A Critique of Methods of Sampling and Reporting Pathogens in Populations of Fish

Abstract

We used maximum likelihood methods to estimate an observed or apparent prevalence for a pathogen in a pooled sample of fish and here provide the program code for such calculations using commonly available statistical software. To illustrate the characteristics and variability of prevalence estimates from pooled samples, we explored the relationships among pathogen prevalence, sample size, and method of pooling samples. We calculated the average width of confidence intervals and the mean square error of the prevalence estimator for samples from populations with pathogen prevalence ranging from 1% to 90% using several pooling strategies for samples of 30 and 60 fish. As an illustration, we calculated the confidence interval and apparent prevalence of Myxobolus cerebralis in samples of fish from Utah screened with pooled sampling strategies. When all pools were positive, the apparent prevalence was 100%, but the bounds of the confidence interval ranged from 8% to 100%. Interpretations of data sets that are based only on the results for positive pools may be misleading, as the percentage of pools that is positive when any single pool scores negative is higher than the maximum likelihood estimate of apparent prevalence. The confidence intervals bounding estimates were generally smaller when larger numbers of groups were used and samples had few fish per pool. In populations with higher prevalence, the use of pooled samples significantly enlarges the confidence interval of estimates.     

"TAGS", a program for the evaluation of test accuracy in the absence of a gold standard

When a perfect reference test (i.e. "gold standard") is not available, it is possible to obtain estimates of test sensitivity and specificity using "latent-class" methods. However, there are few widely available software programs that allow implementation of these procedures. We describe the development of a program (implemented in R and S-Plus software) for this purpose that yields maximum-likelihood estimates of sensitivity, specificity and prevalence. We also have implemented an HTML form, which submits data to a web-based interface to R. The programs can incorporate data obtained from several populations, results of multiple tests, and can account for data obtained from a reference population in which the true status (infected or non-infected) of each individual is known exactly. Two estimation methods are used: a Newton-Raphson procedure and an expectation-maximisation (EM) procedure. The estimation methods assume test independence conditional on the infection status of the individuals and constant test accuracy in each population. A goodness-of-fit statistic and the residuals of pairwise correlation coefficients are calculated to check the validity of these assumptions. Two examples are used to illustrate application and limitations of the programs. The programs are available at www.afssa.fr/interne/tags.htm (Europe) or www.epi.ucdavis.edu/diagnostictests/ (USA).     

Modelling cumulative egg production in laying hens and parent stocks of broiler chickens using classical growth functions

ABSTRACT

1. The objective of the present study is to introduce fresh insight into modelling of egg production by applying classical growth functions to egg production records reported by Aviagen Management Guide to laying hens and the parent stock of broiler chickens.

2. The functions (monomolecular, logistic, Gompertz, Richards and Morgan) were fitted using nonlinear regression procedures of SAS software, and their performance was assessed using goodness-of-fit statistics (coefficient of determination, residual mean squares, Akaike information criterion and Bayesian information criterion).

3. Overall, except for the logistic and Gompertz, the growth functions evaluated gave an acceptable fit to the cumulative egg production curves, with the Morgan equation ranking first followed by the Richards equation. The Morgan and Richards equations provided satisfactory predictions of weekly egg yield at different egg production stages, from early to late production, whereas the least accurate estimates were obtained with the logistic equation.

4. In conclusion, classical growth functions proved feasible alternatives to fit cumulative egg production curves of laying hens and parent stock of broiler chickens, resulting in suitable statistical performance and accurate estimates of production.     

Analyzing BSE surveillance in low prevalence countries

If the prevalence of bovine spongiform encephalopathy (BSE) varies among cohorts within a population, stratified analysis of BSE surveillance data may allow identification of differences in BSE exposure that are important with respect to the design and evaluation of disease prevention and control measures. In low BSE prevalence populations, however, surveillance at levels that meet or exceed international guidelines may provide insufficient statistical power to distinguish prevalence levels among cohorts. Furthermore, overstratification to account for hypothetical variability in the population may inflate uncertainty in BSE risk estimates.     

