Mycobacterium avium subspecies paratuberculosis (MAP). This is the first in a two-part review of the epidemiology and control of paratuberculosis in dairy herds. Paratuberculosis was originally described in 1895 and is now considered endemic among farmed cattle worldwide. MAP has been isolated from a wide range of non-ruminant wildlife as well as humans and non-human primates. In dairy herds, MAP is assumed to be introduced predominantly through the purchase of infected stock with additional factors modulating the risk of persistence or fade-out once an infected animal is introduced. Faecal shedding may vary widely between individuals and recent modelling work has shed some light on the role of super-shedding animals in the transmission of MAP within herds. Recent experimental work has revisited many of the assumptions around age susceptibility, faecal shedding in calves and calf-to-calf transmission. Further efforts to elucidate the relative contributions of different transmission routes to the dissemination of infection in endemic herds will aid in the prioritisation of efforts for control on farm.

Evaluation of national surveillance methods for detection of Irish dairy herds infected with Mycobacterium avium ssp. paratuberculosis

The aim of this study was to evaluate the utility and cost-effectiveness of a range of national surveillance methods for paratuberculosis in Irish dairy herds. We simulated alternative surveillance strategies applied to dairy cattle herds for the detection of Mycobacterium avium ssp. paratuberculosis (MAP)-infected herds (case-detection) or for estimation of confidence of herd freedom from infection (assurance testing). Strategies simulated included whole-herd milk or serum serology, serology on cull cows at slaughter, bulk milk tank serology, environmental testing, and pooled fecal testing. None of the strategies evaluated were ideal for widespread national case-detection surveillance. Herd testing with milk or serum ELISA or pooled fecal testing were the most effective methods currently available for detection of MAP-infected herds, with median herd sensitivity >60% and 100% herd specificity, although they are relatively expensive for widespread use. Environmental sampling shows promise as an alternative, with median herd sensitivity of 69%, but is also expensive unless samples can be pooled and requires further validation under Irish conditions. Bulk tank milk testing is the lowest cost option and may be useful for detecting high-prevalence herds but had median herd sensitivity <10% and positive predictive value of 85%. Cull cow sampling strategies were also lower cost but had median herd sensitivity <40% and herd positive predictive values of <50%, resulting in an increased number of test-positive herds, each of which requires follow-up herd testing to clarify status. Possible false-positive herd testing results associated with prior tuberculosis testing also presented logistical issues for both cull cow and bulk milk testing. Whole-herd milk or serum ELISA testing are currently the preferred testing strategies to estimate confidence of herd freedom from MAP in dairy herds due to the good technical performance and moderate cost of these strategies for individual herd testing. Cull cow serology and bulk tank milk sampling provide only minimal assurance value, with confidence of herd freedom increasing only minimally above the prior estimate. Different testing strategies should be considered when deciding on cost-effective approaches for case-detection compared with those used for building confidence of herd freedom (assurance testing) as part of a national program.

Modeling of alternative testing strategies to demonstrate freedom from Mycobacterium avium ssp. paratuberculosis infection in test-negative dairy herds in the Republic of Ireland

In light of the various adverse effects of Johne's disease on animal productivity and the debate on the role of its causative organism, Mycobacterium avium ssp. paratuberculosis, in the etiology of Crohn's disease, major dairy-producing countries around the world have implemented national control programs aimed at reducing the prevalence of this infection in cattle. A pilot control program was initiated in Ireland in 2013, with a key objective to provide farmers with test-negative dairy herds with tools and knowledge to increase their confidence of freedom over time. The aim of this study was to estimate the confidence of freedom obtained in test-negative Irish dairy herds over time with various sampling scenarios and to evaluate the cost-effectiveness of alternative scenarios for achieving an acceptable level of confidence of freedom in herds with no evidence of infection. A stochastic model was developed to simulate repeated annual testing of individual animals using ELISA and confirmatory assays over a period of 20 yr. Two scenarios modeled the current herd-screening options, whereas 14 alternative scenarios explored the effect of varying parameters from the current testing strategies, such as the frequency of testing, the eligibility criteria for selecting animals, the type of assay, the probability of introduction, and the assay sensitivity. Results showed that the current testing strategy with milk twice a year or serum once a year in all animals over 2 yr old provided the highest annual herd sensitivity, with a median value of 55%. Although the median confidence of freedom increased over time for all scenarios, the time required to reach 90 and 95% confidence of freedom was highly variable between scenarios. Under the testing scenario where serum tests were used once a year, the confidence of freedom reached 90% after 4 yr and 95% after 7 yr of testing. Some of the alternative scenarios achieved an acceptable level of confidence of freedom in a reasonable timeframe and at lesser cost than the current testing strategies. The results of this work are used to provide recommendations for the next phases of the program.

