Visualization and application of disease diagnosis codes for population health management using porcine diseases as a model

Accurate and timely results of diagnostic investigations and laboratory testing guide clinical interventions for the continuous improvement of animal health and welfare. Infectious diseases can severely limit the health, welfare, and productivity of populations of animals. Livestock veterinarians submit thousands of samples daily to veterinary diagnostic laboratories (VDLs) for disease diagnosis, pathogen monitoring, and surveillance. Individual diagnostic laboratory reports are immediately useful; however, aggregated historical laboratory data are increasingly valued by clinicians and decision-makers to identify changes in the health status of various animal populations over time and geographical space. The value of this historical information is enhanced by visualization of trends of agent detection, disease diagnosis, or both, which helps focus time and resources on the most significant pathogens and fosters more effective communication between livestock producers, veterinarians, and VDL professionals. Advances in data visualization tools allow quick, efficient, and often real-time scanning and analysis of databases to inform, guide, and modify animal health intervention algorithms. Value is derived at the farm, production system, or regional level. Visualization tools allow client-specific analyses, benchmarking, formulation of research questions, and monitoring the effects of disease management and precision farming practices. We present here the approach taken to visualize trends of disease occurrence using porcine disease diagnostic code data for the period 2010 to 2019. Our semi-automatic standardized creation of a visualization platform allowed the transformation of diagnostic report data into aggregated information to visualize and monitor disease diagnosis.     

Board-invited review: Using behavior to predict and identify ill health in animals

We review recent research in one of the oldest and most important applications of ethology: evaluating animal health. Traditionally, such evaluations have been based on subjective assessments of debilitative signs; animals are judged ill when they appear depressed or off feed. Such assessments are prone to error but can be dramatically improved with training using well-defined clinical criteria. The availability of new technology to automatically record behaviors allows for increased use of objective measures; automated measures of feeding behavior and intake are increasingly available in commercial agriculture, and recent work has shown these to be valuable indicators of illness. Research has also identified behaviors indicative of risk of disease or injury. For example, the time spent standing on wet, concrete surfaces can be used to predict susceptibility to hoof injuries in dairy cattle, and time spent nuzzling the udder of the sow can predict the risk of crushing in piglets. One conceptual advance has been to view decreased exploration, feeding, social, sexual, and other behaviors as a coordinated response that helps afflicted individuals recover from illness. We argue that the sickness behaviors most likely to decline are those that provide longer-term fitness benefits (such as play), as animals divert resources to those functions of critical short-term value such as maintaining body temperature. We urge future research assessing the strength of motivation to express sickness behaviors, allowing for quantitative estimates of how sick an animal feels. Finally, we call for new theoretical and empirical work on behaviors that may act to signal health status, including behaviors that have evolved as honest (i.e., reliable) signals of condition for offspring-parent, inter- and intra-sexual, and predator-prey communication.     

Assessing human risk of illness with West Nile virus mosquito surveillance data to improve public health preparedness

Surveillance for West Nile virus (WNV) and other mosquito‐borne pathogens involves costly and time‐consuming collection and testing of mosquito samples. One difficulty faced by public health personnel is how to interpret mosquito data relative to human risk, thus leading to a failure to fully exploit the information from mosquito testing. The objective of our study was to use the information gained from historic West Nile virus mosquito testing to determine human risk relative to mosquito infection and to assess the usefulness of our mosquito infection forecasting models to give advance warning. We compared weekly mosquito infection rates from 2004 to 2013 to WNV case numbers in Illinois. We then developed a weather‐based forecasting model to estimate the WNV mosquito infection rate one to 3 weeks ahead of mosquito testing both statewide and for nine regions of Illinois. We further evaluated human illness risk relative to both the measured and the model‐estimated infection rates to provide guidelines for public health messages. We determined that across 10 years, over half of human WNV cases occurred following the 29 (of 210) weeks with the highest mosquito infection rates. The values forecasted by the models can identify those time periods, but model results and data availability varied by region with much stronger results obtained from regions with more mosquito data. The differences among the regions may be related to the amount of surveillance or may be due to diverse landscape characteristics across Illinois. We set the stage for better use of all surveillance options available for WNV and described an approach to modelling that can be expanded to other mosquito‐borne illnesses.     