Assessing Relationships Between Genetic Evaluations Using Robust Regression with an Application to Holsteins in Uruguay

Globalization of dairy cattle breeding has created a need for international sire proofs. Some early methods for converting proofs from one population to another are based on simple linear regression. An alternative robust regression method based on the t-distribution is presented, and maximum likelihood and Bayesian techniques for analysis are described, including the situation in which some proofs are missing. Procedures were used to investigate the relationship between Holstein sire proofs obtained by two Uruguayan genetic evaluation programs. The results suggest that conversion equations developed from data including only sires having proofs in both populations can lead to distorted results, relative to estimates obtained using techniques for incomplete data. There was evidence of non-normality of regression residuals, which constitutes an additional source of bias. A robust estimator may not solve all problems, but can provide simple conversion equations that are less sensitive to outlying proofs and to departures from assumptions.     

Transmission parameters of Mycobacterium avium subspecies paratuberculosis infections in a dairy herd going through a control program

A Johne's disease control program, including stringent management practices and a test-and-cull program (whole-herd fecal-samples taken twice a year), was implemented on a medium-sized Pennsylvania dairy farm that was suffering losses from clinical Johne's disease. The data that emerged from the control program, combined with birthdates, culling dates, lactation information and pedigrees, yielded an extensive longitudinal dataset. The dataset was processed through SAS 9.1 for statistical analysis; herd-level disease dynamics and dam-to-daughter transmission parameters were calculated. After the implementation of the program in 1984, prevalence dropped dramatically from 60% to less than 20% in 1989. After an apparent prevalence peak (25%) in 1991 due to improved test sensitivity, prevalence maintained a plateau of 10% from 1996 to 2000. After the implementation of the program, 9.5% of the offspring from test-negative dams and 26.8% of the offspring from known-infected dams became infected with Mycobacterium avium subspecies paratuberculosis (Map) (χ² = 14.7; p = 0.0001). Calves born shortly following the calving of an infected dam and calves growing up with a future high shedder were more likely to be infected compared to calves without this risk profile. It was concluded that, after the implementation of the control program, the most important causes of infections of susceptible calves were their own dams or infected animals which had calved recently.     

The importance of localized culling in stabilizing chronic wasting disease prevalence in white-tailed deer populations

Strategies to contain the spread of disease often are developed with incomplete knowledge of the possible outcomes but are intended to minimize the risks associated with delaying control. Culling of game species by government agencies is one approach to control disease in wild populations but is unpopular with hunters and wildlife enthusiasts, politically unpalatable, and erodes public support for agencies responsible for wildlife management. We addressed the functional differences between hunting and government culling programs for managing chronic wasting disease (CWD) in white-tailed deer by comparing prevalence over a 10-year period in Illinois and Wisconsin. When both Illinois and Wisconsin were actively culling from 2003 – 2007, there were no statistical differences between state CWD prevalence estimates. Wisconsin government culling concluded in 2007 and average prevalence over the next five years was 3.09 ± 1.13% with an average annual increase of 0.63%. During that same time period, Illinois continued government culling and there was no change in prevalence throughout Illinois. Despite its unpopularity among hunters, localized culling is a disease management strategy that can maintain low disease prevalence while minimizing impacts on recreational deer harvest.     

Technical note: Use of marker-based relationships with multiple-trait derivative-free restricted maximal likelihood

The widespread use of the set of multiple-trait derivative-free REML programs for prediction of breeding values and estimation of variance components has led to significant improvement in traits of economic importance. The initial version of this software package, however, was generally limited to pedigree-based relationships. With continued advances in genomic research and the increased availability of genotyping, relationships based on molecular markers are obtainable and desirable. The addition of a new program to the set of multiple-trait derivative-free REML programs is described that allows users the flexibility to calculate relationships using standard pedigree files or an arbitrary relationship matrix based on genetic marker information. The strategy behind this modification and its design is described. An application is illustrated in a QTL association study for canine hip dysplasia.     

Frequentist and Bayesian approaches to prevalence estimation using examples from Johne's disease

Although frequentist approaches to prevalence estimation are simple to apply, there are circumstances where it is difficult to satisfy assumptions of asymptotic normality and nonsensical point estimates (greater than 1 or less than 0) may result. This is particularly true when sample sizes are small, test prevalences are low and imperfect sensitivity and specificity of diagnostic tests need to be incorporated into calculations of true prevalence. Bayesian approaches offer several advantages including direct computation of range-respecting interval estimates (e.g. intervals between 0 and 1 for prevalence) without the requirement of transformations or large-sample approximations, direct probabilistic interpretation, and the flexibility to model in a straightforward manner the probability of zero prevalence. In this review, we present frequentist and Bayesian methods for animal- and herd-level true prevalence estimation based on individual and pooled samples. We provide statistical methods for detecting differences between population prevalence and frequentist methods for sample size and power calculations. All examples are motivated using Mycobacterium avium subspecies paratuberculosis infection and we provide WinBUGS code for all examples of Bayesian estimation.     