Low accuracy of Bayesian latent class analysis for estimation of herd-level true prevalence under certain disease characteristics-An analysis using simulated data

Estimation of the true prevalence of infected individuals involves the application of a diagnostic test to a population and adjusting according to test performance, sensitivity and specificity. Bayesian latent class analysis for the estimation of herd and animal-level true prevalence, has become increasingly used in veterinary epidemiology and is particularly useful in incorporating uncertainty and variability into analyses in a flexible framework. However, the approach has not yet been evaluated using simulated data where the true prevalence is known. Furthermore, using this approach, the within-herd true prevalence is often assumed to follow a beta distribution, the parameters of which may be modelled using hyperpriors to incorporate both uncertainty and variability associated with this parameter. Recently however, the authors of the current study highlighted a potential issue with this approach, in particular, with fitting the distributions and a tendency for the resulting distribution to invert and become clustered at zero. Therefore, the objective of the present study was to evaluate commonly specified models using simulated datasets where the herd-level true prevalence was known. The specific purpose was to compare findings from models using hyperpriors to those using a simple beta distribution to model within-herd prevalence. A second objective was to investigate sources of error by varying characteristics of the simulated dataset. Mycobacterium avium subspecies paratuberculosis infection was used as an example for the baseline dataset. Data were simulated for 1000 herds across a range of herd-level true prevalence scenarios, and models were fitted using priors from recently published studies. The results demonstrated poor performance of these latent class models for diseases characterised by poor diagnostic test sensitivity and low within-herd true prevalence. All variations of the model appeared to be sensitive to the prior and tended to overestimate herd-level true prevalence. Estimates were substantially improved in different infection scenarios by increasing test sensitivity and within-herd true prevalence. The results of this study raise questions about the accuracy of published estimates for the herd-level true prevalence of paratuberculosis based on serological testing, using latent class analysis. This study highlights the importance of conducting more rigorous sensitivity analyses than have been carried out in previous analyses published to date.

Bovine Tuberculosis in Britain and Ireland - A Perfect Storm? the Confluence of Potential Ecological and Epidemiological Impediments to Controlling a Chronic Infectious Disease

Successful eradication schemes for bovine tuberculosis (bTB) have been implemented in a number of European and other countries over the last 50 years. However, the islands of Britain and Ireland remain a significant aberration to this trend, with the recent exception of Scotland. Why have eradication schemes failed within these countries, while apparently similar programs have been successful elsewhere? While significant socio-economic and political factors have been discussed elsewhere as key determinants of disease eradication, here we review some of the potential ecological and epidemiological constraints that are present in these islands relative to other parts of Europe. We argue that the convergence of these potential factors may interact additively to diminish the potential of the present control programs to achieve eradication. Issues identified include heterogeneity of diagnostic testing approaches, the presence of an abundant wildlife reservoir of infection and the challenge of sustainably managing this risk effectively; the nature, size, density and network structure of cattle farming; potential effects of Mycobacterium bovis strain heterogeneity on disease transmission dynamics; possible impacts of concurrent endemic infections on the disclosure of truly infected animals; climatological differences and change coupled with environmental contamination. We further argue that control and eradication of this complex disease may benefit from an ecosystem level approach to management. We hope that this perspective can stimulate a new conversation about the many factors potentially impacting bTB eradication schemes in Britain and Ireland and possibly stimulate new research in the areas identified.

Seroprevalence of Toxoplasma gondii in pregnant women and livestock in the mainland of China: a systematic review and hierarchical meta-analysis

Primary Toxoplasma gondii infection in pregnant women may result in abortion, stillbirth, or lifelong disabilities of the unborn child. One of the main transmission routes to humans is consumption of raw or undercooked meat containing T. gondii tissue cysts. We aim to determine and compare the regional distribution of T. gondii seroprevalence in pregnant women and meat-producing livestock in China through a systematic literature review. A total of 272 eligible publications were identified from Medline, Scopus, Embase and China National Knowledge Infrastructure. Apparent and true seroprevalence were analysed by region using a novel Bayesian hierarchical model that allowed incorporating sensitivity and specificity of the applied serological assays. The true seroprevalence of T. gondii in pregnant women was 5.0% or less in seven regions of China. The median of the regional true seroprevalences in pigs (24%) was significantly higher than in cattle (9.5%), but it was not significantly higher than in chickens (20%) and small ruminants (20%). This study represents the first use of a Bayesian hierarchical model to obtain regional true seroprevalence. These results, in combination with meat consumption data, can be used to better understand the contribution of meat-producing animals to human T. gondii infection in China.

