Factors influencing the isolation of Mycobacterium avium subsp. paratuberculosis from bovine fecal samples

Introducing a portable electrochemical biosensor for Mycobacterium avium subsp. paratuberculosis detection using graphene oxide and chitosan

In this contribution, a novel, low-cost, high throughput, and ultra-selective electrochemical DNA nanobiosensor was developed for accurate on-site detection of Mycobacterium avium subspecies paratuberculosis (MAP) in real media for practical diagnosis of Johne's disease (JD). The method was designed based on the immobilization of graphene oxide and chitosan biopolymer on the surface of a glassy carbon electrode, modified by electrochemical immobilization of graphene oxide and chitosan biopolymer, followed by activation of biopolymer via 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride and N-hydroxy succinimide (EDC/NHS) coupling system. Afterward, the commercial probe DNA (ssDNA) was stabilized on the activated electrode surface to prepare an ultra-selective ssDNA-stabilized nanobiosensor for MAP sensing called "ssDNA-stabilized GO-CH-EDC/NHS-modified electrode". Several characterization methods distinguished the bioelectrode. The DNA hybridization between the nanobiosensor and target DNA was confirmed by cyclic voltammetry and differential pulse voltammetry. "At optimal experimental conditions, the nanobiosensor showed a linear range of 1.0 × 10-15-1.0 × 10-12 mol L-1, a detection limit as low as 1.53 × 10-13 mol L-1, and a repeatability with a relative standard deviation (%RSD) of 4.7%. The reproducibility was also appropriate, with a %RSD of about 10%. It was used to diagnose MAP in real samples with highly accurate results. Therefore, the developed nanobiosensor can be used for clinical diagnosis of MAP.

Variation in the Performance of Different Batches of Two Mycobacterium avium Subspecies paratuberculosis Antibody ELISAs Used for Pooled Milk Samples

Simple Summary

This article explores variation in the performance of different batches of tests for the detection of antibodies against the ruminant pathogen Mycobacterium avium subspecies paratuberculosis (MAP) in milk. The results indicate that variation is present and that it has sources mainly in the manufacturing process of the test kits and, to a lesser degree, in the test laboratories.

Abstract

Regionally, the monitoring of paratuberculosis at the herd level is performed by the detection of specific antibodies in pooled milk samples by ELISA. The negative/positive cut-off S/P values applied for pooled milk samples are low and particularly vulnerable to variation in the test performance. In this study, a batch variation in the test performance of two ELISA tests was assessed to identify consequences for sample classification. A total of 72 pooled milk samples (50 from MAP-infected herds, 22 from one MAP-non-infected herd) were analyzed using three different batches, each of two different MAP antibody ELISA tests (A and B). Receiver operating characteristic (ROC) analysis was performed, with the results of each batch, S/P values of the samples and optical density (OD) readings of the negative and positive control samples included in the kits being compared between the batches of one test. ROC analysis revealed a considerable variation in the test performance of the batches of the two individual tests, caused by differences in the S/P values of the samples and resulting in different sensitivities at a specificity of 100%. Major sources of variation originate from the manufacturing processes of test batches. These sources have to be better controlled, and the test performance has to be revisited regularly.

Enhanced sensitivity and fast turnaround time in laboratory diagnosis for bovine paratuberculosis in faecal samples

Bovine paratuberculosis (Johne's disease in cattle) is caused by the pathogen Mycobacterium avium subsp. paratuberculosis (MAP) and is a widespread chronic bacterial infectious disease in cattle. Due to the peculiarities of the pathogen, detection of MAP in faeces remains difficult. DNA extraction and real-time PCR for detection of MAP in bovine faeces (direct PCR) have been refined and feasible procedures for rapid, sensitive and automatable detection of the pathogen agent have been developed. Accordingly, in a first step we tested 20 faecal samples using two MAP complete kits (DNA extraction kits based on magnetic beads combined with real-time PCR assays) and six other DNA extraction kits for faeces. MAP-specific DNA was detected by real-time PCR assays. Cultivation of MAP on the solid medium HEYM and in the liquid medium M7H9C served as reference standards. The two complete kits detected significantly more MAP-DNA positive samples than the other procedures applied (p < 0.04). Ct values of 37 and 38 served as cut-off for the respective real-time PCR assays calculated on the basis of standard curves and droplet digital PCR (ddPCR). In a second step, the two MAP complete kits were employed for a comprehensive study including 107 positive and 50 negative faecal samples which had been previously tested on HEYM cultivation. The MAP complete kits yielded sensitivity values of 86% and 89% and specificity values of 100% compared to cultivation of MAP in the liquid medium M7H9C. In detail, cultivation of MAP in M7H9C detected the pathogen in 97% and 100% of the samples tested after an incubation period of six and twelve weeks, respectively. However, the cultivation of MAP on HEYM succeeded in only 74% after twelve weeks of incubation. In all these solid culture positive samples, MAP was also detected using the two complete kits. Additionally, the impact of repeated freezing and thawing of samples on re-cultivation of MAP was tested using 20 faecal samples and resulted in a reduction to 75% and 25% of bacterial growth when using liquid medium M7H9C and solid medium HEYM, respectively. The results of this study show that complete kits with refined automatable protocols for DNA extraction in combination with real-time PCR assays for detection of MAP can compete with sensitive cultivation of the pathogen in liquid medium.

