Evaluation [corrected] of the "Iceberg Phenomenon" in Johne's disease through mathematical modelling

Investigating in vivo Mycobacterium avium subsp. paratuberculosis microevolution and mixed strain infections

Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne's Disease (JD) in ruminants, which is responsible for significant economic loss to the global dairy industry. Mixed strain infection (MSI) refers to the concurrent infection of a susceptible host with genetically distinct strains of a pathogen, whereas within-host changes in an infecting strain leading to genetically distinguishable progeny is called microevolution. The two processes can influence host-pathogen dynamics, disease progression and outcomes, but not much is known about their prevalence and impact on JD. Therefore, we obtained up to 10 MAP isolates each from 14 high-shedding animals and subjected them to whole-genome sequencing. Twelve of the 14 animals examined showed evidence for the presence of MSIs and microevolution, while the genotypes of MAP isolates from the remaining two animals could be attributed solely to microevolution. All MAP isolates that were otherwise isogenic had differences in short sequence repeats (SSRs), of which SSR1 and SSR2 were the most diverse and homoplastic. Variations in SSR1 and SSR2, which are located in ORF1 and ORF2, respectively, affect the genetic reading frame, leading to protein products with altered sequences and computed structures. The ORF1 gene product is predicted to be a MAP surface protein with possible roles in host immune modulation, but nothing could be inferred regarding the function of ORF2. Both genes are conserved in Mycobacterium avium complex members, but SSR1-based modulation of ORF1 reading frames seems to only occur in MAP, which could have potential implications on the infectivity of this pathogen. IMPORTANCE Johne's disease (JD) is a major problem in dairy animals, and concerns have been raised regarding the association of Mycobacterium avium subsp. paratuberculosis (MAP) with Crohn's disease in humans. MAP is an extremely slow-growing bacterium with low genome evolutionary rates. Certain short sequence repeats (SSR1 and SSR2) in the MAP chromosome are highly variable and evolve at a faster rate than the rest of the chromosome. In the current study, multiple MAP isolates with genetic variations such as single-nucleotide polymorphisms, and more noticeably, diverse SSRs, could simultaneously infect animals. Variations in SSR1 and SSR2 affect the products of the respective genes containing them. Since multiple MAP isolates can infect the same animal and the possibility that the pathogen undergoes further changes within the host due to unstable SSRs, this could provide a compensative mechanism for an otherwise slow-evolving pathogen to increase phenotypic diversity for overcoming host responses.

High prevalence of vitamin D insufficiency among South Asian pregnant women: a systematic review and meta-analysis

Insufficiency of vitamin D, during pregnancy, is a common cause of various pregnancy-related complications. Despite such insufficiency being frequently reported among South Asian pregnant women, the absence of systematic review and meta-analysis renders the true extent of this problem being poorly characterised. In this systematic review, three main databases (PubMed, Scopus and Google Scholar) were searched for original studies. We included original studies published between 1January 2001 to 31 December 2019, conducted on pregnant women who lived in South Asian countries and reported the prevalence of vitamin D insufficiency among the study participants. Twenty studies with a total of 7804 participants from four South Asian countries finally met our selection criteria. Overall pooled prevalence of insufficiency was 65 % (95 % CI: 51 %, 78 %) with a significant heterogeneity (I² = 99·37 %; P = 0·00). The average level of vitamin D ranged from 9 ng/ml to 24·86 ng/ml with a weighted mean of 16·37 ng/ml (weighted standard deviation 7·13 ng/ml). The highest prevalence of insufficiency was found in Pakistan (76 %) followed by India (67 %), Bangladesh (64 %) and Nepal (14 %). Results obtained in this study suggest that vitamin D insufficiency is highly prevalent among South Asian pregnant women. Being the first systematic review in this region, findings from this study will help the future studies and strengthen the evidence for policymakers to develop effective mitigation strategies.

