Estimation of sensitivity and specificity of bacteriology, histopathology and PCR for the confirmatory diagnosis of bovine tuberculosis using latent class analysis

Insights into mycobacteriome composition in Mycobacterium bovis-infected African buffalo (Syncerus caffer) tissue samples

Animal tuberculosis significantly challenges global health, agriculture, and wildlife conservation efforts. Mycobacterial cultures are resource-intensive, time-consuming, and challenged by heterogeneous populations. In this study, we employed a culture-independent approach, using targeted long-read-based next-generation sequencing (tNGS), to investigate the mycobacterial composition in 60 DNA samples extracted from Mycobacterium bovis infected culture-confirmed African buffalo tissue. We detected mycobacterial DNA in 93.3% of the samples and the sensitivity for detecting Mycobacterium tuberculosis complex (MTBC) was 91.7%, demonstrating a high concordance of our culture-independent tNGS approach with mycobacterial culture results. In five samples, we identified heterogenous mycobacterial populations with various non-tuberculous mycobacteria, including members of the Mycobacterium avium complex (MAC), M. smegmatis, and M. komaniense. The latter Mycobacterium species was described in South Africa from bovine nasal swabs and environmental samples from the Hluhluwe-iMfolozi Park, which was the origin of the buffalo samples in the present study. This finding suggests that exposure to environmental mycobacteria may confound detection of MTBC in wildlife. In conclusion, our approach represents a promising alternative to conventional methods for detecting mycobacterial DNA. This high-throughput technique enables rapid differentiation of heterogeneous mycobacterial populations, which will contribute valuable insights into the epidemiology, pathogenesis, and microbial synergy during mycobacterial infections.

Pathological findings and differential diagnoses of lymph node diseases in slaughtered cattle in Brazil: A study of 2000 samples

Slaughterhouse inspections play a crucial role in the sanitary control of zoonoses and foodborne diseases. This study aimed to identify and analyze the frequencies of lymph node diseases in cattle slaughtered for human consumption, using the samples sent to the anatomic pathology service of the Federal Laboratory for Agricultural Defense (Laboratório Federal de Defesa Agropecuária), Minas Gerais, Brazil, from January 2015 to September 2022. In total, 2000 lymph node samples were analyzed, and additional information was individually retrieved. Lesions were most frequently identified in thoracic lymph nodes. Bacterial isolation and quantitative polymerase chain reaction (qPCR) were performed using samples suspected of tuberculosis. Tuberculosis cases accounted for 89.3% of the samples. Histopathology was more sensitive than other ancillary tests for diagnosing tuberculosis. Paraffin-embedded tissues from lymphoma cases were subjected to immunophenotyping using anti-CD3 and anti-CD79a immunohistochemistry. Frozen and/or paraffin-embedded tissues from lymphoma cases were used to identify the enzootic bovine leukosis (EBL) retrovirus through qPCR. Other diagnoses included primary (T- and B-cell lymphoma) and metastatic neoplasms (squamous cell carcinoma, pulmonary adenocarcinoma, undifferentiated carcinoma, undifferentiated adenocarcinoma, undifferentiated sarcoma, undifferentiated round cell tumor, mesothelioma, hepatic carcinoid, meningioma, and seminoma), actinogranulomas (pyogranulomatous lymphadenitis [actinobacillosis and actinomycosis]), idiopathic lymphadenitis (neutrophilic and/or histiocytic, granulomatous, and suppurative), and miscellaneous nonspecific lymphadenopathies (depletion/lymphoid atrophy, lymphangiectasia, erythrocyte drainage, parasitic eosinophilic lymphadenitis, follicular hyperplasia, and toxic granulomatous lymphadenitis). The combination of histopathology with complementary techniques is important for successful diagnosis, especially in complex cases of high epidemiological, economic, and zoosanitary importance, such as tuberculosis and EBL.