Assessing risks in relation to international trade with food and animals: a review of methods currently applied

Since approximately 10 years, risk assessments in the context of international trade with animals and food are being conducted. International standards provide guidelines for such assessments. However, the methods to be applied are only very broadly defined. A review of published or otherwise accessible examples demonstrated that most assessments in this field are qualitative in nature. When quantitative risk assessments are conducted, simulation modeling is often used. Further methodological development is required regarding the consideration of uncertainty, the use of expert knowledge and standardization of qualitative risk estimates. In order to maintain quality assurance in risk assessments, a wider use of peer-review is desirable, e.g. through publication of results in scientific journals.     

The application of risk analysis in aquatic animal health management

Risk analysis has only been regularly used in the management of aquatic animal health in recent years. The Agreement on the Application of Sanitary and Phytosanitary measures (SPS) stimulated the application of risk analysis to investigate disease risks associated with international trade (import risk analysis-IRA). A majority (9 of 17) of the risk analyses reviewed were IRA. The other major focus has been the parasite of Atlantic salmon--Gyrodactylus salaris. Six studies investigated the spread of this parasite, between countries, rivers and from farmed to wild stocks, and clearly demonstrated that risk analysis can support aquatic animal health policy development, from international trade and biosecurity to disease interaction between wild and farmed stocks. Other applications of risk analysis included the spread of vertically transmitted pathogens and disease emergence in aquaculture. The Covello-Merkhofer, risk analysis model was most commonly used and appears to be a flexible tool not only for IRA but also the investigation of disease spread in other contexts. The limitations of the identified risk assessments were discussed. A majority were qualitative, partly due to the lack of data for quantitative analysis, and this, it can be argued, constrained their usefulness for trade purposes (i.e. setting appropriate sanitary measures); in other instances, a qualitative result was found to be adequate for decision making. A lack of information about the disease hazards of the large number of fish species traded is likely to constrain quantitative analysis for a number of years. The consequence assessment element of a risk analysis was most likely to be omitted, or limited in scope and depth, rarely extending beyond examining the evidence of susceptibility of farmed and wild species to the identified hazard. The reasons for this are discussed and recommendations made to develop guidelines for a consistent, systematic and multi-disciplinary approach to consequence assessment. Risk analysis has improved decision making in aquatic animal health management by providing a transparent method for using the available scientific information. The lack of data is the main constraint to the application of risk analysis in aquatic animal health. The identification of critical parameters is an important output from risk analysis models which should be used to prioritise research.     

Animal health pharmaceutical industry

The animal health pharmaceutical industry has proactively reported on the volumes of member company antimicrobial active ingredients sold in the U.S. At the individual company level, reporting of finished product distribution data to the FDA is a regulatory requirement, with applications to surveillance and pharmacovigilance. An accounting of product manufactured is done for purposes of good business practices, as well as marketing analyses. Additional applications of antimicrobial usage data might include use in risk assessments, such as for the FDA's Center for Veterinary Medicine Guidance for Industry #152 for the evaluation of the microbiological safety of antimicrobials intended for use in food animals. Compilation of national usage data will be a complex undertaking, hindered by issues such as confidentiality, auditing, field use practice variations, population dynamics (e.g. disease incidence, market conditions for poultry and livestock production), and generic usage. The amounts or volumes in pounds should be considered relative to the large number of animals under husbandry in the United States. Large volumes might seem impressive unless put into proper context. Until such time as a clearly defined application of national usage data is agreed, it is recommended that local usage programs will provide more useful information to perpetuate prudent antimicrobial use in animals.     