Mycobacterium paratuberculosis zoonosis is a One Health emergency

A singular pathogen has been killing animals, contaminating food and causing an array of human diseases. Mycobacterium avium subspecies paratuberculosis (MAP) is the cause of a fatal enteric infectious disease called Johne's (Yo'-nees), a disorder mostly studied in ruminant animals. MAP is globally impacting animal health and imparting significant economic burden to animal agriculture. Confounding the management of Johne's disease is that animals are typically infected as calves and while commonly not manifesting clinical disease for years, they shed MAP in their milk and feces in the interval. This has resulted in a "don't test, don't tell" scenario for the industry resulting in greater prevalence of Johne's disease; furthermore, because MAP survives pasteurization, the contaminated food supply provides a source of exposure to humans. Indeed, greater than 90% of dairy herds in the US have MAP-infected animals within the herd. The same bacterium, MAP, is the putative cause of Crohn's disease in humans. Countries historically isolated from importing/exporting ruminant animals and free of Johne's disease subsequently acquired the disease as a consequence of opening trade with what proved to be infected animals. Crohn's disease in those populations became a lagging indicator of MAP infection. Moreover, MAP is associated with an increasingly long list of human diseases. Despite MAP scientists entreating regulatory agencies to designate MAP a "zoonotic agent," it has not been forthcoming. One Health is a global endeavor applying an integrative health initiative that includes the environment, animals and humans; One Health asserts that stressors affecting one affects all three. Recognizing the impact MAP has on animal and human health as well as on the environment, it is time for One Health, as well as other global regulatory agencies, to recognize that MAP is causing an insidious slow-motion tsunami of zoonosis and implement public health mitigation.

High burden of hypovitaminosis D among the children and adolescents in South Asia: a systematic review and meta-analysis

BACKGROUND

Vitamin D is vital for the growth and development of children. While deficiency and/or insufficiency of vitamin D among South Asian children are frequently reported in the literature, the lack of a meta-analysis has left its true extent poorly characterized. In this study, we aimed to conduct a systematic review and perform meta-analyses of the prevalence of hypovitaminosis D among the children of the South Asian countries.

METHODS

Two major electronic search engines (PubMed and Scopus) and one database (Google scholar) were used; original studies, conducted among South Asian children and adolescents and published between 1 January 2001 and 31 December 2019. A random-effect meta-analysis was also performed to calculate the pooled prevalence of hypovitaminosis D followed by subgroup analyses for countries and age groups.

RESULTS

After applying inclusion and exclusion criteria, a total of 41 studies with a total population size of 18,233 were finally selected. The overall prevalence of hypovitaminosis D was 61% [95% CI: 46% to 71%] with highly significant heterogeneity (I2 = 99.72%; p < 0.0001). The average level of serum vitamin D ranged from 5 ng/mL to 34 ng/mL, with a weighted mean of 19.15 ng/mL (weighted standard deviation 11.59 ng/mL). Country-wise analysis showed that hypovitaminosis D in Afghanistan was the highest [96.2%; 95% CI: 91% to 99%], followed by Pakistan [94%; 95% CI: 90% to 96%], India [64%; 95% CI: 46% to 79%], Bangladesh [35.48%; 95% CI: 32% to 39%], Nepal [35%; 95% CI: 1% to 83%], and Sri Lanka [25%; 95% CI: 16% to 36%]. Age group analyses revealed that hypovitaminosis D was most prevalent among neonates [85%; 95% CI: 76% to 91%], followed by school-going children [57%; 95% CI: 33% to 80%], and preschool children [55%; 95% CI: 35% to 75%].

CONCLUSION

This study generates quantitative evidence and specific extent of hypovitaminosis D in the South Asian countries as a public health concern. Being the first systematic review for this region, results from this study will create awareness and will facilitate adopting mitigation strategies by the policymakers and the governments to address this problem.

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.