Assessment of the diagnostic performance of intradermal tuberculin test and post-mortem inspection for the diagnosis of bovine tuberculosis according to WOAH guidelines

Bovine tuberculosis (bTB) constitutes a global challenge for public and animal health with still some deficiencies regarding its diagnosis. This study aimed to estimate the accuracy of the single intradermal tuberculin test (SIT) and post-mortem inspection for different diagnostic objectives following WOAH guidelines. Tissue samples from 59 microbiological culture/PCR-positive and 58 microbiological culture/PCR-negative cattle were evaluated. The diagnostic sensitivity and specificity, the positive and negative probability indices as well as the positive and negative predictive values (PPV and NPV) of each technique were estimated for different pretest probabilities. The SIT with strict interpretation demonstrated moderate precision in confirming the absence of infection in populations historically free of bTB, with a 12.1% rate of false positives, but also detecting positive animals in the early stage of the eradication programs, with a 13.6% rate of false negatives. The diagnostic performance for ruling out bTB was notably high (NPV > 90%) in animals with a pre-test probability (PTP) below 42%. Post-mortem inspection constituted an interesting alternative tool to confirm suspected and positive cases for SIT, particularly in areas with bTB prevalence exceeding 19%, where implementing SIT and eradication measures may be impractical. In these areas, the likelihood that animals with tuberculosis-like lesions are affected by the disease surpasses 90%. Similarly, in herds with a PTP below 25%, the absence of bTB could be confidently ruled out with over 90% certainty. These findings highlight the effectiveness of SIT and post-mortem inspection as valuable techniques for current eradication programs and controlling bTB in high-prevalence areas where molecular techniques may not be feasible.

Bacteriological culture and direct PCR for detecting the Mycobacterium tuberculosis complex in the Italian eradication campaign: a decade of experience at the National Reference Laboratory

AIMS

Our study evaluates the capacity of direct real-time PCR for detecting Mycobacterium tuberculosis complex (MTBC), with a focus on diagnostic performances and the feasibility of implementing this protocol in an eradication campaign. Specifically, we compare the effectiveness of the direct PCR method to various culture systems used by the Italian National Reference Laboratory over the last decade to detect MTBC.

METHODS AND RESULTS

Bovine tissue samples were routinely tested and analyzed for bovine tuberculosis (bTB) confirmation using microbiological culture (solid and liquid media), histopathological analysis, and a direct PCR assay targeting IS6110, an insertion sequence specific to the MTBC that is widely used for tuberculosis diagnosis. The direct real-time PCR demonstrated a high concordance (K = 0.871) with microbiological culture, as well as good sensitivity (91.84%) and specificity (95.24%). In contrast, histopathology demonstrated lower concordance (K = 0.746) and performance levels (sensitivity 91.41%, specificity 82.88%). Liquid media promoted faster and more efficient growth of MTBC than solid media. M. bovis and M. caprae had the comparable ability to respond to the direct real-time PCR test and grow on the microbiological medium.

CONCLUSIONS

This study confirms that direct real-time PCR can detect MTBC with high diagnostic accuracy within a few days. This study found no significant differences in performance between culture media and direct PCR for M. bovis and M. caprae.

Droplet digital PCR as alternative to microbiological culture for Mycobacterium tuberculosis complex detection in bovine lymph node tissue samples

Introduction

Bovine tuberculosis (bTB) caused by Mycobacterium tuberculosis complex (MTC) remains a significant concern for public health. Direct real-time PCR and droplet digital PCR (ddPCR) are proposed as alternative tools to enhance diagnostic precision and efficiency. This study aims to assess the diagnostic performance of a ddPCR assay targeting IS6110 for the detection of MTC DNA in both microbiological culture and fresh lymph node (LN) tissue samples obtained from cattle, in comparison with the established reference standard, the microbiological culture followed by real-time PCR.

Methods

The fresh LNs (N=100) were collected each from a different cattle carcass at the slaughterhouse. The limit of detection of ddPCR-IS6110 was set to 101 copies per 20 μl reaction.