An intra-laboratory cultural and real-time PCR method comparison and evaluation for the detection of subclinical paratuberculosis in dairy herds

Mycobacterium avium subsp. paratuberculosis (MAP) is a vigorous microorganism which causes incurable chronic enteritis, Johne's disease (JD) in cattle. A target of control programmes for JD is to accurately detect MAP-infected cattle early to reduce disease transmission. The present study evaluated the efficacy of two different cultural procedures and a TaqMan real-time PCR assay for detection of subclinical paratuberculosis in dairy herds. Therefore, sixty-one faecal samples were collected from two Dutch dairy herds (n = 40 and n = 21, respectively) which were known to be MAP-ELISA positive. All individual samples were assessed using two different cultural protocols in two different laboratories. The first cultural protocol (first laboratory) included a decontamination step with 0.75% hexadecylpyridinium chloride (HPC) followed by inoculation on Herrold's egg yolk media (HEYM). The second protocol (second laboratory) comprised of a decontamination step using 4% NaOH and malachite green-oxalic acid followed by inoculation on two media, HEYM and in parallel on modified Löwenstein-Jensen media (mLJ). For the TaqMan real-time PCR assay, all faecal samples were tested in two different laboratories using TaqMan® MAP (Johne's) reagents (Life Technologies). The cultural procedures revealed positive reactions in 1.64% of the samples for cultivation protocol 1 and 6.56 and 8.20% of the samples for cultivation protocol 2, respectively. The results of the TaqMan real-time PCR performed in two different laboratories yielded 13.11 and 19.76% positive reaction. The kappa test showed proportional agreement 0.54 between the mLJ media (second laboratory) and TaqMan® real-time PCR method (second laboratory). In conclusion, the TaqMan real-time PCR could be a strongly useful and efficient assay for the detection of subclinical paratuberculosis in dairy cattle leading to an improvement in the efficiency of MAP control strategies.

Comparison of fecal culture and F57 real-time polymerase chain reaction for the detection of Mycobacterium avium subspecies paratuberculosis in Swiss cattle herds with a history of paratuberculosis

BACKGROUND

Bovine paratuberculosis is an incurable chronic granulomatous enteritis caused by Mycobacterium avium subspecies paratuberculosis (MAP). The prevalence of MAP in the Swiss cattle population is hard to estimate, since only a few cases of clinical paratuberculosis are reported to the Swiss Federal Food Safety and Veterinary Office each year.Fecal samples from 1,339 cattle (855 animals from 12 dairy herds, 484 animals from 11 suckling cow herds, all herds with a history of sporadic paratuberculosis) were investigated by culture and real-time polymerase chain reaction (PCR) for shedding of MAP.

RESULTS

By culture, MAP was detected in 62 of 445 fecal pools (13.9%), whereas PCR detected MAP in 9 of 445 pools (2.0%). All 186 samples of the 62 culture-positive pools were reanalyzed individually. By culture, MAP was grown from 59 individual samples (31.7%), whereas PCR detected MAP in 12 individual samples (6.5%), all of which came from animals showing symptoms of paratuberculosis during the study. Overall, MAP was detected in 10 out of 12 dairy herds (83.3%) and in 8 out of 11 suckling cow herds (72.7%).

CONCLUSIONS

There is a serious clinically inapparent MAP reservoir in the Swiss cattle population. PCR cannot replace culture to identify individual MAP shedders but is suitable to identify MAP-infected herds, given that the amount of MAP shed in feces is increasing in diseased animals or in animals in the phase of transition to clinical disease.

Antemortem and postmortem examinations of the cattle calf naturally infected with Mycobacterium avium subsp. paratuberculosis

A male cattle calf was detected as subclinically and naturally infected with Mycobacterium avium subspecies paratuberculosis (MAP) by a series of antemortem and postmortem tests. The MAP infection was identified by strong antibody and cell-mediated immune (CMI) response by a commercial ELISA kit and an intradermal Johnin test, respectively, in the initial antemortem examination. The antemortem status of the calf was further confirmed by MAP-specific interferon gamma (IFN-γ) response. For detection of IFN-γ response, MAP-specific IFN-γ release assays (IGRAs): (a) immuno capture ELISA (IC-ELISA) and (b) ELISPOT was employed. In addition, the presence of intracellular cytokine IFN-γ was detected by flow cytometry. For all cytokine assays, MAP-specific recombinant antigens HSP65 and 35 kDa were employed to overcome the poor sensitivity and specificity resulting from the use of Johnin, the crude protein purified derivative of MAP. Postmortem examination of the MAP-infected/suspected cattle calf did not reveal any pathognomonic gross lesions in the gastro-intestinal tract. Histopathological examination of multiple organs showed the presence of epithelioid cells/macrophages and edematous lesions in the mesenteric lymph nodes suggestive of MAP; however, no granulomas were observed in the intestinal tract. The necropsy samples of rectum and mesenteric lymph nodes were positive for isolation of MAP by culture in the BACTEC™ MGIT™ 960 system, and acid fast bacilli were demonstrated by fluorescence microscopy confirming the infection. Due to differential and complex expression patterns of MAP antigens reported in literature, a combination of assays such as those based on IGRAs and antibody detection is essential. Therefore, the current experimental evidence confirms the efficacy of the approach adopted. However, further studies will be needed to understand the optimal combination MAP-specific antigens for use in IGRAs or antibody assays that can be used for detecting MAP infection in every stage of the disease.

Diagnosis of paratuberculosis in cattle: microbiological culture, serology and PCR

The aim of this study was to confirm clinical diagnosis of paratuberculosis in two cows showing suggestive clinical signs of the disease. Based on clinical signs, in culture and in IS900 PCR results from the individual milk samples it was possible to diagnose paratuberculosis in the cows studied.

Detection of spatial and temporal spread of Mycobacterium avium subsp. paratuberculosis in the environment of a cattle farm through bio-aerosols

Environmental samples were collected to investigate the spatial and temporal spread of Mycobacterium avium subsp. paratuberculosis (MAP) in a dairy cattle barn before and after the introduction of two groups of MAP-shedding animals. Samples collected off the floor of the barn reflected the moment of sampling whereas samples collected by microfiber wipes at a minimal of 3m height contained the accumulated settled dust over a 3-week period. Samples were analysed by IS900 qPCR for the presence of MAP DNA and by culture for viable MAP bacteria. MAP DNA was detected in a large number of sites both before and after introduction cattle. MAP DNA was detected inside the barn in floor and dust samples from cubicles and slatted floors and in settled dust samples located above the slatted floors and in the ventilation ridge opening. Outside the barn MAP DNA was detected by PCR in samples reflecting the walking path of the farmer despite hygiene measures. No viable MAP was detected before the introduction of shedder cattle. Three weeks later viable MAP was found inside the barn at 7/49 locations but not outside. Fifteen weeks later viable MAP was also detected in environmental samples outside the barn. In conclusion, introduction of MAP shedding cattle lead to widespread contamination of the internal and external environment of a dairy barn, including the presence of viable MAP in settled dust particles suggesting potential transmission of MAP infection through bio-aerosols.