An Embedded Multiscale Modelling to Guide Control and Elimination of Paratuberculosis in Ruminants

In recent years, multiscale modelling approach has begun to receive an overwhelming appreciation as an appropriate technique to characterize the complexity of infectious disease systems. In this study, we develop an embedded multiscale model of paratuberculosis in ruminants at host level that integrates the within-host scale and the between-host. A key feature of embedded multiscale models developed at host level of organization of an infectious disease system is that the within-host scale and the between-host scale influence each other in a reciprocal (i.e., both) way through superinfection, that is, through repeated infection before the host recovers from the initial infectious episode. This key feature is demonstrated in this study through a multiscale model of paratuberculosis in ruminants. The results of this study, through numerical analysis of the multiscale model, show that superinfection influences the dynamics of paratuberculosis only at the start of the infection, while the MAP bacteria replication continuously influences paratuberculosis dynamics throughout the infection until the host recovers from the initial infectious episode. This is largely because the replication of MAP bacteria at the within-host scale sustains the dynamics of paratuberculosis at this scale domain. We further use the embedded multiscale model developed in this study to evaluate the comparative effectiveness of paratuberculosis health interventions that influence the disease dynamics at different scales from efficacy data.

Comparison of Mycobacterium avium subsp. paratuberculosis infection in cattle, sheep and goats in the Khuzestan Province of Iran: Results of a preliminary survey

Background

Paratuberculosis or Johne's disease, the chronic infectious granulomatous enteritis of ruminants, is a worldwide infection, which is caused by Mycobacterium avium subsp. paratuberculosis (MAP). The most common symptoms of this disease in cattle are loss of milk production, weight loss and diarrhoea, whereas in sheep and goats, the symptoms are emaciation, anorexia and severe disability.

Objectives

The aim of this study was to compare the seroprevalence of MAP in cattle, sheep and goats in the southwest of Iran.

Methods

Blood samples were randomly collected from 530 cattle, 568 sheep and 368 goats in southwest of Iran. Sera were tested by a commercial ELISA kit (ID vet; ID Screen® Paratuberculosis Indirect) for detection of antibodies of MAP.

Results

Overall apparent and true seroprevalence rate of MAP was 6.00% (95% CI: 4.90%–7.30%) and 13.25% (95% CI: 11.55%– 14.95%). Apparent and true seroprevalence of MAP, respectively, was 4.34% (95% CI: 3.88%–6.46%) and 9.19% (95% CI: 6.98%–11.98%) in cattle, 6.87% (95% CI: 5.05%–9.27%) and 15.37% (95% CI: 12.60%–16.60%) in sheep and 7.07% (95% CI: 4.82%–10.18%) and 15.86% (95% CI: 12.41%–20.01%) in goats, respectively. As a result, there was no significant relationship between animal species and MAP infection. Moreover, multivariate logistic regression showed that the infection rate is not associated with age, gender and geographical location in cattle, sheep and goats (P > 0.05).

Conclusion

This study confirms that the seroprevalence of MAP is relatively considerable in the cattle, sheep and goats in the southwest of Iran, although in cattle, it is less than goats and sheep. Therefore, preventive and control measures should be considered by animal health authorities and meat and dairy processing units.

How is the iceberg of COVID-19? Results from a rapid literature review

Background: Given the various reports of the clinical spectrum of the disease, the aim of the present study was to determine possible scenarios of Coronavirus 2019 (COVID-19) iceberg using published articles. Methods: The present study was a rapid review of all international databases, including PubMed (Medline), Scopus, Web of Sciences, Embase, and Cochrane Library from January 1 to October 30, 2020. Results: In this review, 7 scenarios were considered for COVID-19 iceberg, in which the range of fatality percentage was estimated to be 0.5% to 7%, the range of asymptomatic cases 1% to 88.6%, the range of cases with mild symptoms 8% to 78%, no symptoms 1 % to 90 %, the range of intensive care unit (ICU) admission was 0.5% to 14.2%, and finally the intubation percentage was estimated to be 0.2% to 12.2%. The Scenarios Diamond Princess Cruise Ship and Iceland are closer to the reality of the clinical spectrum of COVID-19 around the world, which represent 0.6% and 0.5% of deaths, 0.7% and 1% of intubations, 2.5% and 9.7% of ICU admissions, 1.1% and 6% of hospitalizations, 15% and 31% of cases with mild symptoms, and finally 56.9% and 75% of asymptomatic cases of COVID-19, respectively, which should now be considered as the basis of the clinical knowledge of the disease. Conclusion: Understanding the clinical spectrum and natural knowledge of the disease and paying attention to asymptomatic or mild-symptom cases can help to make better decisions and develop more effective interventions to control COVID-19.

