Longitudinal data collection of Mycobacterium avium subspecies Paratuberculosis infections in dairy herds: the value of precise field data

Within-herd mathematical modeling of Mycobacterium avium subspecies paratuberculosis to assess the effectiveness of alternative intervention methods

Johne's disease (JD) in cattle is caused by Mycobacterium avium subspecies paratuberculosis (MAP) and is characterized by chronic, progressive enteritis that can lead to substantial weight loss, severe diarrhea, and eventual death. Economic losses due to JD are primarily driven by reduced milk production in subclinical and clinically infected cows, but also include reduced value when sold to slaughter, and costs associated with premature culling. Controlling the transmission of JD within a dairy herd can be achieved through proactive calf management practices and reactive test-based culling. While effective, test-and-cull interventions have the potential to result in net economic losses, particularly when the intervention includes culling of low-shedding cattle. Proactive calf management practices have been observed to be effective at controlling within-herd JD prevalence. However, assessing the magnitude of effect of interventions in observational and experimental studies can be difficult due to the pathogenesis of MAP and may take many years of data to provide meaningful results. The limitations of studying JD in nature presents an opportunity to use mathematical modelling techniques to assess the effectiveness of various interventions on the simulated within-herd disease dynamics of JD. The objectives of this study were to build a within-herd compartmental disease model of JD and assess the effectiveness of three interventions: 1) strategic insemination of test-positive low-shedding adult cattle to preferentially breed beef calves, 2) using separate calving areas for low- and high-shedding dams, and 3) test-based culling of low- and high-shedding cows. Model outcomes were compared to a base case model (i.e., no interventions) under four endemic within-herd prevalences. In general, simulations of test-based culling performed best at reducing long-term within-herd prevalence of JD. Strategic insemination and separate calving area interventions were both effective and performed similarly to one another, but even when combined were not as effective as test-and-cull alone. Finally, the results from the separate calving area intervention model suggest that increased dam-calf contact time would not result in a substantial increased within-herd prevalence. Given that some of the modelled populations in this study are very small and prevalence is very low, further work is needed to assess these interventions using discrete, stochastic methods, which may result in different outcomes.

Meta-analysis of prevalence of paratuberculosis in cattle using published estimates under serum and milk ELISA

Johne's disease (JD), caused by Mycobacterium avium subspecies paratuberculosis (MAP), poses significant challenges to the global livestock industry, particularly affecting bovine populations. To better understand the prevalence of paratuberculosis and its diagnostic nuances, a comprehensive meta-analysis was conducted. This analysis encompassed 21 studies involving 632,767 cows for milk enzyme-linked immunosorbent assay (ELISA) and 51 studies involving 256,409 cows for serum ELISA. The pooled prevalence estimate for paratuberculosis on a cow-basis was found to be 16% (95% CI: 14%; 18%) for milk ELISA and 8% (95% CI: 7%; 8%) for serum ELISA. Notably, higher confidence intervals (CI) were observed in milk ELISA, the Europe and Asia groups, suggesting variability in prevalence estimates within these regions. Conversely, lower CIs were noted in the USA and Canada groups, indicating greater consistency in prevalence estimates within these countries. However, serum ELISA exhibited high CI values across all regions, underscoring potential variability in diagnostic performance. These findings provide valuable insights for veterinarians, researchers, policymakers, and livestock producers in optimizing paratuberculosis detection and control strategies to mitigate its impact on bovine health and agricultural productivity.

Active surveillance of paratuberculosis in Alpine-dwelling red deer (Cervus elaphus)

Paratuberculosis (Johne's disease) is a globally widespread infectious disease affecting domestic and wild ruminants, caused by Mycobacterium avium subsp. paratuberculosis (MAP). The bacterium is excreted in the feces and is characterized by high environmental resistance. The new Animal Health Law (Regulation EU 2016/429) on transmissible animal diseases, recently in force throughout the European Union, includes paratuberculosis within the diseases requiring surveillance in the EU, listing some domestic and wild Bovidae, Cervidae, and Camelidae as potential reservoirs. Taking advantage of a culling activity conducted in the Stelvio National Park (Italy), this study investigated MAP infection status of red deer (Cervus elaphus) between 2018 and 2022, and evaluated the probability of being MAP-positive with respect to individual and sampling-level variables. A total of 390 subjects were examined macroscopically and tested for MAP, using different diagnostic tools: IS900 qPCR, culture, histopathology, and serology. Twenty-three of them were found positive for MAP by at least one test, with an overall prevalence of 5.9% (95% CI 4.0-8.7), that, respectively, ranged from 12.4% in the first culling season to 2.0 and 2.1% in the 2019-2020 and 2021-2022 culling seasons. Quantitative PCR assay on ileocecal valve and mesenteric lymph nodes detected the highest number of MAP positive animals. The results of the study showed the increased probability of being MAP-positive with increasing age and that red deer with lower body mass values were more likely to be infected with MAP. Overall, the absence of signs of clinical paratuberculosis and gross lesions together with the low level of shedding witness early phases of the disease among the positive red deer and support an improvement of the paratuberculosis status of this population, as shown by the decreased prevalence of the disease over the years.