Factors affecting isolation and identification of Mycobacterium avium subsp. paratuberculosis from fecal and tissue samples in a liquid culture system

Culture of Mycobacterium avium subsp. paratuberculosis is the definitive diagnostic test for Johne's disease, a chronic granulomatous enteropathy of animals. Compared to solid media, the identification of all strains of the organism in liquid media can be more difficult because the appearance of colonies and mycobactin dependence are not observable, and the growth of other organisms needs to be distinguished, commonly by PCR. Factors affecting the isolation rate of S strains and the contamination rate in modified Middlebrook 7H9 broth (Bactec 12B) and 7H10 agar were studied using 11,598 fecal samples and 2,577 tissue samples from sheep from 1,421 farms over 10 years. Minimization of contamination in Bactec cultures required the avoidance of the carryover of fecal particles from the first sedimentation step in the double-incubation centrifugation method, and contamination was reduced significantly by incubating the sample in a solution containing vancomycin, amphotericin B, and nalidixic acid for 3 days compared to 2 days. The growth of irrelevant microorganisms confounded the identification of M. avium subsp. paratuberculosis in liquid culture by inhibiting IS900 PCR and in solid medium culture by inhibiting the growth of M. avium subsp. paratuberculosis or obscuring colonies. The contamination of samples was clustered in certain laboratory submissions and was reduced by including ampicillin in Bactec medium without affecting the odds of isolation of M. avium subsp. paratuberculosis. The long-term contamination rate for fecal cultures was about 7%, and that for tissue cultures was <0.2%. Liquid medium was more sensitive than solid medium culture for M. avium subsp. paratuberculosis. The applicability of these findings for C strains is discussed.

Fabrication of a Novel Conductometric Biosensor for Detecting Mycobacterium avium subsp. paratuberculosis Antibodies

Johne's disease (JD) is one of the most costly bacterial diseases in cattle. In the U.S., economic losses from the disease have been estimated to exceed $1,500,000,000 per year, mainly from the effects of reduced milk production. Current diagnostic tests for JD are laboratory based and many of those tests require specialized equipment and training. Development of rapid and inexpensive diagnostic assays, which are adapted for point-ofcare applications, would aid in the control of JD. In this study, a polyaniline (Pani)-based conductometric biosensor, in an immunomigration format, was fabricated for the detection of serum antibody (IgG) against the causal organism of JD, Mycobacterium avium subsp. paratuberculosis (MAP). Immobilized Mycobacterium avium purified proteins in the capture membrane were used to detect MAP IgG, previously bound with Pani/anti-bovine IgG* conjugate in the conjugate membrane. After detection, the Pani in the sandwiched captured complex bridges an electrical circuit between the silver electrodes, flanking the capture membrane. The electrical conductance, caused by Pani, was measured as drop in electrical resistance. Testing of the biosensor with known JD positive and negative serum samples demonstrated a significant difference in the mean resistance observed between the groups. This proof-of-concept study demonstrated that a conductometric biosensor could detect MAP IgG in 2 minutes. The biosensor's speed of detection and the equipment involved would, among other things, support its application towards the various point-ofcare opportunities aimed at JD management and control.

Assessment of management-related risk factors for paratuberculosis in Danish dairy herds using Bayesian mixture models

Transmission of Mycobacterium avium subsp. paratuberculosis (Map) to susceptible animals is primarily considered to occur via faeces and milk originating from infectious cows. However, studies of factors resulting in increased transmission of Map are difficult to perform due to a long and unpredictable incubation period and inaccurate diagnostic tests. A multi-level Bayesian mixture model has been shown to predict the infection status of an individual cow more precisely than traditional cut-off based methods used for interpretation of diagnostic test-information, thereby increasing the precision of the diagnostic information. The objective of our study was to assess management-related risk factors for within-herd transmission of Map. Management-related risk factors were recorded in 97 Danish dairy herds. Twenty-six months following that recording, the antibody status of all lactating cows (n=7,410) in the same herds was measured by the use of an ELISA. A multi-level Bayesian mixture model was used to assess the association between the probability of infection of individual cows and 41 herd-level management-related risk factors using univariable analyses. In this model, the continuous OD value was used to estimate the probability of infection, corrected for known animal covariates and laboratory factors. The statistical significance of the potential risk factors was assessed by calculating odds ratios and their 95% credibility posterior intervals. Four significant risk factors were identified: housing of cows in bed stalls compared to housing in tie stalls; low level of hygiene in the feeding area of calving areas; low amounts of straw in the bedding of the calving area; high animal density among young stock >12 months of age. Surprisingly, the hygiene level in the calving area was not found to affect the odds of infection.

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

OBJECTIVE

To estimate the sensitivity (Se) and specificity (Sp) for an enhanced direct-fecal PCR procedure, bacterial culture of feces (BCF), and a serum ELISA for detecting Mycobacterium avium subsp paratuberculosis (MAP) infection in adult dairy cattle.

SAMPLE POPULATION

Fecal and serum samples were collected from 669 adult cattle randomly selected from a 4,000-cow dairy herd known to contain animals infected with MAP.

PROCEDURES

Serum samples were evaluated for MAP-specific antibodies via ELISA. Fecal samples were evaluated by BCF and enhanced PCR methods (both gel-based [GB]-PCR and quantitative real-time [qRT]-PCR assays). Fecal samples also were pooled (5:1) and then subjected to GB-PCR assay. Bayesian statistical methods were used to estimate Se and Sp for each diagnostic test without knowledge concerning true MAP infection status.