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.

Presence of Infection by Mycobacterium avium subsp. paratuberculosis in the Blood of Patients with Crohn's Disease and Control Subjects Shown by Multiple Laboratory Culture and Antibody Methods

Mycobacterium avium subspecies paratuberculosis (MAP) has long been suspected to be involved in the etiology of Crohn's disease (CD). An obligate intracellular pathogen, MAP persists and influences host macrophages. The primary goals of this study were to test new rapid culture methods for MAP in human subjects and to assess the degree of viable culturable MAP bacteremia in CD patients compared to controls. A secondary goal was to compare the efficacy of three culture methods plus a phage assay and four antibody assays performed in separate laboratories, to detect MAP from the parallel samples. Culture and serological MAP testing was performed blind on whole blood samples obtained from 201 subjects including 61 CD patients (two of the patients with CD had concurrent ulcerative colitis (UC)) and 140 non-CD controls (14 patients in this group had UC only). Viable MAP bacteremia was detected in a significant number of study subjects across all groups. This included Pozzato culture (124/201 or 62% of all subjects, 35/61 or 57% of CD patients), Phage assay (113/201 or 56% of all subjects, 28/61 or 46% of CD patients), TiKa culture (64/201 or 32% of all subjects, 22/61 or 36% of CD patients) and MGIT culture (36/201 or 18% of all subjects, 15/61 or 25% of CD patients). A link between MAP detection and CD was observed with MGIT culture and one of the antibody methods (Hsp65) confirming previous studies. Other detection methods showed no association between any of the groups tested. Nine subjects with a positive Phage assay (4/9) or MAP culture (5/9) were again positive with the Phage assay one year later. This study highlights viable MAP bacteremia is widespread in the study population including CD patients, those with other autoimmune conditions and asymptomatic healthy subjects.

A Novel Real-Time PCR-Based Screening Test with Pooled Fecal Samples for Bovine Johne's Disease

Johne's disease (JD) is an economically important infectious disease in livestock farming caused by Mycobacterium avium subsp. paratuberculosis As an alternative to serological tests, which are used mainly for the screening of whole herds, we developed a novel ResoLight-based real-time PCR (RL-PCR) assay with pooled fecal samples for the detection of fecal shedders in cattle herds. The RL-PCR assay included an internal amplification control (IC) which was amplified using the same primer pair as the target molecule M. avium subsp. paratuberculosis IS900 and differentiated based on melting temperatures. Individual fecal suspensions were pooled and concentrated by centrifugation to avoid a loss of sensitivity by the dilution effect. Combined with a DNA extraction kit (Johne-PureSpin; FASMAC), no inhibition of PCR amplification was observed with up to 15 fecal samples in a pool. The detection limit of RL-PCR at a pool size of 10 was 10 M. avium subsp. paratuberculosis organisms per gram of feces, which was comparable to that of individual testing. A total of 2,654 animals in 12 infected herds were screened by individual antibody-enzyme-linked immunosorbent assay (ELISA) and the RL-PCR assay using pooled feces. Fifty animals were diagnosed with JD through the screening by RL-PCR, compared with only 5 by ELISA (which were also positive in RL-PCR). In 7 JD-free herds, the results of 4 out of 327 pools (1.2%) were invalid due to the lack of IC amplification, and then animals were confirmed negative individually. Our results suggest that implementation of herd screening by pooled RL-PCR would advance the monitoring and control of JD in cattle herds.