Results

DdPCR-IS6110 detected 44 out of 49 reference-standard positive samples and yielded negative results in 47 out of 51 reference-standard negative samples, resulting in adjusted sensitivity (Se) and specificity (Sp) of 90.76% [95% confidence interval (CI): 82.58 - 98.96%)], and 100% (95% CI: 100%) respectively. The estimated adjusted false negative rate (FNR) was 9.23% (95% CI: 1.04 - 17.42%) and the false positive rate (FPR) was 0% (95% CI: 0%). When directly applied from fresh bovine LN tissues, ddPCR-IS6110 identified 47 out of 49 reference-standard positive samples as ddPCR-IS6110-positive and 42 out of 51 reference-standard negative samples as ddPCR-IS6110-negative, resulting in adjusted Se and Sp values of 94.80% [95% (CI): 88.52 - 100%] and 100% (95% CI: 100%), respectively. The adjusted FNR was 5.20% (95% CI: 0 - 11.50%) and the FPR was 0% (95% CI: 0%). Noteworthy, ddPCR-IS6110 disclosed as positive 9 samples negative to reference-standard.

Discussion

DdPCR-IS6110 proved to be a rapid, highly sensitive, and specific diagnostic tool as an alternative to reference-standard method.

Comparative analysis of tuberculin and defined antigen skin tests for detection of bovine tuberculosis in buffaloes (Bubalus bubalis) in Haryana state, India

BACKGROUND

Bovine tuberculosis (bTB) is a chronic disease that results from infection with any member of the Mycobacterium tuberculosis complex. Infected animals are typically diagnosed with tuberculin-based intradermal skin tests according to World Organization of Animal Health which are presently in use. However, tuberculin is not suitable for use in BCG-vaccinated animals due to a high rate of false-positive reactions. Peptide-based defined skin test (DST) antigens have been identified using antigens (ESAT-6, CFP-10 and Rv3615c) which are absent from BCG, but their performance in buffaloes remains unknown. To assess the comparative performance of DST with the tuberculin-based single intradermal test (SIT) and the single intradermal comparative cervical test (SICCT), we screened 543 female buffaloes from 49 organized dairy farms in two districts of Haryana state in India.

RESULTS

We found that 37 (7%), 4 (1%) and 18 (3%) buffaloes were reactors with the SIT, SICCT and DST tests, respectively. Of the 37 SIT reactors, four were positive with SICCT and 12 were positive with the DST. The results show that none of the animals tested positive with all three tests, and 6 DST positive animals were SIT negative. Together, a total of 43 animals were reactors with SIT, DST, or both, and the two assays showed moderate agreement (Cohen's Kappa 0.41; 95% Confidence Interval (CI): 0.23, 0.59). In contrast, only slight agreement (Cohen's Kappa 0.18; 95% CI: 0.02, 0.34) was observed between SIT and SICCT. Using a Bayesian latent class model, we estimated test specificities of 96.5% (95% CI, 92-99%), 99.7% (95% CI: 98-100%) and 99.0% (95% CI: 97-100%) for SIT, SICCT and DST, respectively, but considerably lower sensitivities of 58% (95% CI: 35-87%), 9% (95% CI: 3-21%), and 34% (95% CI: 18-55%) albeit with broad and overlapping credible intervals.

CONCLUSION

Taken together, our investigation suggests that DST has a test specificity comparable with SICCT, and sensitivity intermediate between SIT and SICCT for the identification of buffaloes suspected of tuberculosis. Our study highlights an urgent need for future well-powered trials with detailed necropsy, with immunological and microbiological profiling of reactor and non-reactor animals to better define the underlying factors for the large observed discrepancies in assay performance, particularly between SIT and SICCT.

Performance of IS6110-LAMP assay for detection of Mycobacterium tuberculosis complex in blood and urine samples from patients with extrapulmonary tuberculosis

BACKGROUND

The diagnosis of extrapulmonary tuberculosis (EPTB) shows numerous difficulties because of non-specific symptomatology and low sensitivity of conventional methods. Loop-mediated isothermal amplification (LAMP) is a fast and low-cost technique, which can amplify under isothermal conditions an amount of target DNA copies into approximately a billion copies.

