Field testing of an enhanced direct-fecal polymerase chain reaction procedure, bacterial culture of feces, and a serum enzyme-linked immunosorbent assay for detectingMycobacterium aviumsubspparatuberculosisinfection in adult dairy cattle

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

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

Control of Mycobacterium avium subsp. paratuberculosis infection on a New Zealand pastoral dairy farm

Background

Johne’s disease is a major production limiting disease of dairy cows caused by infection with Mycobacterium avium subsp. paratuberculosis in calf-hood. The disease is chronic, progressive, contagious and widespread with no treatment and no cure. Economic losses arise from decreased productivity through reduced growth, milk yield, fertility and also capital losses due to premature culling or death. Control chiefly centers upon removing those animals which actively shed bacteria and protecting calves from infection. A prolonged pre-clinical shedding phase, lack of test sensitivity, organism persistence and abundance in the environment as well as management systems that expose susceptible calves to infection make control challenging, particularly in pastoral, seasonal dairy systems. Combining a novel testing strategy to remove infected cows along with limited measures to protect vulnerable calves at pasture, this study reports the successful reduction over a four-year period of seroprevalence of cows testing positive for MAP infection in a New Zealand pastoral dairy herd.

Results

For all age groups considered the apparent seroprevalence of cows testing positive decreased from 297 / 1,122 (26%) in 2013–2014, to 24 / 1,030 (2.3%) in 2016–2017. Over the same period, the apparent seroprevalence in primiparous cows decreased from 39 / 260 (15%) to 7 / 275 (2.5%) and in multiparous cows from 258 / 862 (29.9%) to 17 / 755 (2.3%). The reported proportion of calved cows culled annually from suspected clinical Johne’s disease fell from 55 / 1,201 (5%) in the year preceding the control program to 5 / 1,283 (0.4%) in the final year of the study.

Conclusions

On this farm, reduction in the prevalence of infection was achieved by reducing the infectious pressure through targeted culling of heavily shedding animals together with limited measures to protect calves at pasture from exposure to Mycobacterium avium subsp. paratuberculosis. Whilst greater protection of young animals through separation from infected cows and their colostrum and milk would have reduced the risk of neonatal infection, this study demonstrates, in this case, that these management measures while prudent were not essential for effective reduction in the prevalence of MAP infection.

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

OBJECTIVES

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

METHODS

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

RESULTS

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

CONCLUSIONS

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

Diagnostic accuracy of blood sucrose as a screening test for equine gastric ulcer syndrome (EGUS) in weanling foals

Background

Equine gastric ulcer syndrome is an important cause of morbidity in weanling foals. Many foals are asymptomatic, and the development of an inexpensive screening test to ensure an early diagnosis is desirable. The objective of this study was to determine the diagnostic accuracy of blood sucrose for diagnosis of EGUS in weanling foals.

Results

45 foals were studied 7 days before and 14 days after weaning. The diagnostic accuracy of blood sucrose for diagnosis of gastric lesions (GL); glandular lesions (GDL); squamous lesions (SQL) and clinically significant gastric lesions (CSL) at 45 and 90 min after administration of 1 g/kg of sucrose via nasogastric intubation was assessed using ROC curves and calculating the AUC. For each lesion type, sucrose concentration in blood was compared to gastroscopy; and sensitivities (Se) and specificities (Sp) were calculated across a range of sucrose concentrations. Cut-off values were selected manually to optimize Se. Because of concerns over the validity of the gold standard, additional Se, Sp, and lesion prevalence data were subsequently estimated and compared using Bayesian latent class analysis. Using the frequentist approach, the prevalence of GL; GDL; SQL and CSL before weaning was 21; 9; 7 and 8% respectively; and increased to 98; 59; 97 and 82% respectively after weaning. At the selected cut-off, Se ranged from 84 to 95% and Sp ranged from 47 to 71%, depending upon the lesion type and time of sampling. In comparison, estimates of Se and Sp were consistently higher when using a Bayesian approach, with Se ranging from 81 to 97%; and Sp ranging from 77 to 97%, depending upon the lesion type and time of sampling.

Conclusions

Blood sucrose is a sensitive test for detecting EGUS in weanling foals. Due to its poor specificity, it is not expected that the sucrose blood test will replace gastroscopy, however it may represent a clinically useful screening test to identify foals that may benefit from gastroscopy. Bayesian latent class analysis represents an alternative method to evaluate the diagnostic accuracy of the blood sucrose test in an attempt to avoid bias associated with the assumption that gastroscopy is a perfect test.