Modelling spread and surveillance of Mycobacterium avium subsp. paratuberculosis in the Swedish cattle trade network

To monitor a state of disease freedom and to ensure a timely detection of new introductions of disease, surveillance programmes need be evaluated prior to implementation. We present a strategy to evaluate surveillance of Mycobacterium avium subsp. paratuberculosis (MAP) using simulated testing of bulk milk in an infectious disease spread model. MAP is a globally distributed, chronic infectious disease with substantial animal health impact. Designing surveillance for this disease poses specific challenges because methods for surveillance evaluation have focused on estimating surveillance system sensitivity and probability of freedom from disease and do not account for spread of disease or complex and changing population structure over long periods. The aims of the study were to 1. define a model that describes the spread of MAP within and between Swedish herds; 2. define a method for simulation of imperfect diagnostic testing in this framework; 3. to compare surveillance strategies to support surveillance design choices. The results illustrate how this approach can be used to identify differences between the probability of detecting disease in the population based on choices of the number of herds sampled and the use of risk-based or random selection of these herds. The approach was also used to assess surveillance to detect introduction of disease and to detect a very low prevalence endemic state. The use of bulk milk sampling was determined to be an effective method to detect MAP in the population with as few as 500 herds tested per year if the herd-level prevalence was 0.2 %. However, detection of point introductions in the population was unlikely in the 13-year simulation period even if as many as 2000 herds were tested per year. Interestingly, the use of a risk-based selection strategy was found to be a disadvantage to detect MAP given the modelled disease dynamics.

A single dose polyanhydride-based nanovaccine against paratuberculosis infection

Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis) causes Johne’s disease in ruminants and is characterized by chronic gastroenteritis leading to heavy economic losses to the dairy industry worldwide. The currently available vaccine (inactivated bacterin in oil base) is not effective in preventing pathogen shedding and is rarely used to control Johne’s disease in dairy herds. To develop a better vaccine that can prevent the spread of Johne’s disease, we utilized polyanhydride nanoparticles (PAN) to encapsulate mycobacterial antigens composed of whole cell lysate (PAN-Lysate) and culture filtrate (PAN-Cf) of M. paratuberculosis. These nanoparticle-based vaccines (i.e., nanovaccines) were well tolerated in mice causing no inflammatory lesions at the site of injection. Immunological assays demonstrated a substantial increase in the levels of antigen-specific T cell responses post-vaccination in the PAN-Cf vaccinated group as indicated by high percentages of triple cytokine (IFN-γ, IL-2, TNF-α) producing CD8⁺ T cells. Following challenge, animals vaccinated with PAN-Cf continued to produce significant levels of double (IFN-γ, TNF-α) and single cytokine (IFN-γ) secreting CD8⁺ T cells compared with animals vaccinated with an inactivated vaccine. A significant reduction in bacterial load was observed in multiple organs of animals vaccinated with PAN-Cf, which is a clear indication of protection. Overall, the use of polyanhydride nanovaccines resulted in development of protective and sustained immunity against Johne’s disease, an approach that could be applied to counter other intracellular pathogens.

Implications of Cattle Trade for the Spread and Control of Infectious Diseases in Slovenia

The objectives of this study were to gain insight into the structure of the cattle trade network in Slovenia and to evaluate the potential for infectious disease spread through movements. The study considered cattle movements between different types of premises that occurred between August 1, 2011 and July 31, 2016 with the exclusion of the movements to the end nodes (e.g., slaughterhouses). In the first part, we performed a static network analysis on monthly and yearly snapshots of the network. These time scales reflect our interest in slowly spreading pathogens; namely Mycobacterium avium subsp. paratuberculosis (MAP), which causes paratuberculosis, a worldwide economically important disease. The results showed consistency in the network measures over time; nevertheless, it was evident that year to year contacts between premises were changing. The importance of individual premises for the network connectedness was highly heterogeneous and the most influential premises in the network were collection centers, mountain pastures, and pastures. Compared to random node removal, targeted removal informed by ranking based on local network measures from previous years was substantially more effective in network disassociation. Inclusion of the latest movement data improved the results. In the second part, we simulated disease spread using a Susceptible-Infectious (SI) model on the temporal network. The SI model was based on the empirically estimated true prevalence of paratuberculosis in Slovenia and four scenarios for probabilities of transmission. Different probabilities were realized by the generation of new networks with the corresponding proportion of contacts which were randomly selected from the original network. These diluted networks served as substrates for simulation of MAP spread. The probability of transmission had a significant influence on the velocity of disease spread through the network. The peaks in daily incidence rates of infected herds were observed at the end of the grazing period. Our results suggest that network analysis may provide support in the optimization of paratuberculosis surveillance and intervention in Slovenia. The approach of simulating disease spread on a diluted network may also be used to model other transmission pathways between herds.