RESULTS

Adjusting for Se conditional dependence between serum ELISA and BCR, overall Se and Sp were estimated at 33.7% and 95.9%, 51.3% and 99.0%, and 32.2% and 100% for serum ELISA, qRT-PCR, and BCF, respectively.The GB-PCR assay yielded positive results for 38.3% of the pools known to contain feces from at least 1 cow that had positive GBPCR results.

CONCLUSIONS AND CLINICAL RELEVANCE

Estimated Se values for the serum ELISA and BCF were slightly lower than those reported elsewhere. The enhanced qRT-PCR method offered relative improvements in Se of 52% and 59% over serum ELISA and microbial culture, respectively. Pooling of fecal samples and testing with the GB-PCR assay are not recommended. Additional studies with qRT-PCR and fecal pools are required.

Age at Occurrence of Mycobacterium avium Subspecies paratuberculosis in Naturally Infected Dairy Cows

Paratuberculosis is a chronic infection of ruminants and other species caused by Mycobacterium avium ssp. paratuberculosis (Map). Establishing test strategies for paratuberculosis will require insight into the temporal aspects of certainty with a given test. In this study, the age at which cows tested positive by ELISA and fecal culture (FC) was investigated by use of time-to-event analyses. The effects of herd, parity, and shedding group were evaluated at the age of test-positive ELISA and FC, respectively. Finally, the test frequency was investigated for the probability of cows being tested ELISA-positive. Milk and fecal samples were collected repeatedly over a 3-yr period from 1,776 Danish dairy cows from 8 herds. The milk samples were tested for the presence of antibodies by using an ELISA, and an FC test was used for detection of Map. Repeated ELISA testing detected 98 and 95% of cows classified as high and low shedders, respectively, suggesting that most infected cows develop antibodies. Among the high shedders, 50% were positive before 4.3 yr of age (quartiles 1 to 3: 3.4 to 5.7 yr of age). Repeated FC detected only 72% of the cows that were ELISA-positive, and 50% of the ELISA-positive cows were detected by FC at 7.6 yr of age. The age with the highest probability of testing positive was determined as the interval with the steepest slope in the survival probability plots. The highest probability of testing positive by ELISA was from 2.5 to 4.5 yr of age. The highest probability of testing positive by FC was from 2.5 to 5.5 yr of age. For both ELISA and FC, testing positive was highest in the first 300 d in milk. For cows younger than 4 yr of age, monthly testing with ELISA, compared with testing every 2 yr, could increase the probability of detecting cows with antibodies by 19%. In older cows, there were no apparent differences in the probability of testing positive by monthly sampling compared with sampling every second year. Therefore, for older animals the effect of more frequent sampling would be for early detection rather than to obtain additional information. Cows shedding high numbers of Map will produce antibodies, although not necessarily concomitantly with the shedding. These antibodies can be detected by ELISA with a test strategy that is different for younger and older cows. We suggest testing younger cows more frequently than older cows and that testing should be done prior to 350 d in milk.

Age-specific characteristics of ELISA and fecal culture for purpose-specific testing for paratuberculosis

Paratuberculosis is a chronic infection, and animals are not equally affected by it. Therefore, diagnostic tests that are able to detect different stages of the infection are needed for objective decision making. A longitudinal study was carried out to describe the ability of 2 tests to predict 2 conditions in dairy cattle: "infection" and "infectious," exemplifying 2 different purposes of testing. "Infection" is the term of choice for certification and eradication purposes, and "infectious" is more relevant for control purposes. In the study period of 3 yr, repeated sampling of milk (n = 23,219) and feces (n = 8,832) was performed. A total of 1,985 Danish dairy cows provided material for the study. Milk samples were analyzed for antibodies using an ELISA, and fecal samples were analyzed for mycobacteria by culture. A reference test to correctly classify cattle antemortem does not exist; thus, "infection" and "infectious" were defined by repeated testing using one test as the condition to be detected by the other test. Fecal culture responses were evaluated against antibody status, and ELISA responses were evaluated against detected bacterial shedding. The results of this study indicate that the ability of both tests to detect "infection" increases almost linearly from 2 to 5 yr of age, whereas the ability of both tests to detect "infectious" is not affected by age. Purpose-specific tests are required to appropriately interpret and use test results for management of paratuberculosis, and relevant covariates, such as age, should be included when possible.

Effect of egg yolk on the detection of Mycobacterium avium subsp. paratuberculosis using the ESP II liquid culture system

Rapid diagnosis of paratuberculosis in infected cattle is important for the successful control of Johne disease within herds. Thus, improving culture methods for Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis) will aid in the identification of asymptomatic animals. Egg yolk is a component of the media used for growing M. paratuberculosis, but its requirement as a supplement has not been reported. Using the ESP II liquid culture system, 2 different sources and 5 concentrations (3.3%, 1.6%, 0.8%, 0.4%, and 0%) of egg yolk were analyzed. Egg yolk source did not affect either recovery rate or time to detection, but both parameters were significantly improved when the 3.3% egg yolk concentrations (final volume) were used over media containing no egg yolk. This study also assessed the recovery of M. paratuberculosis from fecal samples that were cultured multiple times using Herrold egg yolk agar (HEY). Specimens containing greater than 70 cfu/g feces could routinely be identified as positive for M. paratuberculosis after only 1 culture attempt, whereas specimens with fewer bacteria were only intermittently positive, even after 5 replicate cultures. Therefore, this study indicates that the sensitivity of the Trek Diagnostic ESP II liquid culture system for M. paratuberculosis is affected by egg yolk concentration and that single culture attempts using HEY solid media may not identify specimens containing low numbers of bacteria.