Should they stay,or should they go? Relative future risk of bovine tuberculosis for interferon-gamma test-positive cattle left on farms

Bovine tuberculosis (bTB), caused by Mycobacterium bovis, is a serious infectious disease that remains an ongoing concern for cattle farming worldwide. Tuberculin skin-tests are often used to identify infected animals (reactors) during test-and-cull programs, however, due to relatively poor sensitivity, additional tests can be implemented in parallel. For example, in Northern Ireland interferon-gamma (IFN-g) testing is used in high-risk herds. However, skin-test negative animals which are positive to the IFN-g test are not required by law to be slaughtered – therefore the final choice for these animals’ fate is left with the owner. During this study we investigated whether these animals represented a greater risk of becoming a skin reactor, relative to IFN-g test negative animals from the same herds. Our study population included 1107 IFN-g positive animals from 239 herds. A Cox-proportional hazard model indicated that animals which tested IFN-g positive were 2.31 times (95% CI: 1.92-2.79; P < 0.001) more likely to become a reactor compared with IFN-g negative animals. Animals from dairy herds, and from herds in the south-east, were of higher risk than animals from beef herds and other regions, respectively. Our findings suggest that IFN-g positive animals represent a higher risk of failing a skin-test in the future, indicating the value of IFN-g testing for identifying early-stage infected animals. These IFN-g positive animals are not under any disease restriction, and may move freely (trade), which may put recipient herds at increased risk. Our findings provide important evidence for stakeholders engaged in bTB eradication programs.

Electronic supplementary material

The online version of this article (doi:10.1186/s13567-015-0242-8) contains supplementary material, which is available to authorized users.     

Mycotoxins. Contemporary issues of food animal health and productivity.

Modern agriculture and production animal medicine require attention to high-quality feeds that are free from mycotoxin contamination that can cause economically important decreases in productivity. Maintaining current information about effects of mycotoxins on feed intake and growth, reproductive efficiency, and possible immunosuppression aid in effective consultation with livestock producers. Investigation and determination of potential production losses related to mycotoxins should use historical, clinical, laboratory, and experimental information to objectively evaluate whether mycotoxin contamination is clinically relevant. The practicing veterinarian or veterinary consultant can provide valuable clinical and interpretive assistance to producers who may have a real or potential mycotoxin contamination. Thorough diagnostic evaluation of animals, appropriate testing of feeds and forages, and rational consideration of differential diagnoses help to put mycotoxins in the proper perspective as a production-related management problem.     

Animal models of listeriosis: a comparative review of the current state of the art and lessons learned

ABSTRACT: Listeriosis is a leading cause of hospitalization and death due to foodborne illness in the industrialized world. Animal models have played fundamental roles in elucidating the pathophysiology and immunology of listeriosis, and will almost certainly continue to be integral components of the research on listeriosis. Data derived from animal studies helped for example characterize the importance of cell-mediated immunity in controlling infection, allowed evaluation of chemotherapeutic treatments for listeriosis, and contributed to quantitative assessments of the public health risk associated with L. monocytogenes contaminated food commodities. Nonetheless, a number of pivotal questions remain unresolved, including dose-response relationships, which represent essential components of risk assessments. Newly emerging data about species-specific differences have recently raised concern about the validity of most traditional animal models of listeriosis. However, considerable uncertainty about the best choice of animal model remains. Here we review the available data on traditional and potential new animal models to summarize currently recognized strengths and limitations of each model. This knowledge is instrumental for devising future studies and for interpreting current data. We deliberately chose a historical, comparative and cross-disciplinary approach, striving to reveal clues that may help predict the ultimate value of each animal model in spite of incomplete data.     

Preliminary estimates of the direct costs associated with endemic diseases of livestock in Great Britain.

Many 'economic' studies of livestock diseases in Great Britain have been carried out over time. Most studies have considered just one or two diseases and used a different methodology and valuation base from other studies, hampering any comparative assessment of the economic impact of diseases. A standardized methodology was applied to the estimation of the direct costs to livestock production of some 30 endemic diseases/conditions of farm animals in Great Britain. This involved identification of the livestock populations at risk, estimation of the annual incidence of each disease in these populations, identification of the range and incidence of physical effects of each disease on production, valuation of the physical effects of each disease and estimation of the financial value of output losses/resource wastage due to a disease and the costs of specific treatment and prevention measures. The wider economic impacts of disease (such as the implications for human health, animal welfare and markets) were not included in the assessments. Using this standardized methodology with common financial values, a simple spreadsheet model was constructed for each disease. Given the paucity of appropriate disease data for economic assessment, 'low' and 'high' values were used to reflect uncertainties surrounding key disease parameters. Preliminary estimates of the value of disease output losses/resource wastage, treatment and prevention costs are presented for each disease. Despite the limitations of the spreadsheet models and of the estimates derived from them, we conclude that the models represent a useful start in developing a system for the comparative economic assessment of livestock diseases in Great Britain.     