Construction of a Bacterial Lipidomics Analytical Platform: Pilot Validation with Bovine Paratuberculosis Serum

Lipidomics analyses of bacteria offer the potential to detect and monitor infections in a host since many bacterial lipids are not present in mammals. To evaluate this omics approach, we first built a database of bacterial lipids for representative Gram-positive and Gram-negative bacteria. Our lipidomics analysis of the reference bacteria involved high-resolution mass spectrometry and electrospray ionization with less than a 1.0 ppm mass error. The lipidomics profiles of bacterial cultures clearly distinguished between Gram-positive and Gram-negative bacteria. In the case of bovine paratuberculosis (PTB) serum, we monitored two unique bacterial lipids that we also monitored in Mycobacterium avian subspecies PTB. These were PDIM-B C82, a phthiodiolone dimycocerosate, and the trehalose monomycolate hTMM 28:1, constituents of the bacterial cell envelope in mycolic-containing bacteria. The next step will be to determine if lipidomics can detect subclinical PTB infections which can last 2-to-4 years in bovine PTB. Our data further suggest that it will be worthwhile to continue building our bacterial lipidomics database and investigate the further utility of this approach in other infections of veterinary and human clinical interest.

Investigating effective testing strategies for the control of Johne's disease in western Canadian cow-calf herds using an agent-based simulation model

Johne's disease is an insidious infectious disease of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). Johne's disease can have important implications for animal welfare and risks causing economic losses in affected herds due to reduced productivity, premature culling and replacement, and veterinary costs. Despite the limited accuracy of diagnostic tools, testing and culling is the primary option for controlling Johne's disease in beef herds. However, evidence to inform specific test and cull strategies is lacking. In this study, a stochastic, continuous-time agent-based model was developed to investigate Johne's disease and potential control options in a typical western Canadian cow-calf herd. The objective of this study was to compare different testing and culling scenarios that included varying the testing method and frequency as well as the number and risk profile of animals targeted for testing using the model. The relative effectiveness of each testing scenario was determined by the simulated prevalence of cattle shedding MAP after a 10-year testing period. A second objective was to compare the direct testing costs of each scenario to identify least-cost options that are the most effective at reducing within-herd disease prevalence. Whole herd testing with individual PCR at frequencies of 6 or 12 months were the most effective options for reducing disease prevalence. Scenarios that were also effective at reducing prevalence but with the lowest total testing costs included testing the whole herd with individual PCR every 24 months and testing the whole herd with pooled PCR every 12 months. The most effective method with the lowest annual testing cost per unit of prevalence reduction was individual PCR on the whole herd every 24 months. Individual PCR testing only cows that had not already been tested 4 times also ranked well when considering both final estimated prevalence at 10 years and cost per unit of gain. A more in-depth economic analysis is needed to compare the cost of testing to the cost of disease, taking into account costs of culling, replacements and impacts on calf crops, and to determine if testing is an economically attractive option for commercial cow-calf operations.

Bovine Immunity and Vitamin D3: An Emerging Association in Johne's Disease

Mycobacterium avium subspecies paratuberculosis (MAP) is an environmentally hardy pathogen of ruminants that plagues the dairy industry. Hallmark clinical symptoms include granulomatous enteritis, watery diarrhea, and significant loss of body condition. Transition from subclinical to clinical infection is a dynamic process led by MAP which resides in host macrophages. Clinical stage disease is accompanied by dysfunctional immune responses and a reduction in circulating vitamin D3. The immunomodulatory role of vitamin D3 in infectious disease has been well established in humans, particularly in Mycobacterium tuberculosis infection. However, significant species differences exist between the immune system of humans and bovines, including effects induced by vitamin D3. This fact highlights the need for continued study of the relationship between vitamin D3 and bovine immunity, especially during different stages of paratuberculosis.

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.

Modeling Paratuberculosis Transmission in a Small Dairy Herd Typical of Slovenia Suggests That Different Models Should Be Used to Study Disease Spread in Herds of Different Sizes

This study aimed to investigate the possible dynamics of paratuberculosis or Johne’s disease in a typical Slovenian dairy herd of about 17 cows. Paratuberculosis is a worldwide endemic disease of cattle caused by Mycobacterium avium subsp. paratuberculosis (MAP) and is associated with significant economic losses. We developed a stochastic compartmental model with two pathways of disease progression, infections of adult cows and infections of young animals through horizontal and vertical transmission, and transmission through animal movements. The average proportions of subclinically and clinically infected cows were 4% and 0.47%, respectively. The prevalence within the herd, which included latently infected animals, averaged 7.13% and ranged from 0% to 70.59%. Under the given circumstances, the results showed a relatively high rate of spontaneous elimination (0.22 per herd per year) of the disease and a high rate of reinfection (0.18 per herd per year) facilitated by active animal trade. To our knowledge, this stochastic compartmental model is the first to be developed specifically to represent a small dairy herd and could apply to other countries with a similar structure of dairy farms. The results suggest that different models should be used to study MAP spread in herds of various sizes.

Effective control of Johne’s disease in large Czech dairy herds

Introduction

Johne’s disease, caused by infection with Mycobacterium avium subsp. paratuberculosis (MAP), causes economic losses in dairy herds due to reduced milk production and premature culling. A test-and-cull strategy coupled with changes in calf rearing management preventing new infections has been introduced into infected herds to control MAP prevalence. This study appraised the effectiveness of these practice changes.

Material and Methods

In 19 large dairy herds (of a median 470 milk-producing cows), implementing MAP control measures for 3–7 years, a serum ELISA was used to detect infected cows in their dry-off period. The number of ELISA-positive animals per year (EPAY) was calculated and statistical analysis was used to test whether the EPAY total decreased during the control period and to analyse the EPAY in relationship to the duration of the control programme.

Results

Statistical support was found for a decrease of EPAY over time (P < 0.01, odds ratio 0.756) and in 14 herds a significant fall in the percentages of EPAY during the test period (P ≤ 0.05) was noted.