Knowledge gaps that hamper prevention and control of Mycobacterium avium subspecies paratuberculosis infection

In the last decades, many regional and country-wide control programmes for Johne's disease (JD) were developed due to associated economic losses, or because of a possible association with Crohn's disease. These control programmes were often not successful, partly because management protocols were not followed, including the introduction of infected replacement cattle, because tests to identify infected animals were unreliable, and uptake by farmers was not high enough because of a perceived low return on investment. In the absence of a cure or effective commercial vaccines, control of JD is currently primarily based on herd management strategies to avoid infection of cattle and restrict within-farm and farm-to-farm transmission. Although JD control programmes have been implemented in most developed countries, lessons learned from JD prevention and control programmes are underreported. Also, JD control programmes are typically evaluated in a limited number of herds and the duration of the study is less than 5 year, making it difficult to adequately assess the efficacy of control programmes. In this manuscript, we identify the most important gaps in knowledge hampering JD prevention and control programmes, including vaccination and diagnostics. Secondly, we discuss directions that research should take to address those knowledge gaps.

Estimating the true prevalence of bovine digital dermatitis in taranaki, New Zealand using a bayesian latent class model

A Bayesian latent class model was developed to estimate the true prevalence of bovine digital dermatitis (BDD) in Taranaki, New Zealand. This model allowed farms to have zero prevalence as well as also accounting for between farm heterogeneity that was conditional on whether a farm was positive for bovine digital dermatitis. The estimated true farm level prevalence was 68.9% (95% credible interval [CrI]: 50.0%-85.7%), while on infected farms the overall cow level prevalence (number of infected cows/total number of cows on infected farms) was 2.9% (95%CrI: 2.1%-4.3%). The sensitivity analyses suggested that the prevalence estimates were reasonably robust when the variation of the priors fell within the biologically plausible range. These results indicated that visual inspection of standing animals during milking was sufficiently accurate to identify infected farms. However, for every 100 animals identified through visual inspection, 84 animals with lesions were missed. In other words, 46% (calculated as 84/184) of true positives at the animal level could be missed by visual inspection. The high and robust specificity (99.9%, 95%CrI: 99.8%-99.9%) suggested that lesions reported as BDD were very unlikely to be false positives.

Relative importance of herd-level risk factors for probability of infection with paratuberculosis in Irish dairy herds

Control of paratuberculosis is challenging due to the relatively poor performance of diagnostic tests, a prolonged incubation period, and protracted environmental survival. Prioritization of herd-level interventions is not possible because putative risk factors are often not supported by risk factor studies. The objective for this study was to investigate the relative importance of risk factors for an increased probability of herd paratuberculosis infection. Risk assessment data, comprehensive animal purchase history, and diagnostic test data were available for 936 Irish dairy herds. Both logistic regression and a Bayesian β regression on the outcome of a latent class analysis were conducted. Population attributable fractions and proportional reduction in variance explained were calculated for each variable in the logistic and Bayesian models, respectively. Routine use of the calving area for sick or lame cows was found to be a significant explanatory covariate in both models. Purchasing behavior for the previous 10 yr was not found to be significant. For the logistic model, length of time calves spend in the calving pen (25%) and routine use of the calving pen for sick or lame animals (14%) had the highest attributable fractions. For the Bayesian model, the overall R² was 16%. Dry cow cleanliness (7%) and routine use of the calving area for sick or lame cows (6%) and had the highest proportional reduction in variance explained. These findings provide support for several management practices commonly recommended as part of paratuberculosis control programs; however, a large proportion of the observed variation in probability of infection remained unexplained, suggesting other important risks factors may exist.

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.

Johne's disease in the eyes of Irish cattle farmers: A qualitative narrative research approach to understanding implications for disease management

Bovine Johne's Disease (JD) is a disease characterised by chronic granulomatous enteritis which manifests clinically as a protein-losing enteropathy causing diarrhoea, hypoproteinaemia, emaciation and, eventually death. Some research exists to suggest that the aetiologic pathogen Mycobacterium avium subspecies paratuberculosis may pose a zoonotic risk. Nationally coordinated control programmes have been introduced in many of the major milk producing countries across the world. However, JD is challenging to control in infected herds owing to limitations of diagnostic tests and the long incubation period of the disease. Internationally, research increasingly recognises that improved understanding of farmers' subjective views and behaviours may inform and enhance disease management strategies and support the identification and implementation of best practice at farm level. The aim of this study was to use qualitative research methods to explore the values and knowledges of farmers relative to the control of JD at farm level. The Biographical Narrative Interpretive Method (BNIM) was used to generate data from both infected and presumed uninfected farms in Ireland. Qualitative analysis revealed that cultural and social capital informed farmers' decisions on whether to introduce control and preventive measures. Cultural capital refers to the pride and esteem farmers associate with particular objects and actions whereas social capital is the value that farmers associate with social relationships with others. On-farm controls were often evaluated by farmers as impractical and were frequently at odds with farmers' knowledge of calf management. Knowledge from farmers of infected herds did not disseminate among peer farmers. Owners of herds believed to be uninfected expressed a view that controls and preventive measures were not worthy of adoption until there was clear evidence of JD in the herd. These findings highlight important barriers and potential aids to prevention and control in both infected and uninfected herds.