OBJECTIVE

The present study aimed to evaluate a IS6110-LAMP system for Mycobacterium tuberculosis detection in blood and urine samples from patients with EPTB.

METHODS

The collected samples (n = 122) were stratified in two groups: Group EPTB - patient samples with confirmed EPTB (n = 61); Group non-TB - patient samples without TB (n = 61). The urine samples underwent decontamination, and the components of blood samples were separated (plasma and PBMC). DNA extractions were performed in all biological samples followed by IS6110-LAMP assay technique. The detection limit was evaluated through dilution curves (1:10) using Mtb reference strain (H37Rv) genomic DNA.

FINDINGS

The detection limit of IS6110-LAMP was 10 fg/μL (∼10-20 bacilli/μL). The IS6110-LAMP technique sensitivity and specificity were 95.65 % and 79.25 %, respectively, with a general kappa agreement index of 0.762.

MAIN CONCLUSIONS

Based on these results, IS6110-LAMP test showed considerable diagnostic parameters, being able to aid in the speed and accuracy of the final EPTB diagnosis.

Animal tuberculosis control in a disease-free country, France: does the long and winding road really lead to eradication?

It took France almost fifty years to attain its officially animal tuberculosis (TB) free status in 2000, granting the country a favourable position for international live animal trading. The initial TB control program has been adapted at different times in its history in order to suit changing epidemiological contexts: it was first focused on detection and elimination of infected animals while later on protecting TB free herds became a priority.In spite of all the efforts put into the program, final eradication has still not been achieved. Instead, the eradication process has stalled, most probably due to changes in breeding practices in the last 30 years. Indeed, the beef industry has overtaken the milk industry, which has led to the occurrence of new TB risks. Novel epidemiological situations in some regions of extensive beef cattle farming, where wildlife species (wild boar, badger) are also infected, have emerged. More adapted measures have thus been implemented, progressively evaluated and improved in order to reinforce prevention of infection, to follow up with the eradication goal and to strengthen, coordinate and re-motivate field resources. These include, among others, introduction of biosecurity measures in the herd, risk based surveillance and management of wildlife and cattle, improvement of screening in the field and at the abattoir, better diagnosis, but also improvement of communication, awareness, training activities of the main field actors. Very importantly, this new plan has been established through the participation of the majority of involved stakeholders -the farmer industry, hunter associations, veterinarians, scientists and the government-, through coordinated specific steering committees and ad hoc working groups.Without doubt, the main challenge for the next few years is reinforcing communication to encourage and strengthen the program in an already faltering agro-social system. In addition, it will be essential to continue sustaining national research and international collaborations to feed the program with relevant scientific data enabling the authorities to undertake the most pertinent measures for tackling the disease in the short term.

LAP-MALDI MS Profiling and Identification of Potential Biomarkers for the Detection of Bovine Tuberculosis

Detecting bovine tuberculosis (bTB) primarily relies on the tuberculin skin test, requiring two separate animal handling events with a period of incubation time (normally 3 days) between them. Here, we present the use of liquid atmospheric pressure (LAP)-MALDI for the identification of bTB infection, employing a three-class prediction model that was obtained by supervised linear discriminant analysis (LDA) and tested with bovine mastitis samples as disease-positive controls. Noninvasive collection of nasal swabs was used to collect samples, which were subsequently subjected to a short (<4 h) sample preparation method. Cross-validation of the three-class LDA model from the processed nasal swabs provided a sensitivity of 75.0% and specificity of 90.1%, with an overall classification accuracy of 85.7%. These values are comparable to those for the skin test, showing that LAP-MALDI MS has the potential to provide an alternative single-visit diagnostic platform that can detect bTB within the same day of sampling.