Conclusion

Our results demonstrated the effectiveness of the control measures in place to reduce MAP infection in herds with initial EPAY ≥3.36%. The missing decreasing trend in the remaining five herds with low average initial EPAY suggested the need for additional measures to reduce the number of infected animals in these herds.

Who infects whom?-Reconstructing infection chains of Mycobacterium avium ssp. paratuberculosis in an endemically infected dairy herd by use of genomic data

Recent evidence of circulation of multiple strains within herds and mixed infections of cows marks the beginning of a rethink of our knowledge on Mycobacterium avium ssp. paratuberculosis (MAP) epidemiology. Strain typing opens new ways to investigate MAP transmission. This work presents a method for reconstructing infection chains in a setting of endemic Johne’s disease on a well-managed dairy farm. By linking genomic data with demographic field data, strain-specific differences in spreading patterns could be quantified for a densely sampled dairy herd. Mixed infections of dairy cows with MAP are common, and some strains spread more successfully. Infected cows remain susceptible for co-infections with other MAP genotypes. The model suggested that cows acquired infection from 1–4 other cows and spread infection to 0–17 individuals. Reconstructed infection chains supported the hypothesis that high shedding animals that started to shed at an early age and showed a progressive infection pattern represented a greater risk for spreading MAP. Transmission of more than one genotype between animals was recorded. In this farm with a good MAP control management program, adult-to-adult contact was proposed as the most important transmission route to explain the reconstructed networks. For each isolate, at least one more likely ancestor could be inferred. Our study results help to capture underlying transmission processes and to understand the challenges of tracing MAP spread within a herd. Only the combination of precise longitudinal field data and bacterial strain type information made it possible to trace infection in such detail.

Characterizing infectious disease progression through discrete states using hidden Markov models

Infectious disease management relies on accurate characterization of disease progression so that transmission can be prevented. Slowly progressing infectious diseases can be difficult to characterize because of a latency period between the time an individual is infected and when they show clinical signs of disease. The introduction of Mycobacterium avium ssp. paratuberculosis (MAP), the cause of Johne’s disease, onto a dairy farm could be undetected by farmers for years before any animal shows clinical signs of disease. In this time period infected animals may shed thousands of colony forming units. Parameterizing trajectories through disease states from infection to clinical disease can help farmers to develop control programs based on targeting individual disease state, potentially reducing both transmission and production losses due to disease. We suspect that there are two distinct progression pathways; one where animals progress to a high-shedding disease state, and another where animals maintain a low-level of shedding without clinical disease. We fit continuous-time hidden Markov models to multi-year longitudinal fecal sampling data from three US dairy farms, and estimated model parameters using a modified Baum-Welch expectation maximization algorithm. Using posterior decoding, we observed two distinct shedding patterns: cows that had observations associated with a high-shedding disease state, and cows that did not. This model framework can be employed prospectively to determine which cows are likely to progress to clinical disease and may be applied to characterize disease progression of other slowly progressing infectious diseases.

Characterization of potential superspreader farms for bovine tuberculosis: A review

Background

Variation in host attributes that influence their contact rates and infectiousness can lead some individuals to make disproportionate contributions to the spread of infections. Understanding the roles of such ‘superspreaders’ can be crucial in deciding where to direct disease surveillance and controls to greatest effect. In the epidemiology of bovine tuberculosis (bTB) in Great Britain, it has been suggested that a minority of cattle farms or herds might make disproportionate contributions to the spread of Mycobacterium bovis, and hence might be considered ‘superspreader farms’.

Objectives and Methods

We review the literature to identify the characteristics of farms that have the potential to contribute to exceptional values in the three main components of the farm reproductive number ‐ R_f: contact rate, infectiousness and duration of infectiousness, and therefore might characterize potential superspreader farms for bovine tuberculosis in Great Britain.

Results

Farms exhibit marked heterogeneity in contact rates arising from between‐farm trading of cattle. A minority of farms act as trading hubs that greatly augment connections within cattle trading networks. Herd infectiousness might be increased by high within‐herd transmission or the presence of supershedding individuals, or infectiousness might be prolonged due to undetected infections or by repeated local transmission, via wildlife or fomites.

Conclusions

Targeting control methods on putative superspreader farms might yield disproportionate benefits in controlling endemic bovine tuberculosis in Great Britain. However, real‐time identification of any such farms, and integration of controls with industry practices, present analytical, operational and policy challenges.

Identification of the ABCC4, IER3, and CBFA2T2 candidate genes for resistance to paratuberculosis from sequence-based GWAS in Holstein and Normande dairy cattle

Background

Bovine paratuberculosis is a contagious disease, caused by Mycobacterium avium subsp. paratuberculosis (MAP), with adverse effects on animal welfare and serious economic consequences. Published results on host genetic resistance to MAP are inconsistent, mainly because of difficulties in characterizing the infection status of cows. The objectives of this study were to identify quantitative trait loci (QTL) for resistance to MAP in Holstein and Normande cows with an accurately defined status for MAP.