The effect of sub-clinical infection with Mycobacterium avium subsp. paratuberculosis on milk production in a New Zealand dairy herd

Background

Johne’s disease is a major production limiting disease of dairy cows. The disease is chronic, progressive, contagious and widespread; there is no treatment and there is no cure. Economic losses arise from decreased productivity through reduced growth, milk yield and fertility and capital losses due to premature culling or death. This study attempts to address the effect of subclinical JD on milk production under New Zealand pastoral dairy farming conditions using a new testing approach. Blood samples were taken from all lactating animals from a single seasonally calving New Zealand dairy herd in the autumn of 2013 and 2014. Samples were subject to serological assay for antibodies to Mycobacterium avium subsp. paratuberculosis using a combination of four ELISA tests in parallel followed by selective quantitative fecal PCR to confirm the fecal shedding characteristics of ELISA positive cows. ELISA status was classified as Not-Detected, Low, Moderate or High and fecal PCR status as Not-Detected, Moderate or High.

Results

A mixed generalized regression model indicated that, compared to cows where MAP was not detected, daily milk solids production was 4% less for high ELISA positive cows (p = 0.004), 6% less for moderate fPCR cows (p = 0.036) and 12% less for high fPCR cows (p < 0.001).

Conclusions

This study confirms that sub-clinical JD can have a significant impact on milk production and that the testing methodology used stratified the animals in this herd on their likely impact on production and disease spread. This allowed the farmer to prioritize removal of heavily shedding, less-productive animals and so reduce the risk of infection of young stock. This is the first longitudinal study based in New Zealand looking at the effect of Johne’s infection status on daily milk production allowing for intermediary and confounding factors.

Evaluation of different diagnostic methods for the detection of Mycobacterium avium subsp. paratuberculosis in boot swabs and liquid manure samples

Background

Environmental sampling based on boot swabs and/or liquid manure samples is an upcoming strategy for the identification of paratuberculosis (paraTB) positive herds, but only limited data are available regarding the diagnostic performance of molecular detection methods (qPCR) versus faecal culture (FC) for this purpose. In the present study, the test characteristics of two different qPCR protocols (A and B) and a standardized FC protocol, for the detection of Mycobacterium avium subsp. paratuberculosis in boot swabs and liquid manure samples were evaluated.

Results

In 19 paraTB unsuspicious and 58 paraTB positive herds boot swabs and liquid manure were sampled simultaneously and analyzed in three different diagnostic laboratories. Using boot swabs and liquid manure, a substantial to excellent accordance was found between both qPCRs, for boot swabs also with culture, while for liquid manure the detection rate of culture was decreased after prolonged storage at −20 °C. The quantitative results of both qPCR methods correlated well for the same sample and also for boot swabs and liquid manure from the same herd. When cut-off threshold cycle (C_T-)-values were applied as recommended by the manufacturers, herd level specificity (Sp) of qPCR B was below 100% for boot swabs and for both qPCRs for liquid manure. A decreased herd level sensitivity was encountered after adjustment of Sp to 100% and re-calculation of the cut-off C_T-values.

Conclusions

qPCR is equally suitable as bacterial culture for the detection of Mycobacterium avium subsp. paratuberculosis in boot swabs and liquid manure samples. Both matrices represent easily accessible composite environmental samples which can be tested with reliable results. The data encourage qPCR testing of composite environmental samples for paraTB herd diagnosis.

Association between caudal fold tuberculin test responses and results of an ELISA for Mycobacterium avium subsp paratuberculosis and mycobacterial culture of feces in tuberculosis-free dairy herds

OBJECTIVE--To evaluate associations between Mycobacterium avium subsp paratuberculosis (MAP) and caudal fold tuberculin (CFT) test results in cattle. DESIGN--Longitudinal and cross-sectional evaluations. ANIMALS--1 California (approx 3,600 cows) and 3 Colorado (approx 640, 1,190, and 1,480 cows) dairy herds considered free of Mycobacterium bovis infection. PROCEDURES--In the California herd, the association between CFT response and MAP status was determined with ELISA and mycobacterial culture of feces within 1 year before and after CFT testing. The association between CFT and MAP status in all herds was modeled with mixed-effects logistic regression. RESULTS--In the California herd, significantly higher odds of being classified as suspect by CFT were found for cows with results of MAP ELISA negative before and positive after CFT testing (OR, 5.6) and cows positive before and after CFT testing (OR, 8.1). Higher odds were found for cows positive for mycobacterial culture of feces before and negative for culture after CFT testing (OR, 4.6) and cows negative for mycobacterial culture of feces before and positive for culture after CFT testing (OR, 13.2). All herds had higher odds of being classified as suspect by CFT testing for cows with positive results for ELISA (OR, 2.9) or mycobacterial culture of feces (OR, 5.0), compared with cows with negative results of the same tests. CONCLUSIONS AND CLINICAL RELEVANCE--A strong association was found between positive MAP test results and being classified as a suspect by CFT testing. Within-herd MAP prevalence may affect specificity of CFT testing for tuberculosis in cattle.