The Replication-Transmission Relativity Theory for Multiscale Modelling of Infectious Disease Systems

It is our contention that for multiscale modelling of infectious disease systems to evolve and expand in scope, it needs to be founded on a theory. Such a theory would improve our ability to describe infectious disease systems in terms of their scales and levels of organization, and their inter-relationships. In this article we present a relativistic theory for multiscale modelling of infectious disease systems, that can be considered as an extension of the relativity principle in physics, called the replication-transmission relativity theory. This replication-transmission relativity theory states that at any level of organization of an infectious disease system there is no privileged/absolute scale which would determine, disease dynamics, only interactions between the microscale and macroscale. Such a relativistic theory provides a scientific basis for a systems level description of infectious disease systems using multiscale modelling methods. The central idea of this relativistic theory is that at every level of organization of an infectious disease system, the reciprocal influence between the microscale and the macroscale establishes a pathogen replication-transmission multiscale cycle. We distinguish two kinds of reciprocal influence between the microscale and the macroscale based on systematic differences in their conditions of relevancy. Evidence for the validity of the replication-transmission relativity theory is presented using a multiscale model of hookworm infection that is developed at host level when the relationship between the microscale and the macroscale is described by one of the forms of reciprocal influence.

Application of Transcriptomics to Enhance Early Diagnostics of Mycobacterial Infections, with an Emphasis on Mycobacterium avium ssp. paratuberculosis

Mycobacteria cause a wide variety of disease in human and animals. Species that infect ruminants include M. bovis and M. avium ssp. paratuberculosis (MAP). MAP is the causative agent of Johne’s disease in ruminants, which is a chronic granulomatous enteric infection that leads to severe economic losses worldwide. Characteristic of MAP infection is the long, latent phase in which intermittent shedding can take place, while diagnostic tests are unable to reliably detect an infection in this stage. This leads to unnoticed dissemination within herds and the presence of many undetected, silent carriers, which makes the eradication of Johne’s disease difficult. To improve the control of MAP infection, research is aimed at improving early diagnosis. Transcriptomic approaches can be applied to characterize host-pathogen interactions during infection, and to develop novel biomarkers using transcriptional profiles. Studies have focused on the identification of specific RNAs that are expressed in different infection stages, which will assist in the development and clinical implementation of early diagnostic tests.

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.

Deciphering the virulence of Mycobacterium avium subsp. paratuberculosis isolates in animal macrophages using mathematical models

Understanding why pathogenic Mycobacterium avium subsp. paratuberculosis (Map) isolates cause disparate disease outcomes with differing magnitudes of severity is important in designing and implementing new control strategies. We applied a suite of mathematical models: i) general linear, ii) and neurofuzzy logic, to explain how the host of origin of several Map isolates, Map genotype, host, macrophage-based in vitro model and time post-infection contributed to the infection. A logistic growth ordinary differential equation (ODE) model was applied to estimate within macrophage growth rates for the different Map isolates. The models revealed different susceptibilities of bovine and ovine macrophages to Map infection and confirmed distinct virulence profiles for the isolates, judged by their ability to grow within macrophages. Ovine macrophages were able to internalize Map isolates more efficiently than bovine macrophages. While bovine macrophages were able to internalize Map isolates from cattle with more efficiency, ovine macrophages were more efficient in internalizing ovine isolates. Overall, Map isolates from goat and sheep grew minimally within macrophages or did not grow but were able to persist by maintaining its initial population. In contrast, the ability of the bovine isolates and the non-domesticated animal isolates to grow to higher CFU numbers within macrophages suggests that these isolates are more virulent than the sheep and goat isolates, or that these isolates are better adapted to infect domestic ruminants. Overall, our study confirms the different virulence levels for the Map isolates and susceptibility profiles of host macrophages, which is crucial in increasing our understanding of Map infection.