Evaluation of three ELISAs for Mycobacterium avium subsp. paratuberculosis using tissue and fecal culture as comparison standards

Three serum ELISAs for detection of antibodies against Mycobacterium avium subsp. paratuberculosis (Mptb) were evaluated against culture of tissue and feces samples from 994 dairy cows collected at slaughter. Culture of ileum and associated lymph nodes for Mptb were positive for 160 (16.1%) of the 994 cows and 36 (3.6%) were fecal culture-positive for Mptb. Two of the ELISAs evaluated were absorbed indirect assays and the third was a non-absorbed indirect assay. Estimated sensitivities of the absorbed ELISAs when compared to tissue culture were 8.8% and 6.9%, while the unabsorbed ELISA had a sensitivity of 16.9%. Specificities were 97.6%, 96.0% and 90.8%, respectively. When compared to fecal culture, the sensitivities of the absorbed ELISAs were 16.6% and 13.9%, respectively, and the sensitivity of the unabsorbed ELISA was 27.8%. Specificities were 97.1%, 95.9% and 90.1%, respectively. Area under the curve (AUC) of receiver operator characteristic curves for the absorbed ELISAs when tissue culture was the standard were 0.553 and 0.547, while the unabsorbed ELISA had an AUC of 0.540. When fecal culture was the comparison standard, the AUC of the absorbed ELISAs was 0.575 and 0.574, while the unabsorbed ELISA was 0.529. Overall, the sensitivities of the ELISAs when compared to tissue culture were low. The apparent advantage of the unabsorbed ELISA with respect to sensitivity is at the cost of lowered specificity and test accuracy.

Detection of Mycobacterium avium subspecies paratuberculosis in Swiss dairy cattle by real-time PCR and culture: a comparison of the two assays

AIMS

To compare the two different diagnostic assays for the detection of Mycobacterium avium ssp. paratuberculosis, the aetiological agent of paratuberculosis.

METHODS AND RESULTS

Faecal samples were derived from 310 cows, representing 13 commercial dairy herds in various locations in Switzerland with expected increased risk because of a past history of disease. Detection assays for M. avium ssp. paratuberculosis were culture (gold standard) and a newly designed real-time PCR. Real-time PCR identified 31 of 310 animals as positive within this risk population whereas culture identified 20 positive animals. The specificity of real-time PCR was confirmed by DNA sequencing of the PCR product. Depending on the test used, the paratuberculosis prevalence in our tested risk population ranged from 6.5 to 10%.

CONCLUSIONS

Real-time PCR and culture data were in good agreement, and real-time PCR generates data in a short time in contrast to culture.

SIGNIFICANCE AND IMPACT OF THE STUDY

We consider real-time PCR as a suitable alternative method to culture for the detection of M. avium ssp. paratuberculosis in a national surveillance programme.

Fecal shedding of Mycobacterium avium subsp. paratuberculosis by dairy cows

Between 1982 and 2000, fecal samples were obtained from 786 cows that were shedding Mycobacterium avium subsp. paratuberculosis (Map). These cows were resident on 93 Pennsylvania dairies (mean herd size, 64 milk cows) that had no or minimal previous testing for Map. Feces were cultured on four tubes of Herrold's egg yolk medium and the distribution of mean Map colony forming units (CFU) was evaluated. Most cows were light (< 10 CFU/tube, 51.4%) or high (> 50 CFU/tube, 30.8%) fecal shedders with fewer cows in the moderate category (10-50 CFU/tube). Of the 786 cows, 192 (24.4%) had colonies in only one of four tubes. In the multivariable negative binomial model, there were significant associations between mean CFU/tube and prevalence, herd size, and season and an interaction between herd size and season. The linear mixed model of continuous tube counts with a random herd effect yielded similar findings with associations with herd size as a continuous variable, season, and an interaction between categorized prevalence and continuous herd size. Variability in CFU/tube was greatest among cows in the same herd, intermediate for replicate tubes from the same cow, and smallest among cows in different herds. Reduction in the number of replicate tubes from four would have reduced the sensitivity of fecal culture for Map by approximately 6% (for three tubes) to 12% (for two tubes).

Certification of herds as free of Mycobacterium paratuberculosis infection: actual pooled faecal results versus certification model predictions

Dutch dairy herds closed for at least 3 years with no history of paratuberculosis were recruited for a study on herd-certification. One hundred dairy herds were tested for Mycobacterium paratuberculosis at 6-month intervals by pooled faecal culture (five individual animal samples per pool) with solid media. Ninety of the herds completed 9 herd tests and 10 herds dropped out of the study for reasons other than a paratuberculosis diagnosis. Of the 90 herds completing the full study, 61% eventually were found to be M. paratuberculosis-infected. The number of infected herds detected decreased with each round of testing. Assuming that all infected herds had been detected by the ninth herd test, the observed percentage of herds that were truly noninfected (P-free) after each round of testing was calculated. The observed P-free was compared to the predicted P-free based on a previously reported herd-certification model. The P-free predicted by the model was significantly different from the observed P-free. When a single assumption in the model was changed and a diagnostic sensitivity of 40-50% was selected, the predicted P-free closely approximated the observed P-free for the 90 Dutch dairy herds studied. The critical assumption that was changed for Version 2.0 of the model was within-herd infection prevalence for infected but test-negative herds after each round of serial testing. Model Version 1.0 had assumed a 50% decrease in within-herd prevalence but Version 2.0 assumed a stable within-herd prevalence. Culture of pooled faecal samples provides a high-sensitive, high-specific, low-cost test for herd-certification programs.