Results

From MAP-infected herds, cows without clinical signs of disease were subjected to at least four repeated serum ELISA and fecal PCR tests over time to determine both infected and non-infected statuses. Clinical cases were confirmed using PCR. Only cows that had concordant results for all tests were included in further analyses. Positive and control cows were matched within herd according to their birth date to ensure a same level of exposure to MAP. Cows with accurate phenotypes, i.e. unaffected (control) or affected (clinical or non-clinical cases), were genotyped with the Illumina BovineSNP50 BeadChip. Genotypes were imputed to whole-genome sequences using the 1000 Bull Genomes reference population (run6). A genome-wide association study (GWAS) of MAP status of 1644 Holstein and 649 Normande cows, using either two (controls versus cases) or three classes of phenotype (controls, non-clinical and clinical cases), revealed three regions, on Bos taurus (BTA) chromosomes 12, 13, and 23, presenting significant effects in Holstein cows, while only one of those was identified in Normande cows (BTA23). The most significant effect was found on BTA13, in a short 8.5-kb region. Conditional analyses revealed that only one causal variant may be responsible for the effects observed on each chromosome with the ABCC4 (BTA12), CBFA2T2 (BTA13), and IER3 (BTA23) genes as good functional candidates.

Conclusions

A sequence-based GWAS on cows for which resistance to MAP was accurately defined, was able to identify candidate variants located in genes that were functionally related to resistance to MAP; these explained up to 28% of the genetic variance of the trait. These results are very encouraging for efforts towards implementation of a breeding strategy aimed at improving resistance to paratuberculosis in Holstein cows.

Identification of Sero-Diagnostic Antigens for the Early Diagnosis of Johne's Disease using MAP Protein Microarrays

Considerable effort has been directed toward controlling Johne’s disease (JD), a chronic granulomatous intestinal inflammatory disease caused by Mycobacterium avium subsp. paratuberculosis (MAP) in cattle and other ruminants. However, progress in controlling the spread of MAP infection has been impeded by the lack of reliable diagnostic tests that can identify animals early in the infection process and help break the transmission chain. To identify reliable antigens for early diagnosis of MAP infection, we constructed a MAP protein array with 868 purified recombinant MAP proteins, and screened a total of 180 well-characterized serum samples from cows assigned to 4 groups based on previous serological and fecal test results: negative low exposure (NL, n = 30); negative high exposure (NH, n = 30); fecal-positive, ELISA-negative (F + E−, n = 60); and both fecal- and ELISA-positive (F + E+, n = 60). The analyses identified a total of 49 candidate antigens in the NH, F + E−, and F + E+ with reactivity compared with the NL group (p < 0.01), a majority of which have not been previously identified. While some of the antigens were identified as reactive in only one of the groups, others showed reactivity in multiple groups, including NH (n = 28), F + E− (n = 26), and F + E+ (n = 17) groups. Using combinations of top reactive antigens in each group, the results reveal sensitivities of 60.0%, 73.3%, and 81.7% in the NH, F + E−, and F + E+, respectively at 90% specificity, suggesting that early detection of infection in animals may be possible and enable better opportunities to reduce within herd transmission that may be otherwise missed by traditional serological assays that are biased towards more heavily infected animals. Together, the results suggest that several of the novel candidate antigens identified in this study, particularly those that were reactive in the NH and F + E− groups, have potential utility for the early sero-diagnosis of MAP infection.

Longitudinal study of Mycobacterium avium ssp. paratuberculosis fecal shedding patterns and concurrent serological patterns in naturally infected dairy cattle

Mycobacterium avium ssp. paratuberculosis (MAP) is the etiological agent of paratuberculosis, a disease that affects ruminants worldwide. Despite global interest in the control of this disease, gaps exist in our knowledge of fecal shedding patterns and concurrent serological patterns. This longitudinal study in dairy cattle herds with high MAP seroprevalence in France aimed at accurately describing fecal shedding patterns over 1 year; relating those shedding patterns to individual animal characteristics (age, breed, parity); and exploring the association between fecal shedding patterns and serological patterns. To describe temporal fecal shedding patterns and continuity of shedding, along with the standard quantitative PCR (qPCR) threshold cycle we used a cutoff value that related to low or nonculturable fecal shedding. We also defined a threshold cycle indicative of shedding in high quantities to describe infection progression patterns. Twenty-one herds completed the study, and 782 cows were tested 4 times each. We obtained 4 sets of paired fecal qPCR and serum ELISA results from 757 cows. Although we targeted highly likely infectious animals, we found a large diversity of shedding patterns, as well as high variability between herds in the proportion of animals showing a given pattern. The fecal qPCR results of almost 20% of the final study sample were positioned at least once in the range that indicated low or nonculturable fecal shedding (between the adjusted and the standard cutoff value). Although these animals would typically be classified as non-shedders, they could be important to infection dynamics on the farm. Animals that shed at least twice consecutively and animals that shed in high quantities rarely reverted to negativity. Repeated fecal qPCR can be used to detect temporal fecal shedding traits, and the decision to cull an animal could practically be based on temporal, semiquantitative results. Overall, we found a mismatch between fecal shedding and ELISA seropositivity (637 animals were ELISA-negative 4 times, but only 13% of those animals were qPCR-negative 4 times). We found that having more than 2 ELISA-positive samples was strongly related to persistent and continuous shedding. We suggest that although serological testing is much less sensitive than qPCR, it can also be used, particularly over the course of multiple testing events, to identify animals that are most likely to contribute to the contamination of the farm environment.