Johne's disease in Canada Part I: clinical symptoms, pathophysiology, diagnosis, and prevalence in dairy herds

Recent international developments in the area of infectious disease control and nontariff trade barriers, along with possible zoonotic concerns, have provoked a revival of interest in Johne's disease in Canada and elsewhere. The bacterium causing Johne's disease, Mycobacterium avium subspecies paratuberculosis, is distributed worldwide and causes chronic granulomatous enteritis, also known as paratuberculosis, in domestic and exotic ruminants, including cattle. The subclinical form of this disease results in progressive weight loss, reduced milk production, lower slaughter value, and premature culling, with possible impacts on fertility and udder health. Eventually, infection can lead to the clinical form that manifests as chronic diarrhea, emaciation, debilitation, and eventual death. Currently, available tests to detect infected animals produce many false-negative results and some false-positives, particularly in subclinically infected animals, thus making their interpretation and utilization challenging in control programs. The objective of this 2-part review is to critically review the literature about Johne's disease in dairy cattle for bovine practitioners in Canada. Part I covers the clinical stages, pathophysiology, diagnosis, and prevalence of infection in Canada, while Part II discusses impacts, risk factors, and control programs relevant to Canadian dairy farms. By reviewing the scientific literature about Johne's disease, control of the disease could be pursued through informed implementation of rational biosecurity efforts and the strategic use of testing and culling.     

The price of the precautionary principle: Cost-effectiveness of BSE intervention strategies in the Netherlands

Since 1996, bovine spongiform encephalopathy (BSE) in cattle has been linked to a new variant of Creutzfeldt-Jakob disease (vCJD), a fatal brain disease in man. This paper assessed the cost-effectiveness of BSE control strategies instituted by the European Commission. In a Monte Carlo simulation model, a non-intervention baseline scenario was compared to three intervention strategies: removal of specified risk materials from slaughter animals, post-mortem testing for BSE and the culling of feed and age cohorts of BSE cases. The food risk in the baseline scenario ranged from 16.98 lost life years in 2002 to 2.69 lost life years in 2005. Removing specified risk materials removal practices, post-mortem testing and post-mortem testing plus cohort culling reduced this risk with 93%, 82.7% and 83.1%. The estimated cost-effectiveness of all BSE measures in the Netherlands ranged from 4.3 million euros per life year saved in 2002 to 17.7 million euros in 2005. It was discussed that the cost-effectiveness of BSE control strategies will further deviate from regular health economics thresholds as BSE prevalence and incidence declines.     

An object-oriented Bayesian network modeling the causes of leg disorders in finisher herds

The implementation of an effective control strategy against disease in a finisher herd requires knowledge regarding the disease level in the herd. A Bayesian network was constructed that can estimate risk indexes for three cause-categories of leg disorders in a finisher herd. The cause-categories of leg disorders were divided into infectious causes (arthritis caused by infectious pathogens), physical causes (e.g. fracture and claw lesions), and inherited causes (osteochondrosis). Information about the herd (e.g. the herd size, floor type and number of suppliers) and information about individual pigs (e.g. results from diagnostic tests) were used to estimate the most likely cause of leg disorders at herd level. As information to the model originated from two different levels, we used an object-oriented structure in order to ease the specification of the Bayesian network. Hence, a Herd class and a Pig class comprised the basic components of the object-oriented structure. The causal structure of the model was based on evidence from published literature. The conditional probabilities used in the model were elicited from experts within the field and from the published literature. To illustrate the behaviour of the model, we investigated the value of different levels of evidence in two fictitious herds with different herd characteristics related to the risk of leg disorders (e.g. purchase policy, production type and the stocking density in pens). The model enabled us to demonstrate the value of performing systematic collection of additional information (i.e. clinical, pathological and bacteriological examination) when identifying causes of leg disorders at herd level.     