Simulation of alternatives for the Dutch Johne's disease certification-and-monitoring program

To identify optimal method(s) for certification and subsequent monitoring of Mycobacterium avium subsp. paratuberculosis (Map)-unsuspected herds, certification-and-monitoring schemes were studied using a stochastic simulation model ("JohneSSim"). JohneSSim simulated the within-herd transmission and economic aspects of Map in closed Dutch dairy herds. The model was validated with field observations on Map-unsuspected herds. The current Dutch certification-and-monitoring schemes were compared with 11 alternative schemes in which individual and pooled fecal culture, ELISA, Johnin-intradermal test and gamma-IFN ELISA were used, varying the test frequency, tested age group and number of tested animals. On reaching the 'Map-free' status with the standard certification scheme, 11% of the simulated herds were not truly Map-free. Therefore, the designation 'Map-free' should be changed into, for instance, 'low-risk Map'. In the most-attractive alternative certification scheme, the 'Map-free' status was reached after four herd examinations (at 2-year intervals) consisting of serial testing of all cattle > or = 2 years of age with a pooled fecal culture and individual fecal culture of positive pools. This scheme resulted in lower total and annual discounted costs and a lower animal-level prevalence at reaching the 'Map-free' status compared to the standard scheme, assuming that there was no new introduction of the infection. Schemes to monitor the 'Map-free' status were compared, assuming that this status was reached with the standard certification scheme. In comparison to the standard monitoring scheme, none of the alternative monitoring schemes resulted in both a lower animal-level prevalence of undetected pre-existing Map infections in closed herds, and lower median annual discounted costs. Results of the model were very sensitive to the assumed sensitivity of the fecal culture test and to management measures that prevent within-herd transmission of Map. If these preventive measures were taken, the probability of undetected Map infections in closed 'Map-free' herds was decreased substantially.

Development of a polymerase chain reaction test to confirm Mycobacterium avium subsp. paratuberculosis in culture

A polymerase chain reaction (PCR) assay for confirmation of Mycobacterium avium subsp. paratuberculosis was developed using the primer set derived from ISMav2. The PCR product was 494 base pairs (bp) and could be digested with ClaI, which produced 311- and 183-bp fragments. No amplification of 494-bp DNA fragment was detected from DNA of other Mycobacterium spp., including Mycobacterium avium complex, other bacteria, including Escherichia coli, Pseudomonas aeruginosa, Actinobacillus pleuropneumoniae, Leptospira interrogans serovar pomona, Corynebacterium pseudotuberculosis, Salmonella typhimurium, Borrelia burgdorferi, and Staphylococcus aureus, and the Scedosporium sp. This PCR assay could detect 5-8 genome equivalents.

Evaluation of IS900-PCR Assay for Detection ofMycobacterium aviumSubspeciesParatuberculosisInfection in Cattle Using Quarter Milk and Bulk Tank Milk Samples

A study was conducted to evaluate sensitivity, specificity, and predictive value of IS900-PCR assay for detection of Mycobacterium avium subspecies paratuberculosis in pooled quarter milk and bulk tank milk. Feces, blood and pooled quarter milk from 1493 lactating cattle on 29 herds were analyzed. Bulk tank milk (n = 29 bulk tanks) samples were also examined. Culture analysis revealed that 10.9%, 2.8%, and 20.6% of fecal, pooled quarter milk samples and bulk tanks were positive for M. avium subsp. paratuberculosis, respectively. While 13.5% and 27.5% of pooled quarter milk samples and bulk tanks were positive by IS900 PCR assay, respectively. Moderate to high antibody titers for M. avium subsp. paratuberculosis were detected in 223 of 1493 (14.4%) cows. Cows positive on fecal culture were taken as true positives relative to which the IS900 PCR assay was evaluated. The sensitivity and predictive value of KELA, pooled quarter milk culture, and IS900 PCR assay increased with lactation age. While the specificity of the tests decreased with increase in lactation age. Overall, the IS900 PCR assay using pooled quarter milk samples had a sensitivity, specificity and predictive value of 0.87, 0.95 and 0.71, respectively. The IS900 PCR assay using bulk tank milk had poor sensitivity (0.21), specificity (0.5) and predictive value (0.6). Pooled quarter milk culture analysis had a very low sensitivity (0.17). The kinetics ELISA had lower sensitivity (0.59), specificity (0.90) and predictive value (0.43) as compared to the IS900 PCR assay using pooled quarter milk samples. Results from our study suggest that IS900 PCR assay using bulk tank milk may not be useful for screening herds with M. avium subsp. paratuberculosis infected animals. In conclusion, use of IS900 PCR assay for cows in 2(nd) lactation and higher, using aseptically collected pooled quarter milk samples, can be a useful tool for screening and monitoring lactating cattle in herds with M. avium subsp. paratuberculosis infection.

Evaluation of four DNA extraction methods for the detection of Mycobacterium avium subsp. paratuberculosis by polymerase chain reaction

Polymerase chain reaction (PCR) has been widely used due to its high specificity, sensitivity, and rapid turn-around time. However, inhibitory factors may be co-extracted with the target nucleic acid that will hinder the performance of PCR. In this study, DNA extraction methods for Mycobacterium avium subsp. paratuberculosis were evaluated including rapid lysis, organic extraction, silica-based and magnetic particle-based (MagaZorb) technologies on bacterial cells, and spiked bovine feces. Efficiency of the extraction was determined by PCR end point titration with primers targeting the insertion sequence, IS900. Results of the end point titrations are identical for bacterial cells and spiked feces. Inhibition was observed in PCR with DNA isolated from spiked feces, and a 1/100 dilution was able to alleviate this problem with DNA extracted by MagaZorb. A 1/1000 dilution was required for the other three methods. MagaZorb proved to be more efficient at removing inhibitory factors and required the least labor and completion time. Further evaluation is required for its utilization in other clinical specimens.

Development of the Dutch Johne's disease control program supported by a simulation model

The development of a simulation model, "JohneSSim", was part of a research program aimed at designing a national Johne's disease control program for The Netherlands. Initially, the focus was mainly directed towards different compulsory "test-and-cull" strategies. However, the results from the JohneSSim model showed that eradication of Johne's disease based on such strategies would not be possible within 20 years and that it was also economically unattractive. However, improved calf management seemed to be more effective in reducing the prevalence within the same time period. Simulation of a strategy using an "ideal test" (80% sensitivity in all infected animals) showed a considerably faster decrease in prevalence. However, this strategy proved to be economically unattractive because of the high culling rate of (young) test-positive animals. The simulation model was also adapted to study beef cow herds. However, the results indicated that none of the strategies were able to reduce the mean true prevalence to almost zero for such herds. Only strategies based on "separation of calves and adult animals" proved to significantly reduce the prevalence but such a strategy is unpractical and uneconomic for Dutch beef cow herds. Due to this finding and the relative low number of Dutch beef cow farms, first priority has been given to the development of a Johne's disease control program for dairy farms. Based on the results of the "JohneSSim" model, the new national voluntary Johne's disease control program for dairy, Paratuberculosis Program Netherlands (PPN), started in September 2000. The PPN is based on a stepwise improvement of calf hygiene, with little dependency on "test and culling". The model results indicated that, if dairy farmers consistently carried out the necessary management adaptations, PPN considerably decreased prevalence and that it was economically more attractive than any previous plans.