Genetic association of polymorphisms in bovine TLR2 and TLR4 genes with Mycobacterium avium subspecies paratuberculosis infection in Indian cattle population

Toll like receptors (TLRs) are pattern recognition molecules involved in cellular recognition of Mycobacterium avium subspecies paratuberculosis (MAP), the infectious agent causing Paratuberculosis (PTB), a notified disease of domestic and wild ruminants. The present study was undertaken to investigate the presence of single nucleotide polymorphisms (SNPs) in TLR2 and TLR4 gene and to evaluate association of these SNPs with occurrence of PTB in Indian cattle. A total of 213 cattle, were subjected to multiple diagnostic tests viz. Johnin PPD, ELISA test (Indigenous and Parachek kit method), fecal microscopy and fecal culture for detection of MAP infection. Based on screening results 51 animals each were assigned to case and control population. Two SNPs viz. rs55617172, rs41830058 in TLR2 gene and two SNPs viz. rs8193046, rs8193060 in TLR4 gene and were genotyped by PCR-RFLP method. All SNPs were found to be polymorphic except rs41830058 in the case-control population. Both SNPs in TLR4 gene but none in TLR2 genes were significantly associated with the occurrence of PTB in our population. The genotypes in SNP rs8193046 and SNP rs8193060 were significantly (P < 0.01) different in case-control population. These findings suggest that SNPs rs8193046 and rs8193060 are likely a potential marker against MAP infection and a selection programme eliminating AG genotype for rs8193046 and CT genotype for rs8193060 might be beneficial in conferring resistance to MAP infection in Indian cattle population.

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.

Resilience to infection by Mycobacterium avium subspecies paratuberculosis following direct intestinal inoculation in calves

Mycobacterium avium subspecies paratuberculosis (Map) is the cause of Johne’s disease, a chronic enteritis of cattle. A significant knowledge gap is how persistence of Map within the intestinal tract after infection contributes to progression of disease. To address this, we exposed calves to Map by direct ileocecal Peyer’s patch injection. Our objective was to characterize the persistence of Map in tissues, associated intestinal lesions, fecal Map shedding, and serum antibody responses, through the first 28-weeks post-inoculation (wpi). Previous work using this model showed 100% rate of Map infection in intestine and lymph node by 12 wpi. We hypothesized that direct inoculation of Map into the distal small intestine would induce intestinal Map infection with local persistence and progression towards clinical disease. However, our data show decreased persistence of Map in the distal small intestine and draining lymph nodes. We identified Map in multiple sections of distal ileum and draining lymph node of all calves at 4 and 12 wpi, but then we observed reduced Map in distal ileum at 20 wpi, and by 28 wpi we found that 50% of animals had no detectable Map in intestine or the lymph node. This provides evidence of resilience to Map infection following direct intestinal Map inoculation. Further work examining the immune responses and host–pathogen interactions associated with this infection model are needed to help elicit the mechanisms underlying resilience to Map infection.

Serum lipidomics of bovine paratuberculosis: Disruption of choline-containing glycerophospholipids and sphingolipids

OBJECTIVES

Bovine paratuberculosis is a devastating infection with Mycobacterium avium subspecies paratuberculosis that ultimately results in death from malnutrition. While the infection is characterized by a long (2-4 years) subclinical phase with immune activation, ultimately host defense mechanisms fail and the bacteria spread from the small intestine to other organs. Since both the gastrointestinal tract and liver are essential for the biosynthesis of structural glycerophospholipids, we investigated the circulating levels of these lipids in field infections and experimentally infected cattle.

METHODS

Serum lipidomics of control and M. avium subspecies paratuberculosis-infected cattle were performed utilizing high-resolution mass spectrometry.

RESULTS

In M. avium subspecies paratuberculosis-positive cattle, demonstrating clinical signs, we monitored large decreases in the levels of circulating phosphocholine-containing lipids. These included phosphatidylcholines, choline plasmalogens, and sphingomyelins. Next, we monitored the time course of these lipid alterations in experimentally infected calves and found that altered lipid levels were only detected in cattle with clinical signs of infection.

CONCLUSIONS

Our data indicate that altered availability of choline-containing lipids occurs late in the disease process and is most likely a result of malnutrition and altered biosynthetic capacities of the liver and gastrointestinal tract. Alterations in the bioavailability of these critical structural lipids presumably contributes to the demise of M. avium subspecies paratuberculosis-infected cattle. In light of increasing concern that M. avium subspecies paratuberculosis may be a zoonotic bacterium that contributes to the development of Crohn's disease and multiple sclerosis, our data also have human clinical relevance.

Identifying individual animal factors associated with Mycobacterium avium subsp. paratuberculosis (MAP) milk ELISA positivity in dairy cattle in the Midwest region of the United States

BACKGROUND

Mycobacterium avium subsp. paratuberculosis (MAP) is a widespread chronic disease of ruminants that causes severe economic losses to the dairy cattle industry worldwide. The objective of this study was to evaluate the association between individual cow MAP-ELISA and relevant milk production predictors in dairy cattle using data routinely collected as part of quality and disease control programs in the Midwest region of the U.S. Milk ELISA results of 45,652 animals from 691 herds from November 2014 to August 2016 were analyzed.

RESULTS

The association between epidemiological and production factors and ELISA results for MAP in milk was quantified using four individual-level mixed multivariable logistic regression models that accounted for clustering of animals at the farm level. The four fitted models were one global model for all the animals assessed here, irrespective of age, and one for each of the categories of < 4 year-old, 4-8 year-old, and > 8 year-old cattle, respectively. A small proportion (4.9%; n = 2222) of the 45,652 tested samples were MAP-seropositive. Increasing age of the animals and higher somatic cell count (SCC) were both associated with increased odds for MAP positive test result in the model that included all animals, while milk production, milk protein and days in milk were negatively associated with MAP milk ELISA. Somatic cell count was positively associated with an increased risk in the models fitted for < 4 year-old and 4-8 year-old cattle. Variables describing higher milk production, milk protein content and days in milk were associated with significantly lower risk in the models for 4-8 year-old cattle and for all cattle.