Problems associated with the serological diagnosis of Leptospira interrogans serovar hardjo infection in bovine populations

Data combining sequential bacteriology and serology from a longitudinal study of a dairy herd were used to demonstrate the limitations of serology as a diagnostic method in cross-sectional sampling of bovine populations. Whole-herd point serological prevalences showed considerable variation over a two-year sampling period (38.8 to 76.2 per cent), and this was mainly due to varying age-specific prevalence. Owing to the rapid decline in titres and the varying persistence of infection, point serological prevalences failed to approximate to cumulative infection rates (either past or present) at different times of the year. A higher estimate of the number of susceptible animals in the herd than is the case results in inaccurate information on true incidence rates and can confuse assessments of the susceptibility of different age groups, especially if only small numbers are sampled. A sampling exercise demonstrated that a 10-cow sample usually provided little useful information other than establishing the presence or absence of hardjo in the herd. Increasing the sample size markedly improved epidemiological information, investigations of clinical disease, assessments of vaccination needs and public health tracebacks. Preferably 10 sera from each of the yearling, first calver, second calver and older age groups should be tested. Serology was an inadequate indicator of infection in individual animals. Group geometric mean titres taken from a mean serological response curve were shown to have limited application in the interpretation of field data, unless infection had occurred in the previous two months.     

Antimicrobial susceptibility testing of bacteria isolated from animals: methods for in-vitro susceptibility testing and their suitability with regard to the generation of the most useful data for therapeutic applications

In-vitro susceptibility testing provides valuable informations for choosing the most suitable antimicrobial agent for the control of bacterial infections in animals. Different diffusion and dilution methods, as conducted according to various approved performance standards, can be used to determine the in-vitro susceptibility of bacterial pathogens. In the present article, problems are discussed which arise from the use of different methods and the difficulty to interpret such results. While most approved performance standards were designed for testing of bacteria from human sources, the NCCLS document M31-A2 exclusively focusses on susceptibility testing of bacteria isolated from animals and--in contrast to all other standards--includes veterinary specific breakpoints for a number of antimicrobial agents used in veterinary medicine. Therefore, performance of in-vitro susceptibility testing of veterinary pathogens should follow the recommendations given in the NCCLS document M31-A2. The microdilution method is recommended as the method of choice for susceptibility testing. The result of a microdilution test is given as the minimum inhibitory concentration (MIC). This value provides a quantitative result which precisely indicates the degree of susceptibility of the tested bacterial strain and in return gives the veterinarian a clear guidance whether therapeutic intervention with the antibiotic in question will be successful.     

Regional risk of exporting cattle seropositive for bluetongue virus from the United States

OBJECTIVE: To create a stochastic model to quantify the risk that shipments of cattle from regions within the United States would contain animals seropositive for bluetongue virus and to determine shipment-level accuracy of serologic testing by use of a competitive ELISA (c-ELISA). SAMPLE POPULATION: 19,216 shipments containing 528,918 cattle and calves. PROCEDURE: Data were obtained on number of animals and state of origin of cattle in export shipments originating within the United States between January 1994 and March 2002. Probability distributions for size of export shipments were determined for all states within the United States, and distributions for agar gel immunodiffusion and c-ELISA accuracy (sensitivity and specificity) were determined from expert opinion and review of the literature. The model simulated selection of a shipment and then determined the probability that a threshold number or percentage of cattle within that shipment would have a positive c-ELISA result. Shipment-level sensitivity, specificity, positive-predictive value, and negative-predictive value were calculated. RESULTS: Substantial differences were evident in the regional probability of a shipment being declared positive, with shipments from northeastern states having the lowest probability and shipments from southwestern states having the highest probability. The c-ELISA had variable predictive values at the shipment level, depending on the threshold used and the prevalence of antibody-positive cattle within the region. CONCLUSIONS AND CLINICAL RELEVANCE: Results from this study will aid importers in making scientifically based decisions regarding risk of importing antibody-positive cattle.     