Development of Multispecies,Long-Term Monitoring Programs for Resource Management

There is growing interest among resource managers in implementing long-term wildlife monitoring. The process to develop such a program may seem daunting, however, because it requires determining the species, metrics, sampling methods, experimental design, and level of effort necessary to achieve the desired power for detecting meaningful changes. Failure to give these decisions proper attention often leads to suboptimal information for decisions and planning objectives. Our primary objectives were to develop alternative scenarios for a monitoring program, including power estimates and sampling effort required to detect population changes for small mammals on rangelands in southern Texas. Our secondary objective was to present a framework for developing customized monitoring programs for tracking wildlife populations over time. We trapped small mammals using ~ 28 000 trap nights each year from 2014 to 2016 resulting in 13 183 captures of nine species. We estimated abundances and occupancy in each year for each species and conducted power analyses using simulations. We used these results to develop four multispecies monitoring scenarios: two with distinctly different levels of effort with abundance as the focal metric and two for monitoring occupancy. The most effort-intensive scenario required trapping 40 grids for 6 consecutive nights each yr. With this effort, we predicted it would be possible to detect annual changes in abundance of ≤ 10% after 10 yr for four species and net declines in occupancy of ≤ 50% after 10 yr for five species with a power of 0.90. The least effort-intensive scenario required trapping 30 transects for 4 consecutive nights each yr. We predicted this effort would allow for the detection of annual changes in occupancy rates between 35% and 55% after 10 yr for five species. Our study is an example for land managers, providing general guidelines for developing rigorous, long-term monitoring programs specific to their objectives.     

PCR-based detection of Toxoplasma gondii from cattle in southern Iran

ObjectiveToxoplasma gondii is a protozoan parasite that is widely prevalent in most warm-blooded vertebrates. Humans mainly become infected by eating raw or undercooked meat. This study was designed to investigate the infection of cattle with T. gondii in Jahrom, southern Iran.MethodsTissue samples consisting of heart, diaphragm, and tongue were collected from 125 slaughtered cattle. DNA samples were extracted from the homogenized tissues. T. gondii was detected and genotyped using nested-polymerase chain reaction (Nested-PCR) and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) based on GRA6 and SAG2 (3', 5' terminal regions) genes, respectively.ResultsThe prevalence of T. gondii DNA was 56% in cattle. The most infected tissue was the diaphragm (54.4%) followed by the heart (48.8%) and tongue (43.2%). Type II was the most prevalent genotype (70%) among T. gondii isolates.ConclusionIn this study, the high prevalence of T. gondii infection in cattle meat indicates the important role of cattle in the transmission of infection to humans. Therefore, incorporating the correct method of consuming meat in health education programs is crucial to prevent human infection.     

Impact of imperfect Mycobacterium avium subsp. paratuberculosis vaccines in dairy herds: A mathematical modeling approach

The objective of this study was to investigate the potential impacts of imperfect Mycobacterium avium subsp. paratuberculosis (MAP) vaccines on the dynamics of MAP infection in US dairy herds using a mathematical modeling approach. Vaccine-based control programs have been implemented to reduce the prevalence of MAP infection in some dairy herds; however, MAP vaccines are imperfect. Vaccines can provide partial protection for susceptible calves, reduce the infectiousness of animals shedding MAP, lengthen the latent period of infected animals, slow the progression from low shedding to high shedding in infectious animals, and reduce clinical disease. To quantitatively study the impacts of imperfect MAP vaccines, we developed a deterministic multi-group vaccination model and performed global sensitivity analyses. Our results explain why MAP vaccination might have a beneficial, negligible, or detrimental effect in the reduction of prevalence and show that vaccines that are beneficial to individual animals may not be useful for a herd-level control plan. The study suggests that high efficacy vaccines that are aimed at reducing the susceptibility of the host are the most effective in controlling MAP transmission. This work indicates that MAP vaccination should be integrated into a comprehensive control program that includes test-and-cull intervention and improved calf rearing management.     