CONCLUSIONS

Our results suggest that testing cows with high SCC (> 26 × 1000/ml), low milk production and within the first 60 days of lactation may maximize the odds of detecting seropositive animals. These results could be useful in helping to design better surveillance strategies based in testing of milk.

Use of an Individual-based Model to Control Transmission Pathways of Mycobacterium avium Subsp. paratuberculosis Infection in Cattle Herds

Johne’s disease (JD) is a chronic enteric disease in cattle caused by Mycobacterium avian subsp. paratuberculosis (MAP). Eradicating JD is a difficult task due to the long incubation period of MAP, inefficient diagnostic tests, and delayed clinical signs. Effective control strategies can help farmers to reduce prevalence, but those most acceptable to farmers combine specific information about lactation performance and testing results, which existing models do not provide. This paper presents an individual-based model of MAP infection dynamics and assesses the relative performance of the applied alternative control strategies. The base dairy herd model included the daily life events of a dairy cow and reflects several current dairy management processes. We then integrated MAP infection dynamics into the model. The model adopted four different test-based control strategies based on risk-based culling decisions and three hygiene scenarios. The model tracked the source of each infection and quantified the efficacy of each control strategy in reducing the risks of different transmission routes. The results suggest that risk-based culling can reduce prevalence compared with no control, but cannot eliminate the infection. Overall, this work provides not only a valuable tool to investigate MAP transmission dynamics but also offers adaptability to model similar infectious diseases.

More S, Bøtner A, Butterworth A, Calistri P, Depner K, Edwards S, Garin-Bastuji B, Good M, Gortázar Schmidt C, Michel V, Miranda MA, Nielsen SS, Raj M, Sihvonen L, Spoolder H, Stegeman JA, Thulke HH, Velarde A, Willeberg P, Winckler C, Baldinelli F, Broglia A, Zancanaro G, Beltrán-Beck B, Kohnle L, Morgado J, Bicout D. Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation (EU) No 2016/429): paratuberculosis

Paratuberculosis has been assessed according to the criteria of the Animal Health Law (AHL), in particular criteria of Article 7 on disease profile and impacts, Article 5 on the eligibility of paratuberculosis to be listed, Article 9 for the categorisation of paratuberculosis according to disease prevention and control rules as in Annex IV and Article 8 on the list of animal species related to paratuberculosis. The assessment has been performed following a methodology composed of information collection and compilation, expert judgement on each criterion at individual and, if no consensus was reached before, also at collective level. The output is composed of the categorical answer, and for the questions where no consensus was reached, the different supporting views are reported. Details on the methodology used for this assessment are explained in a separate opinion. According to the assessment performed, paratuberculosis can be considered eligible to be listed for Union intervention as laid down in Article 5(3) of the AHL. The disease would comply with the criteria in Sections 3, 4 and 5 of Annex IV of the AHL, for the application of the disease prevention and control rules referred to in points (c), (d) and (e) of Article 9(1). The animal species to be listed for paratuberculosis according to Article 8(3) criteria are several species of mammals and birds as susceptible species and some species of the families Bovidae, Cervidae and Leporidae as reservoirs.

Inferring biomarkers for Mycobacterium avium subsp. paratuberculosis infection and disease progression in cattle using experimental data

Available diagnostic assays for Mycobacterium avium subsp. paratuberculosis (MAP) have poor sensitivities and cannot detect early stages of infection, therefore, there is need to find new diagnostic markers for early infection detection and disease stages. We analyzed longitudinal IFN-γ, ELISA-antibody and fecal shedding experimental sensitivity scores for MAP infection detection and disease progression. We used both statistical methods and dynamic mathematical models to (i) evaluate the empirical assays (ii) infer and explain biological mechanisms that affect the time evolution of the biomarkers, and (iii) predict disease stages of 57 animals that were naturally infected with MAP. This analysis confirms that the fecal test is the best marker for disease progression and illustrates that Th1/Th2 (IFN-γ/ELISA antibodies) assays are important for infection detection, but cannot reliably predict persistent infections. Our results show that the theoretical simulated macrophage-based assay is a potential good diagnostic marker for MAP persistent infections and predictor of disease specific stages. We therefore recommend specifically designed experiments to test the use of a based assay in the diagnosis of MAP infections.

Economic consequences of paratuberculosis control in dairy cattle: A stochastic modeling study

The cost of paratuberculosis to dairy herds, through decreased milk production, early culling, and poor reproductive performance, has been well-studied. The benefit of control programs, however, has been debated. A recent stochastic compartmental model for paratuberculosis transmission in US dairy herds was modified to predict herd net present value (NPV) over 25 years in herds of 100 and 1000 dairy cattle with endemic paratuberculosis at initial prevalence of 10% and 20%. Control programs were designed by combining 5 tests (none, fecal culture, ELISA, PCR, or calf testing), 3 test-related culling strategies (all test-positive, high-positive, or repeated positive), 2 test frequencies (annual and biannual), 3 hygiene levels (standard, moderate, or improved), and 2 cessation decisions (testing ceased after 5 negative whole-herd tests or testing continued). Stochastic dominance was determined for each herd scenario; no control program was fully dominant for maximizing herd NPV in any scenario. Use of the ELISA test was generally preferred in all scenarios, but no paratuberculosis control was highly preferred for the small herd with 10% initial prevalence and was frequently preferred in other herd scenarios. Based on their effect on paratuberculosis alone, hygiene improvements were not found to be as cost-effective as test-and-cull strategies in most circumstances. Global sensitivity analysis found that economic parameters, such as the price of milk, had more influence on NPV than control program-related parameters. We conclude that paratuberculosis control can be cost effective, and multiple control programs can be applied for equivalent economic results.