Stakeholder position paper: the need for antimicrobial use data for risk assessment

Risk assessment seeks to estimate the probability and impact of human health effects due to antimicrobial resistance arising from antimicrobial use in animals. Potential ecological pathways for the flow of antimicrobial resistant bacteria and resistance determinants through the food supply and environment are diverse and complicated and this has been a logistical barrier to direct epidemiological measure of risk. Consequently, a number of indirect approaches to assessment have been developed. This paper provides some examples of risk assessments that have been conducted with and without antimicrobial use data, and identifies possible benefits and applications of quantitative antimicrobial use data for risk assessment.     

Improving the assessment of the economic impact of parasitic diseases and of their control in production animals.

This paper reviews the ways in which the economic impact of parasitic diseases of production animals have been evaluated. It then discusses the shortfalls of such studies, as well as the opportunities for improving the quality of economic impact assessments and their value to decision makers in the future. The paper first identifies the impacts that are specific to parasitic diseases. It then goes on to review the abundant literature on estimating the total costs of diseases. The authors argue that this approach severely limits the opportunity for economic assessments to aid decisions in disease control and research. The paper then reviews the literature on studies of avoidable costs, before discussing ways in which economic impact assessments can be enhanced. These issues include greater emphasis on incorporating the lost productivity potential caused by parasitic diseases, greater emphasis on valuing actual rather than intended control measures, and greater emphasis on quantifying the productivity effects at the societal level, particularly in the developing world.     

Emerging technologies for identifying superior dairy cows in New Zealand

The performance of animals is determined by the interaction of their genes with environmental circumstances. Accordingly, animals exhibiting superior performance are not necessarily the animals with the best genes nor are they the best choice of parents. Statistical analyses of production records for repeated traits, e.g. lactation yields and reproductive performance, show that part of the variation in performance among animals in the same herd and year is due to genetic differences, and the remainder is due to so-called residual or environmental factors that are not passed on to offspring. These within-herd environmental factors can be partitioned into a component that affects performance throughout an animal's lifetime, and a part that is unique to each observation. The process of animal evaluation from pedigree and performance records partitions the superiority of each cow into these three components. Reliable assessment of the genetic merit of bulls has required progeny testing, and for cows has required observation of their own individual performance. Selection on the genetic or breeding value component has systematically improved animal performance over recent decades, but has been limited by the age at which assessments of genetic merit are available. Emerging molecular technologies can read DNA sequences or measure RNA expression and have allowed the identification of a number of chromosome regions, and a few specific genes in those regions, that influence economic performance. This information allows better characterisation of the relationships between animals and more accurate predictions of genetic merit in bulls without progeny information and in cows that have yet to produce their own performance record. At some stage, enough genes responsible for variation in performance will be identified to allow faster genetic progress through selection of animals at young ages and therefore more rapid turnover of the generations. Mechanisms that modify gene expression have been identified and these may ultimately allow animals to be selected at an early age for lifetime productivity, accounting for processes that modify gene expression and lead to differences in performance that are not reflected by DNA sequence information. This review describes the status of these emerging technologies and their likely role in the improvement of dairy cattle.     

草坪草病害风险性评估体系的初步建立及应用

为探索建立统一的草坪草病害风险性评价尺度，本研究引入有害生物风险分析（Pest Risk Analysis）理论。基于有害生物风险分析的规定程序，结合草坪绿地生态系统特点及模糊数学理论，利用德尔菲法及层次分析法，探讨了草坪绿地病害风险分析体系的建立、评价指标和评价值的计算方法。初步建立了三层次17个评价指标的综合评价模型R=5P1×P2×P3×P4×P5，并运用此模型评价了草坪草5种主要病害的风险性危害值。结果表明，草坪草褐斑病(Rhizoctonia solani)、腐霉病(Phythium ultimum)和镰刀菌枯萎病(Fusarium spp.)3种病害的风险性危害值在0.6～0.8，风险级别为高风险；草坪草锈病(Puccinia spp.)和德氏霉叶枯病(Drechslera spp.)2种病害的风险性危害值在0.4～0.6，风险级别为中等风险。在实际工作中，应根据不同的病害风险等级制定相对应的风险管理策略及具体办法。