Echocardiographic and electrocardiographic effects of atenolol versus sotalol in dogs with severe subaortic stenosis

BackgroundSubaortic stenosis (SAS) is a commonly diagnosed canine congenital cardiac defect, with severe forms of carrying a poor long-term prognosis. To date, an effective treatment strategy has not been developed in veterinary medicine. This study sought to determine if sotalol, a class III antiarrhythmic, may have salient echocardiographic and antiarrhythmic benefits for medical management for dogs affected with severe SAS.MethodsTen dogs diagnosed with severe SAS were enrolled in this prospective, double-blinded, crossover study. Dogs underwent physical exam, non-invasive blood pressure measurement, electrocardiography, echocardiography, and 24-h Holter monitoring. Diagnostics were repeated 12–16 days following randomization to oral atenolol (0.5–1 mg/kg) or sotalol (1–2 mg/kg) twice daily. After a medication taper and four-day washout, dogs were crossed-over to the alternate study medication, and the diagnostics were repeated in 12–16 days. Linear and multinomial mixed models were developed to evaluate the effects of treatments on echocardiographic and electrocardiographic variables.ResultsIndices of left ventricular systolic function were reduced based on the volumetric assessment when dogs received sotalol compared to atenolol. No difference was noted between groups in left ventricular systolic function based on the linear assessment. No difference was observed in the reduction in left ventricular outflow tract velocity. No significant differences were observed between treatment groups for any variable on 24-h Holter monitor.ConclusionsSotalol may be a viable therapy to consider for dogs with severe SAS based on this pilot study. A larger, prospective study is necessary to investigate further.     

Bayesian estimation of diagnostic accuracy of a new bead-based antibody detection test to reveal Toxoplasma gondii infections in pig populations

The success of a Toxoplasma gondii surveillance program in European pig production systems depends partly on the quality of the test to detect infection in the population. The test accuracy of a recently developed serological bead-based assay (BBA) was investigated earlier using sera from experimentally infected animals. In this study, the accuracy of the BBA was determined by the use of sera from animals from two field subpopulations. As no T. gondii infection information of these animals was available, test accuracy was determined through a Bayesian approach allowing for conditional dependency between BBA and an ELISA test. The priors for prevalence were based on available information from literature, whereas for specificity vague non-informative priors were used. Priors for sensitivity were based either on available information or specified as non-informative. Posterior estimates for BBA sensitivity and specificity were (mode) 0.855 (Bayesian 95% credibility interval (bCI) 0.702–0.960) and 0.913 (bCI 0.893–0.931), respectively. Comparing the results of BBA and ELISA, sensitivity was higher for the BBA while specificity was higher for ELISA. Alternative priors for the sensitivity affected posterior estimates for sensitivity of both BBA and ELISA, but not for specificity. Because the difference in prevalence between the two subpopulations is small, and the number of infected animals is small as well, the precision of the posterior estimates for sensitivity may be less accurate in comparison to the estimates for specificity. The estimated value for specificity of BBA is at least optimally defined for testing pigs from conventional and organic Dutch farms.     

A scoping review of autoantibodies as biomarkers for canine autoimmune disease

BackgroundAutoantibody biomarkers are valuable tools used to diagnose and manage autoimmune diseases in dogs. However, prior publications have raised concerns over a lack of standardization and sufficient validation for the use of biomarkers in veterinary medicine.ObjectivesSystematically compile primary research on autoantibody biomarkers for autoimmune disease in dogs, summarize their methodological features, and evaluate their quality; synthesize data supporting their use into a resource for veterinarians and researchers.AnimalsNot used.MethodsFive indices were searched to identify studies for evaluation: PubMed, CAB Abstracts, Web of Science, Agricola, and SCOPUS. Two independent reviewers (AET and ELC) screened titles and abstracts for exclusion criteria followed by full‐text review of remaining articles. Relevant studies were classified based on study objectives (biomarker, epitope, technique). Data on study characteristics and outcomes were synthesized in independent data tables for each classification.ResultsNinety‐two studies qualified for final analysis (n = 49 biomarker, n = 9 epitope, and n = 34 technique studies). A high degree of heterogeneity in study characteristics and outcomes reporting was observed. Opportunities to strengthen future studies could include: (1) routine use of negative controls, (2) power analyses to inform sample sizes, (3) statistical analyses when appropriate, and (4) multiple detection techniques to confirm results.ConclusionsThese findings provide a resource that will allow veterinary clinicians to efficiently evaluate the evidence supporting the use of autoantibody biomarkers, along with the varied methodological approaches used in their development.     