Paratuberculosis in buffaloes in Northeast Brazil

Several farms in the Northeast of Brazil were investigated for Mycobacterium avium subsp. paratuberculosis infection in order to identify the occurrence of paratuberculosis in buffaloes. Samples were obtained from 17 farms, two slaughter houses, and a quarantine area in the Northeast. About 15,000 buffaloes of the Murrah, Mediterranean, and Jafarabadi breed as well as their crossbreeds were evaluated for meat, dairy, and mixed farms with semi-intensive or extensive breeding practices. For diagnostic purposes, postmortem and histopathological examination, including Ziehl-Neelsen test of fecal smears and scraped intestinal mucosa were performed. PCR was applied for fecal samples, mesenteric lymph nodes, and intestines. Six Johne's disease-positive farms, which together with those previously identified, indicate that the disease is spread through the Brazilian Northeast, similar to what occurs in cattle herds in other regions of the country. The increase in prevalence of paratuberculosis is a consequence of introduction of animals from other regions without adequate veterinary assistance and due to the little official attention paid to this initially silent and chronic disease.

Impact of the shedding level on transmission of persistent infections in Mycobacterium avium subspecies paratuberculosis (MAP)

Super-shedders are infectious individuals that contribute a disproportionate amount of infectious pathogen load to the environment. A super-shedder host may produce up to 10,000 times more pathogens than other infectious hosts. Super-shedders have been reported for multiple human and animal diseases. If their contribution to infection dynamics was linear to the pathogen load, they would dominate infection dynamics. We here focus on quantifying the effect of super-shedders on the spread of infection in natural environments to test if such an effect actually occurs in Mycobacterium avium subspecies paratuberculosis (MAP). We study a case where the infection dynamics and the bacterial load shed by each host at every point in time are known. Using a maximum likelihood approach, we estimate the parameters of a model with multiple transmission routes, including direct contact, indirect contact and a background infection risk. We use longitudinal data from persistent infections (MAP), where infectious individuals have a wide distribution of infectious loads, ranging upward of three orders of magnitude. We show based on these parameters that the effect of super-shedders for MAP is limited and that the effect of the individual bacterial load is limited and the relationship between bacterial load and the infectiousness is highly concave. A 1000-fold increase in the bacterial contribution is equivalent to up to a 2-3 fold increase in infectiousness.

Implications of PCR and ELISA results on the routes of bulk-tank contamination with Mycobacterium avium ssp. paratuberculosis

Mycobacterium avium ssp. paratuberculosis (MAP), the etiologic agent of Johne's disease in dairy cattle, may enter the bulk tank via environmental contamination or direct excretion into milk. Traditionally, diagnostics to identify MAP in milk target either MAP antibodies (by ELISA) or the organism itself (by culture or PCR). High ELISA titers may be directly associated with excretion of MAP into milk but only indirectly linked to environmental contamination of the bulk tank. Patterns of bulk-milk ELISA and bulk-milk PCR results could therefore provide insight into the routes of contamination and level of infection or environmental burden. Coupled with questionnaire responses pertaining to management, the results of these diagnostic tests could reveal correlations with herd characteristics or on-farm practices that distinguish herds with high and low environmental bulk-tank MAP contamination. A questionnaire on hygiene, management, and Johne's specific parameters was administered to 292 dairy farms in New York, Oregon, and Wisconsin. Bulk-tank samples were collected from each farm for evaluation by real-time PCR and ELISA. Before DNA extraction and testing of the unknown samples, bulk-milk template preparation was optimized with respect to parameters such as MAP fractionation patterns and lysis. Two regression models were developed to explore the relationships among bulk-tank PCR, ELISA, environmental predictors, and herd characteristics. First, ELISA optical density (OD) was designated as the outcome in a linear regression model. Second, the log odds of being PCR positive in the bulk tank were modeled using binary logistic regression with penalized maximum likelihood. The proportion of PCR-positive bulk tanks was highest for New York and for organic farms, providing a clue as to the geographical patterns of MAP-positive bulk-tank samples and relationship to production type. Bulk-milk PCR positivity was also higher for large relative to small herds. The models revealed that bulk-milk PCR result could predict ELISA OD, with PCR-positive results corresponding to high bulk-milk ELISA titers. Similarly, ELISA was a predictor of PCR result, although the association was stronger for organic farms. Despite agreement between high bulk-milk ELISA titers and positive PCR results, a large proportion of high ELISA farms had PCR-negative bulk tanks, suggesting that farms are able to maintain satisfactory hygiene and management despite a presence of MAP in these herds.

A new compartmental model of Mycobacterium avium subsp. paratuberculosis infection dynamics in cattle

Models of Mycobacterium avium subsp. paratuberculosis (MAP), a chronic infectious agent of cattle, are used to identify effective control programs. However, new biological findings show that adult infections occur and that infected animals can be separated into 2 paths: animals that will become high-shedding and, eventually, experience clinical disease (high-path); and animals that will shed only small quantities of MAP and will remain subclinical (low-path). Longitudinal data analysis found that high-path animals progress more quickly than previously believed. A standard model of MAP transmission in dairy herds was modified to include adult low-path infections and 2 infection pathways for infected calves. Analysis of this model showed that adult infection may play an important role in MAP dynamics on a dairy farm, and that the increased rate of progression for high-path animals influences both the prevalence and the persistence of MAP on a dairy farm. This new model will be able to determine the effectiveness of MAP control programs more accurately than previous models.