Sensitivity and specificity of real-time reverse transcription polymerase chain reaction, histopathology, and immunohistochemical labeling for the detection of Rift Valley fever virus in naturally infected cattle and sheep

Real-time reverse transcription polymerase chain reaction (real-time RT-PCR), histopathology, and immunohistochemical labeling (IHC) were performed on liver specimens from 380 naturally infected cattle and sheep necropsied during the 2010 Rift Valley fever (RVF) epidemic in South Africa. Sensitivity (Se) and specificity (Sp) of real-time RT-PCR, histopathology, and IHC were estimated in a latent-class model using a Bayesian framework. The Se and Sp of real-time RT-PCR were estimated as 97.4% (95% confidence interval [CI] = 95.2-98.8%) and 71.7% (95% CI = 65-77.9%) respectively. The Se and Sp of histopathology were estimated as 94.6% (95% CI = 91-97.2%) and 92.3% (95% CI = 87.6-95.8%), respectively. The Se and Sp of IHC were estimated as 97.6% (95% CI = 93.9-99.8%) and 99.4% (95% CI = 96.9-100%), respectively. Decreased Sp of real-time RT-PCR was ascribed to cross-contamination of samples. Stratified analysis of the data suggested variations in test accuracy with fetuses and severely autolyzed specimens. The Sp of histopathology in fetuses (83%) was 9.3% lower than the sample population (92.3%). The Se of IHC decreased from 97.6% to 81.5% in the presence of severe autolysis. The diagnostic Se and Sp of histopathology was higher than expected, confirming the value of routine postmortem examinations and histopathology of liver specimens. Aborted fetuses, however, should be screened using a variety of tests in areas endemic for RVF, and results from severely autolyzed specimens should be interpreted with caution. The most feasible testing option for countries lacking suitably equipped laboratories seems to be routine histology in combination with IHC.

Evaluation of combined high-efficiency DNA extraction and real-time PCR for detection of Mycobacterium avium subsp. paratuberculosis in subclinically infected dairy cattle: comparison with faecal culture, milk real-time PCR and milk ELISA

Background

Johne’s disease is caused by Mycobacterium avium subsp. paratuberculosis (Map) and it is one of the most important diseases in cattle worldwide. Several laboratory tests for Map detection are available; however, these are limited by inadequate sensitivity and specificity when used in subclinically infected populations. To identify Map shedders in subclinically infected cattle, we used a new, high-yield method for DNA-extraction from Map in faeces combined with quantitative real-time PCR (qPCR) for amplification of the insertion sequence IS900 of Map (HYDEqPCR). Evaluation of HYDEqPCR was carried out in comparison with faecal culture, milk qPCR, and milk enzyme-linked immunosorbent assay (ELISA), on 141 faecal and 91 milk samples, from 141 subclinically infected dairy cattle.

Results

The qPCR proved to be highly sensitive, with a detection limit of 2 IS900 DNA copies/μl in 67 % of the reactions. It also showed 100 % specificity, as determined from 50 Map and non-Map strains, and by the sequencing of qPCR amplicons. The detection limit of HYDEqPCR was 90 Map/g Map-spiked faeces, which corresponds to 2.4 colony forming units/g Map-spiked faeces, with an estimated efficiency of 85 % (±21 %). When tested on the field samples, HYDEqPCR showed 89 % of the samples as positive for Map, whereas faecal culture, milk qPCR, and milk ELISA detected 19 %, 36 % and 1 %, respectively. Fisher’s exact tests only show statistical significance (p ≤0.05) for the correlation between HYDEqPCR and faecal culture. The agreement between HYDEqPCR and milk qPCR and milk ELISA was poor, slight, and non-significant.

Conclusions

This study highlights the advantages of HYDEqPCR for detection of Map in subclinically infected populations, in comparison with faecal culture, milk qPCR and milk ELISA. HYDEqPCR can detect low-level Map shedders that go undetected using these other methods, which will thus underestimate the proportions of Map-shedders in herds. Identification of these shedding animals is extremely important for prevention of the spread of Map infection in an animal population. Due to the relatively high sensitivity and specificity of HYDEqPCR, it can be applied to test for Map at the herd or individual level, regardless of animal age or production stage. HYDEqPCR will allow early detection and control of Map in any population at risk.