A data-driven individual-based model of infectious disease in livestock operation: A validation study for paratuberculosis

Chronic livestock diseases cause large financial loss and affect animal health and welfare. Controlling these diseases mostly requires precise information on both individual animal and population dynamics to inform the farmer’s decisions, but even successful control programmes do by no means assure elimination. Mathematical models provide opportunities to test different control and elimination options rather than implementing them in real herds, but these models require robust parameter estimation and validation. Fitting these models to data is a difficult task due to heterogeneities in livestock processes. In this paper, we develop an infectious disease modeling framework for a livestock disease (paratuberculosis) that is caused by Mycobacterium avium subsp. paratuberculosis (MAP). Infection with MAP leads to reduced milk production, pregnancy rates, and slaughter value and increased culling rates in cattle and causes significant economic losses to the dairy industry. These economic effects are particularly important motivations in the control and elimination of MAP. In this framework, an individual-based model (IBM) of a dairy herd was built and MAP infection dynamics was integrated. Once the model produced realistic dynamics of MAP infection, we implemented an evaluation method by fitting it to data from three dairy herds from the Northeast region of the US. The model fitting exercises used least-squares and parameter space searching methods to obtain the best-fitted values of selected parameters. The best set of parameters were used to model the effect of interventions. The results show that the presented model can complement real herd statistics where the intervention strategies suggest a reduction in MAP prevalence without elimination. Overall, this research not only provides a complete model for MAP infection dynamics in a dairy herd but also offers a method for estimating parameters by fitting IBM models.

A nested compartmental model to assess the efficacy of paratuberculosis control measures on U.S. dairy farms

Paratuberculosis, also known as Johne's disease (JD), is a chronic contagious disease, caused by Mycobacterium avium subsp. paratuberculosis (MAP). The disease is incurable, fatal and causes economic losses estimated to exceed 200 million dollars to the U.S. dairy industry annually. Several preventive and control measures have been recommended; however, only a few of these measures have been validated empirically. Using a nested compartmental (NC) modeling approach, the main objective of this research was to identify the best combination of control and preventive measures that minimizes the prevalence and incidence of JD and the risk of MAP occurrence in a dairy herd. The NC model employs both MAP transmission estimates and data on pen movement of cattle on a dairy to quantify the effectiveness of control and preventive measures. To obtain reasonable ranges of parameter values for between-pen movements, the NC model was fitted to the movement data of four typical California dairy farms. Using the estimated ranges of the movement parameters and those of JD from previous research, the basic reproduction number was calculated to measure the risk of MAP occurrence in each pen environment as well as the entire dairy. Although the interventions evaluated by the NC model were shown to reduce the infection, no single measure alone was capable of eradicating the infection. The numerical simulations suggest that a combination of test and cull with more frequent manure removal is the most effective method in reducing incidence, prevalence and the risk of MAP occurrence. Other control measures such as limiting calf-adult cow contacts, raising calves in a disease-free herd or colostrum management were less effective.

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.

Control measures to prevent the increase of paratuberculosis prevalence in dairy cattle herds: an individual-based modelling approach

Paratuberculosis, a gastrointestinal disease caused by Mycobacterium avium subsp. paratuberculosis (Map), can lead to severe economic losses in dairy cattle farms. Current measures are aimed at controlling prevalence in infected herds, but are not fully effective. Our objective was to determine the most effective control measures to prevent an increase in adult prevalence in infected herds. We developed a new individual-based model coupling population and infection dynamics. Animals are characterized by their age (6 groups) and health state (6 states). The model accounted for all transmission routes and two control measures used in the field, namely reduced calf exposure to adult faeces and test-and-cull. We defined three herd statuses (low, moderate, and high) based on realistic prevalence ranges observed in French dairy cattle herds. We showed that the most relevant control measures depend on prevalence. Calf management and test-and-cull both were required to maximize the probability of stabilizing herd status. A reduced calf exposure was confirmed to be the most influential measure, followed by test frequency and the proportion of infected animals that were detected and culled. Culling of detected high shedders could be delayed for up to 3 months without impacting prevalence. Management of low prevalence herds is a priority since the probability of status stabilization is high after implementing prioritized measures. On the contrary, an increase in prevalence was particularly difficult to prevent in moderate prevalence herds, and was only feasible in high prevalence herds if the level of control was high.