Differences in intermittent and continuous fecal shedding patterns between natural and experimental Mycobacterium avium subspecies paratuberculosis infections in cattle

The objective of this paper is to study shedding patterns of cows infected with Mycobacterium avium subsp. paratuberculosis (MAP). While multiple single farm studies of MAP dynamics were reported, there is not large scale meta-analysis of both natural and experimental infections. Large difference in shedding patterns between experimentally and naturally infected cows were observed. Experimental infections are thus probably driven by different pathological mechanisms. For further evaluations of shedding patterns only natural infections were used. Within such infections, the transition to high shedding was studied as a proxy to the development of a clinical disease. The majority of studied cows never developed high shedding levels. Those that do, typically never reduced their shedding level to low or no shedding. Cows that eventually became high shedders showed a pattern of continuous shedding. In contrast, cows with an intermittent shedding pattern had a low probability to ever become high shedders. In addition, cows that start shedding at a younger age (less than three years of age) have a lower hazard of becoming high shedders compared to cows starting to shed at an older age. These data suggest the presence of three categories of immune control. Cows that are intermittent shedders have the infection process under control (no progressive infection). Cows that start shedding persistently at a young age partially control the infection, but eventually will be high shedders (slow progressive infection), while cows that start shedding persistently at an older age cannot effectively control the infection and become high shedders rapidly.

Agent-based model for Johne's disease dynamics in a dairy herd

Johne’s disease is an infectious gastrointestinal disease in ruminants caused by Mycobacterium avium subsp. paratuberculosis that causes diarrhea, emaciation, decreased milk production and eventually death. The disease is transmitted in utero and via milk and colostrums to calves, and fecal-orally to all age classes. Financial losses due to the disease are estimated to be over $200 million in the US dairy industry. The goal of this study was to evaluate the cost effectiveness of control measures based on diagnosis with a sensitive ELISA, EVELISA. An agent-based, discrete time model was developed to simulate Johne’s disease dynamics in a US dairy herd. Spatial aspects of disease transmission were taken into account by using six spatial compartments. The effects on disease prevalence were studied with and without transmission routes included in the model. Further, using the model, cost effectiveness of ELISA-based Johne’s disease control was evaluated. Using the parameters we collected and assumed, our model showed the initial prevalence of Johne’s disease (33.1 ± 0.2%) in the farm increased to 87.7 ± 1.7% in a 10 year-simulation. When ELISA-based control measures were included in the simulation, the increase in prevalence was significantly slowed down, especially when EVELISA was used. However, the level of the prevalence was still higher than the initial level after 10 year simulation even with the ELISA-based diagnostic intervention. The prevalence was further reduced when quarterly ELISA testing was included. The cost analysis showed that the quarterly ELISA and EVELISA testing could bring $44.8 and $51.5/animal/year more revenues, respectively, to a dairy farm.

Evaluating contribution of the cellular and humoral immune responses to the control of shedding of Mycobacterium avium spp. paratuberculosis in cattle

Mycobacterium avium spp. paratuberculosis (MAP) causes a persistent infection and chronic inflammation of the gut in ruminants leading to bacterial shedding in feces in many infected animals. Although there are often strong MAP-specific immune responses in infected animals, immunological correlates of protection against progression to disease remain poorly defined. Analysis of cross-sectional data has suggested that the cellular immune response observed early in infection is effective at containing bacterial growth and shedding, in contrast to humoral immune responses. In this study, 20 MAP-infected calves were followed for nearly 5 years during which MAP shedding, antigen-specific cellular (LPT) and humoral (ELISA) immune responses were measured. We found that MAP-specific cellular immune response developed slowly, with the peak of the immune response occurring one year post infection. MAP-specific humoral immunity expanded only in a subset of animals. Only in a subset of animals there was a statistically significant negative correlation between the amount of MAP shedding and magnitude of the MAP-specific cellular immune response. Direct fitting of simple mechanistic mathematical models to the shedding data suggested that MAP-specific immune responses contributed significantly to the kinetics of MAP shedding in most animals. However, whereas the MAP-specific cellular immune response was predicted to suppress shedding in some animals, in other animals it was predicted to increase shedding. In contrast, MAP-specific humoral response was always predicted to increase shedding. Our results illustrate the use of mathematical methods to understand relationships between mycobacteria and immunity in vivo but also highlight problems with establishing cause-effect links from observational data.

Two state model for a constant disease hazard in paratuberculosis (and other bovine diseases)

Many diseases are characterized by a long and varying sub-clinical period. Two main mechanisms can explain such periods: a slow progress toward disease or a sudden transition from a healthy state to a disease state induced by internal or external events. We here survey epidemiological features of the amount of bacteria shed during Mycobacterium Avium Paratuberculosis (MAP) infection to test which of these two models, slow progression or sudden transition (or a combination of the two), better explains the transition from intermittent and low shedding to high shedding. Often, but not always, high shedding is associated with the occurrence of clinical signs. In the case of MAP, the clinical signs include diarrhea, low milk production, poor fertility and eventually emaciation and death. We propose a generic model containing bacterial growth, immune control and fluctuations. This proposed generic model can represent the two hypothesized types of transitions in different parameter regimes. The results show that the sudden transition model provides a simpler explanation of the data, but also suffers from some limitations. We discuss the different immunological mechanism that can explain and support the sudden transition model and the interpretation of each term in the studied model. These conclusions are applicable to a wide variety of diseases, and MAP serves as a good test case based on the large scale measurements of single cow longitudinal profiles in this disease.