Design and standards for genetic evaluation of swine seedstock populations

The purpose of this article is to describe a program for evaluation of seedstock populations in the swine industry. Differences among seedstock populations for economically important traits must be identified in order for pork producers to efficiently use available genetic resources. National genetic evaluation programs have the potential to identify the important differences among populations and to increase the rate of genetic improvement in a population. Program results provide performance benchmarks that stimulate testing and selection procedures by seedstock suppliers that further increase the rate of genetic improvement. A Terminal Sire Line Genetic Evaluation Program was designed and conducted in the United States by the National Pork Producers Council (Des Moines, IA) to compare seedstock populations for use in crossbreeding systems. High levels of statistical accuracy for program results were established; the ability to detect differences of 0.25 SD per trait, a power of test of 75%, and a 5% significance level were selected. Pure breeds and breeding company sire lines were nominated for the program. Semen was collected from nominated boars and distributed to cooperating commercial producers during eight 1-wk breeding periods. Pigs were produced in 136 commercial herds and transported to testing facilities at 8 to 23 d of age. Nine of the 11 sire lines originally entered in the program completed the sampling requirements for statistical analysis. High levels of statistical accuracy and a large, representative sample of boars with restrictions on genetic relationships ensured that the program results included unbiased, highly accurate sire line data for growth, carcass, meat quality, and eating quality traits of economic importance. This program has shown commercial producers that they have several choices of sire lines for changing their crossbreeding programs in desired trait areas. Commercial product evaluation must be an ongoing process, and this program serves as a model for future testing and evaluation of diverse genetic seedstock populations.     

A Marteilia-Like Parasite in Blue Mussels Mytilus edulis in China

Abstract

Species of the genus Marteilia (Phylum Paramyxea) are protozoan parasites of marine mollusks. Marteilia spp. have been detected in mollusks from different parts of the world, but the presence of these parasites in China has not been previously reported. Therefore, a survey was conducted to look for the presence of Marteilia spp. in blue mussels Mytilus edulis and Asian green mussels Perna viridis collected along China's coasts. Histological and PCR analyses revealed that 5 of 180 M. edulis (prevalence = 2.8%) were positive for infection with a Marteilia-like organism, whereas the parasite was not detected in any of the 80 P. viridis individuals tested. Total genomic DNA was extracted from the infected tissue sections for PCR amplification. The PCR amplification with Marteilia primers SS1 and SAS1 yielded the expected 641-bp product. Sequencing results showed that the 18S ribosomal RNA gene fragment from the protozoans found in M. edulis from China was 88% similar to that of Marteilia refringens, a species that was reported from M. edulis and European flat oysters Ostrea edulis collected in France. This is the first report of a Marteilia-like organism infecting M. edulis in China.

Received May 9, 2011; accepted March 4, 2012     

Fish pathogen screening and its influence on the likelihood of accidental pathogen introduction during fish translocations

Fish translocations are an important tool in fisheries management, yet translocating fish carries the risk of introducing unwanted pathogens. Although pathogen screening can be a useful tool for managing the risk associated with fish translocations, screening cannot eliminate this risk. This paper addresses these problems by demonstrating that two elements must be considered when designing efficient and effective aquatic pathogen screening programs: (1) how many fish to screen and (2) how long to continue screening programs when repeated testing detects zero infected individuals. The chance that infected fish are translocated despite screening is the joint probability of (1) the failure of the screening to detect infected fish in the sample and (2) the actual presence of infected fish in the translocation batch. Our analysis demonstrates that transfer of an infected fish is most likely to occur at moderately low levels of pathogen prevalence because the probability of detecting at least one infected fish through screening increases as pathogen prevalence increases. Small screening samples (i.e., with a low number of individuals) are most likely to detect infected fish when pathogen prevalence is relatively high (i.e., > 5%). Screening programs should terminate after some number of successive screening events in which no infected individuals have been detected. The number of screening events is a function of the cost of the screening program, the cost of a pathogen translocation, and the probability that an infected fish will be transferred. Furthermore, our analysis indicates that the cost of a disease outbreak has relatively little effect on the length of time the screening program should continue. A more pronounced result is that screening programs that are inexpensive or allow a higher probability of pathogen translocation should be continued longer.