Consensus-based reporting standards for diagnostic test accuracy studies for paratuberculosis in ruminants

The Standards for Reporting of Diagnostic Accuracy (STARD) statement (www.stard-statement.org) was developed to encourage complete and transparent reporting of key elements of test accuracy studies in human medicine. The statement was motivated by widespread evidence of bias in test accuracy studies and the finding that incomplete or absent reporting of items in the STARD checklist was associated with overly optimistic estimates of test performance characteristics. Although STARD principles apply broadly, specific guidelines do not exist to account for unique considerations in livestock studies such as herd tests, potential use of experimental challenge studies, a more diverse group of testing purposes and sampling designs, and the widespread lack of an ante-mortem reference standard with high sensitivity and specificity. The objective of the present study was to develop a modified version of STARD relevant to paratuberculosis (Johne's disease) in ruminants. Examples and elaborations for each of the 25 items were developed by a panel of experts using a consensus-based approach to explain the items and underlying concepts. The new guidelines, termed STRADAS-paraTB (Standards for Reporting of Animal Diagnostic Accuracy Studies for paratuberculosis), should facilitate improved quality of reporting of the design, conduct and results of paratuberculosis test accuracy studies which were identified as "poor" in a review published in 2008 in Veterinary Microbiology.

Attitudes towards biosecurity practices relevant to Johne's disease control on beef cattle farms

The success of control programs can be improved when producers' attitudes towards these programs are positive. Implementation of control programs for chronic diseases are more challenging than those for acute diseases because of the absence of the "cues-to-action" that are associated with acute diseases. Johne's disease (JD) is a chronic diarrheal disease of ruminants, and national voluntary control programs exist in several countries. We used a mailed cross-sectional survey to describe the attitudes of producers towards biosecurity practices and veterinarians' beliefs relevant to the control of JD on beef farms. Another objective was to describe and compare the attitudes of producers and veterinarians towards specific measures recommended by the Texas Voluntary Johne's Disease Program (TVJDP) for cattle. Questionnaires were mailed to 1100 producers and 840 veterinarians in the state of Texas, USA. Two hundred and eighty-five producers (26%) and 153 veterinarians (18%) returned questionnaires for analysis. Fifty-nine percent of producers and 50% of veterinarians agreed that JD is responsible for substantial losses in beef cattle production. Sixty-four percent of veterinarians had educated producers on management strategies for the control or elimination of JD. However, only 36% had participated in the training program and 29% were certified to develop risk assessments and implement testing. Only 20% of producers reported that they were familiar with the TVJDP and 16% had considered participating in this program. There is a need for greater promotion of the control program among veterinarians and producers. Reasons for the apparent difference in opinions need to be understood to increase the likelihood of control measures adoption and to subsequently reduce the impact of JD on beef cattle operations.

Development of a method for Bayesian nonparametric ROC analysis with application to an ELISA for Johne's disease in dairy cattle

Six hundred and sixty-eight dairy cattle were tested for Johne's disease using a direct-fecal real-time polymerase chain reaction (rt-PCR), fecal culture, and serum enzyme-linked immunosorbent assay (ELISA). Likelihood ratios (LRs) were estimated for five categories of sample-to-positive (S/P) values for the ELISA: <0.1, 0.1-0.249, 0.25-0.399, 0.4-0.999, > or =1.0. The statistical method assumed a single multinomial model for cross-classified rt-PCR, fecal culture results, and ELISA category strata. Conditional dependence between tests was investigated by the inclusion of all possible pairwise dependence terms. Sensitivity covariance between ELISA and fecal culture was estimated as 0.017. Estimates for the accuracy of the ELISA at the usual cutoff of 0.25S/P was 67.2% and 95.2% for sensitivity and specificity, respectively for a model that adjusted for the dependence between ELISA and fecal culture. The area under the receiver-operating characteristic (ROC) curve (95% probability interval) for the ELISA was 0.867 (0.796, 0.928). Point estimates for likelihood ratios (95% probability intervals) were 0.24 (0.11, 0.38), 1.52 (0.48, 3.27), 2.49 (0.31, 13.4), 6.33 (2.54, 16.5), and 103 (25.0, 2412) for the categories <0.1, 0.1-0.249, 0.25-0.399, 0.4-0.999, >/=1.0, respectively. Assumptions concerning the underlying distribution of test results for infected and uninfected animals were not necessary and this model can be employed for the general estimation of LRs and ROC curves in absence of knowledge concerning true disease status.