The results of using faecal culture as confirmation test of paratuberculosis-seropositive dairy cattle

A total of 15,822 cattle aged 3 years and older, belonging to 378 randomly selected herds, were tested for paratuberculosis using an absorbed enzyme-linked immunosorbent assay (ELISA); 3.3% tested positive. This percentage was lowest for the group of cattle aged 3-4 years (2.3%) and highest for cattle with the age of 5-6 years (4.5%). The mean Sample to Positive (S/P) ratio of seropositive cattle vaccinated against paratuberculosis was higher (0.75 +/- 0.33) than that of seropositive, non-vaccinated cattle (0.58 +/- 0.26). Faecal samples of 422 ELISA-positive cattle were cultured for the presence of Mycobacterium avium subsp. paratuberculosis, 12% of these were contaminated. The percentage of non-contaminated samples with positive culture results was 17.3%, with a substantial difference between vaccinated (1.7%) and non-vaccinated cattle (20.2%). Of the positive cultures, the number of colonies varied from 1-10 (22% of cultures), 11-100 (22%), to more than 100 (55%). The percentage of ELISA-positive, non-vaccinated cattle tested culture-positive was positively correlated with the magnitude of the S/P ratio. This percentage varied from 12% (S/P ratio 0.3-0.5) to 58% (S/P ratio > 1.1), a result that might have implications for interpretation of the test. In this study, the percentage of ELISA-positive cattle with positive faecal culture results was limited and these individuals were mostly moderate to heavy shedders.

Detection by immunomagnetic PCR of Mycobacterium avium subsp. paratuberculosis in milk from dairy goats in Norway

Milk samples from 340 individual goats in 34 dairy herds throughout Norway were examined for Mycobacterium avium subsp. paratuberculosis (M.a. paratuberculosis) by culture and immunomagnetic separation combined with PCR (IMS-PCR). The samples included three categories; (A) vaccinated dairy goats in herds with paratuberculosis; (B) vaccinated dairy goats in herds with no history of paratuberculosis; (C) unvaccinated goats in herds with no history of paratuberculosis. Viable M.a. paratuberculosis were not detected by culture in any sample, but 24 samples (7.1%) tested positive by IMS-PCR when the PCR products were visualised by dot blot hybridisation. PCR products from five milk samples originating from five different herds were sequenced; all showed 99% homology with the IS900 sequence from M.a. paratuberculosis.M.a. paratuberculosis were detected in all sampled categories. The percentage of IMS-PCR positive samples from herds where paratuberculosis had previously been reported was significantly lower than from herds where the infection had never been diagnosed (3.3 and 9.1%, respectively, P=0.048). Similar proportions of milk samples from vaccinated and non-vaccinated goats tested positive for the presence of M.a. paratuberculosis. Vaccinated goats older than 4 years tested positive more often than vaccinated animals less than 2 years old. Samples collected in May tested significantly more often positive than milk sampled during February-March (13.8 and 2.9%, respectively, P=0.001). This study showed that raw goats' milk in Norway might be contaminated with M.a. paratuberculosis.

Evaluation of two absorbed enzyme-linked immunosorbent assays and a complement fixation test as replacements for fecal culture in the detection of cows shedding Mycobacterium avium subspecies paratuberculosis

Control of paratuberculosis in dairy herds is based on preventing the transmission of Mycobacterium avium subsp. paratuberculosis (Mptb) from cows to calves by management measures, supported by removal of cows excreting these bacteria by the fecal route (Mptb shedders). Fecal culture is the most accurate test for identifying Mptb shedders, but this technique is expensive and takes up to 16 weeks for results to be available. Serologic tests are inexpensive, rapid, and easy to perform. Of serologic tests, the complement fixation test (CFT) and absorbed enzyme-linked immunosorbent assay (ELISA) are the serologic tests used most frequently; the CFT is considered less accurate than the ELISA with respect to sensitivity and specificity. The commonly accepted absorbed ELISA is from the Australian Central Serum Laboratory. However, a European supplier has marketed a second ELISA that is supposed to be more sensitive in detecting Mptb shedders. These 2 absorbed ELISAs, designated ELISA-A and ELISA-B, and an in-house CFT were compared with data from 2 serum panels. The Mptb shedding panel consisted of sera from 198 culture-positive cows from 53 infected herds. The method used for culture of fecal samples was a modified Jørgensen method on individual samples. The Mptb shedder detection rate by the 3 serologic tests ranged from 29.8% to 39.4%. Detection rate for ELISA-A was lower than that for ELISA-B and CFT. For all 3 tests, detection rate was dependent on the level of Mptb shedding and the age of the animals. Detection rates increased as cattle age increased to 4 years. The specificity panel was initially composed of sera from 811 cows randomly selected from 41 herds without clinical paratuberculosis that were negative for Mptb based on whole-herd fecal culture. The modified Jørgensen method for culture was used on pooled fecal samples. Serologic test specificity ranged from 93.4% to 99.8%. The specificity of ELISA-A was higher than that of ELISA-B and CFT. Specificity of ELISA-B between herds was 75-100%. Specificity of CFT between herds was 62-100%. The low specificity of ELISA-B and CFT could not be explained by a higher sensitivity for Mptb-infected cows before onset of shedding, because in the 19 herds with 8 more subsequent negative whole-herd fecal cultures in the 4 years after sampling, specificity was not improved. The insufficient specificity of ELISA-B was not corrected sufficiently by heightening the cutoff value because Mptb shedder detection rate was lowered to 28.9%, equal to that of ELISA-A, and specificity only rose to 97%, much lower than that of ELISA-A. Taking into account the different test characteristics, serologic tests are a cost-effective alternative to fecal culture in high-prevalence herds. For certification programs, only ELISA-A is recommended because in a large number of nonsuspect herds specificity remained almost 100%.