Can Immune Response Mechanisms Explain the Fecal Shedding Patterns of Cattle Infected with Mycobacterium avium Subspecies paratuberculosis?

Johne’s disease (JD) is a chronic disease in ruminants and is caused by infection with Mycobacterium avium subspecies paratuberculosis (MAP). At late stages of the disease, MAP bacilli are shed via feces excretion and in turn create the potential for oral-fecal transmission. The role of the host immune response in MAP bacteria shedding patterns at different stages of JD is still unclear. We employed mathematical modeling to predict if the variation in MAP shedding could be correlated to the immune response in infected animals. We used a novel inverse modeling approach that assumed biological interactions among the antigen-specific lymphocyte proliferation response (cell-mediated response), antibody/humoral immune responses, and MAP bacteria. The modeling framework was used to predict and test possible biological interactions between the measured variables and returns only the essential interactions that are relevant in explaining the observed cattle MAP experimental infection data. Through confronting the models with data, we predicted observed effects (enhancement or suppression) and extents of interactions among the three variables. This analysis enabled classification of the infected cattle into three different groups that correspond to the unique predicted immune responses that are essential to explain the data from cattle within these groups. Our analysis highlights the strong and weak points of the modeling approach, as well as the key immune mechanisms predicted to be expressed in all animals and those that were different between animals, hence giving insight into how animals exhibit different disease dynamics and bacteria shedding patterns.

Predicting the Role of IL-10 in the Regulation of the Adaptive Immune Responses in Mycobacterium avium Subsp. paratuberculosis Infections Using Mathematical Models

Mycobacterium avium subsp. paratuberculosis (MAP) is an intracellular bacterial pathogen that causes Johne’s disease (JD) in cattle and other animals. The hallmark of MAP infection in the early stages is a strong protective cell-mediated immune response (Th1-type), characterized by antigen-specific γ-interferon (IFN-γ). The Th1 response wanes with disease progression and is supplanted by a non-protective humoral immune response (Th2-type). Interleukin-10 (IL-10) is believed to play a critical role in the regulation of host immune responses to MAP infection and potentially orchestrate the reversal of Th1/Th2 immune dominance during disease progression. However, how its role correlates with MAP infection remains to be completely deciphered. We developed mathematical models to explain probable mechanisms for IL-10 involvement in MAP infection. We tested our models with IL-4, IL-10, IFN-γ, and MAP fecal shedding data collected from calves that were experimentally infected and followed over a period of 360 days in the study of Stabel and Robbe-Austerman (2011). Our models predicted that IL-10 can have different roles during MAP infection, (i) it can suppress the Th1 expression, (ii) can enhance Th2 (IL-4) expression, and (iii) can suppress the Th1 expression in synergy with IL-4. In these predicted roles, suppression of Th1 responses was correlated with increased number of MAP. We also predicted that Th1-mediated responses (IFN-γ) can lead to high expression of IL-10 and that infection burden regulates Th2 suppression by the Th1 response. Our models highlight areas where more experimental data is required to refine our model assumptions, and further test and investigate the role of IL-10 in MAP infection.

An immuno-epidemiological model for Johne's disease in cattle

To better understand the mechanisms involved in the dynamics of Johne’s disease in dairy cattle, this paper illustrates a novel way to link a within-host model for Mycobacterium avium ssp. paratuberculosis with an epidemiological model. The underlying variable in the within-host model is the time since infection. Two compartments, infected macrophages and T cells, of the within-host model feed into the epidemiological model through the direct transmission rate, disease-induced mortality rate, the vertical transmission rate, and the shedding of MAP into the environment. The epidemiological reproduction number depends on the within-host bacteria load in a complex way, exhibiting multiple peaks. A possible mechanism to account for the switch in shedding patterns of the bacteria in this disease is included in the within-host model, and its effect can be seen in the epidemiological reproduction model.