Application of IS900 PCR for detection of Mycobacterium avium subsp. paratuberculosis directly from raw milk

A polymerase chain reaction (PCR)-based assay was developed for detection of insertion sequence 900 (IS900) of Mycobacterium avium subsp. paratuberculosis in raw milk. This IS900 PCR assay included DNA extraction and PCR assay using commercially available kits. The DNA extraction and PCR assay were optimized to detect the IS900 sequence directly from raw milk. The IS900 PCR assay was evaluated by inoculating raw bulk milk and Middlebrook's 7H9 broth with 0 to 10(8) cfu/ml of each of four American Type Culture Collection strains of M. paratuberculosis. Under experimental conditions, both milk culture on Herrold's egg yolk medium slants, and IS900 PCR could detect 10 to 100 cfu/ml of M. paratuberculosis. Detection of M. paratuberculosis by IS900 PCR was consistent (24/24 PCR assays) when about 100 cfu/ml were present, whereas detection was variable (12/24 PCR assays) at concentrations as low as 10 cfu/ml. Based on the findings of the experimental study, IS900 PCR was further evaluated with pooled quarter milk samples from 211 cows from five herds with known history of Johne's disease. Out of 211 animals examined, nine (4%) and 69 (33%) were positive for M. paratuberculosis by milk culture and IS900 PCR from milk, respectively. A total of 20 bulk tank milk sample aliquots (one sample, four aliquots from each herd) were also examined, of which 10 (50%) were positive for M. paratuberculosis by IS900 PCR. By contrast, only one out of 20 (5%) bulk tank milk sample aliquots was positive by culture. The IS900 PCR amplified product of 229-bp obtained on testing of quarter milk and bulk tank milk samples was confirmed to be the IS900 of M. paratuberculosis by DNA sequence analysis. The results of this study suggest that M. paratuberculosis can be detected directly from quarter milk and bulk tank milk by IS900 PCR.

Paratuberculosis with special reference to cattle. A review

Paratuberculosis is a chronic, granulomatous enteritis caused by Mycobacterium avium subspecies paratuberculosis affecting domestic and wild ruminants. The symptoms of clinical paratuberculosis are chronic diarrhoea and progressive weight loss while subclinically infected animals mainly have decreased production. The infection is widespread throughout the world and causes substantial financial losses for the farming industry. One of the major obstacles in the control of this disease, is the difficulty of identifying subclinically infected animals. This review gives a summary of several aspects of paratuberculosis including clinical importance, pathology, immunology and properties of the infectious agent. Special emphasis will be on the available diagnostic methods, their use and limitations.

Culture of strategically pooled bovine fecal samples as a method to screen herds for paratuberculosis

Fecal samples from 733 cows in 11 dairy herds with a low prevalence of paratuberculosis were cultured for the presence of Mycobacterium avium subsp. paratuberculosis both individually and after combining (pooling) in groups of 5. The culture procedure was the modified Jorgensen method, which uses NaOH and oxalic acid for decontamination and modified Lowenstein-Jensen agar slants for cultivation. Pooling was performed by mixing fecal samples from 5 animals ordered by age, herein referred to as strategic pooling. Culture of individual fecal samples detected M. a. paratuberculosis infections in 43 of the 733 cows and 7 of 11 infected herds (herd sensitivity = 64%). Culture of pooled fecal samples detected M. a. paratuberculosis in 28 of 151 pooled samples representing 8 of the infected 11 herds (herd sensitivity = 73%). Feces of the 43 culture-positive cows was included in 32 pools: of these 32 pools, 26 were culture positive and 6 were culture negative. In addition to the 26 positive pools containing feces from cows that were found culture positive on individual fecal samples, another 2 pools were culture positive, although comprised of feces from cows with negative results after culture of individual fecal samples. From the total of 45 infected cows that were found (43 by individual fecal culture and an additional 2 by pooled fecal culture), individual fecal culture detected 43 of these 45 (96%), while pooled fecal culture detected 39 (87%). Culture of strategically pooled fecal samples using the modified Jorgensen method was equivalent in herd sensitivity to the culture of individual fecal samples and is significantly less expensive.

Duplex PCR for differential identification of Mycobacterium bovis, M. avium, and M. avium subsp. paratuberculosis in formalin- fixed paraffin-embedded tissues from cattle

We previously isolated and sequenced two genomic segments of Mycobacterium avium subsp. paratuberculosis, namely, f57, a species-specific sequence, and the p34 gene, coding for a 34-kDa antigenic protein. Comparison of sequences upstream of the p34 open reading frame (us-p34) from M. avium subsp. paratuberculosis and M. tuberculosis showed a 79-base deletion in M. tuberculosis. Sequence analysis of the p34 genes in another two species, M. bovis (strain BCG) and M. avium (strain D4), confirmed the differences observed between tuberculous and nontuberculous species. A duplex diagnostic PCR strategy based on coamplification of nonhomologous us-p34 and species-specific f57 sequences was therefore developed. Duplex PCR yielded three different patterns, specific either for tuberculous bacilli (M. tuberculosis, M. bovis, and M. africanum), for both nontuberculous mycobacteria M. avium and M. intracellulare, or for M. avium subsp. paratuberculosis. The specificity of this single-step DNA-based assay was assessed on DNA from cultured mycobacterial strains, as well as on a panel of formalin-fixed and paraffin-embedded tissues from cattle. Molecular assay results from tissular DNA were compared to conventional bacteriological and histological test results, including those obtained by Ziehl-Neelsen staining on tissue biopsy specimens. Molecular discrimination was successful and confirmed the value of duplex us-p34 and f57 sequence amplification for differential diagnosis of tuberculosis, paratuberculosis, or infections caused by other members of the M. avium complex.