Optimization of real-time PCR protocols from lymph node bovine tissue for direct detection of Mycobacterium tuberculosis complex

Bovine tuberculosis (bTB) is a zoonotic disease and a global health problem that is subjected to obligatory eradication programs in the European Union. Microbiological culture is an imperfect technique for bTB diagnosis. This study aims to compare and validate two DNA isolation protocols and three different specific DNA targets, IS6110, IS4, and mpb70, to confirm Mycobacterium tuberculosis complex (MTC) infection by real-time PCR directly from fresh tissue samples. Fresh lymph node samples were collected from 81 cattle carcasses at the slaughterhouse. A comparison of both extraction protocols was performed with IS6110-real-time PCR, showing an adjusted sensitivity (SE) of 78.34% and 95.9% for protocols 1 and 2, respectively, while the specificity (SP) was 100% in both cases. Afterward, the comparison between IS4 and mpb70 targets was performed from the samples extracted with protocol 2, obtaining an adjusted SE of 90.87% and 83.3%, respectively, and an SP of 100% in both cases. The positive likelihood ratio was ∞ for the three targets, and the negative likelihood ratio was 0.04, 0.091, and 0.16 for IS6110, IS4, and mpb70, respectively. Negative predictive values were ≥90%, ≥85%, and ≥80% for real-time PCR targeting IS6110, IS4, and mpb70, respectively, when the true prevalence is ≤60%, and the positive predictive value is 100% in any scenario of true prevalence. According to these results, the DNA extraction protocol 2 and real-time PCR targeting IS6110 or IS4 could be potential first-choice molecular assays to detect MTC directly in fresh bovine tissue samples. IMPORTANCE Bovine tuberculosis (bTB), a chronic infectious and zoonotic disease caused by Mycobacterium tuberculosis complex (MTC), is considered a neglected disease of global importance, causing a detrimental impact on public health, particularly in developing countries where tuberculosis remains a major health problem. However, debate around the efficacy of control measures is still an ongoing matter of concern, with poor diagnostic performance being considered one of the most relevant factors involved in the failure to eradicate the disease since many truly infected animals will be misclassified as bTB-free. This study highlights a DNA extraction protocol and real-time PCR targeting IS6110 or IS4 as potential first-choice molecular assays to detect MTC directly in fresh bovine tissue samples, providing rapid, highly sensitive, and specific diagnostic tools as an alternative to microbiology, which could take up to 3 months to complete, shortening the turnaround time for decision makers to be promptly informed.

Detection of Mycobacterium tuberculosis complex field infections in cattle using fecal volatile organic compound analysis through gas chromatography-ion mobility spectrometry combined with chemometrics

Bovine tuberculosis is considered a re-emerging disease caused by different species from the Mycobacterium tuberculosis complex (MTC), important not only for the livestock sector but also for public health due to its zoonotic character. Despite the numerous efforts that have been carried out to improve the performance of the current antemortem diagnostic procedures, nowadays, they still pose several drawbacks, such as moderate to low sensitivity, highlighting the necessity to develop alternative and innovative tools to complement control and surveillance frameworks. Volatilome analysis is considered an innovative approach which has been widely employed in animal science, including animal health field and diagnosis, due to the useful and interesting information provided by volatile metabolites. Therefore, this study assesses the potential of gas chromatography coupled to ion mobility spectrometry (GC-IMS) to discriminate cattle naturally infected (field infections) by MTC from non-infected animals. Volatile organic compounds (VOCs) produced from feces were analyzed, employing the subsequent information through chemometrics. After the evaluation of variable importance for the projection of compounds, the final discriminant models achieved a robust performance in cross-validation, as well as high percentages of correct classification (>90%) and optimal data of sensitivity (91.66%) and specificity (99.99%) in external validation. The tentative identification of some VOCs revealed some coincidences with previous studies, although potential new compounds associated with the discrimination of infected and non-infected subjects were also addressed. These results provide strong evidence that a volatilome analysis of feces through GC-IMS coupled to chemometrics could become a valuable methodology to discriminate the infection by MTC in cattle. IMPORTANCE Bovine tuberculosis is endemic in many countries worldwide and poses important concerns for public health because of their zoonotic condition. However, current diagnostic techniques present several hurdles, such as low sensitivity and complexity, among others. In this regard, the development of new approaches to improve the diagnosis and control of this disease is considered crucial. Volatile organic compounds are small molecular mass metabolites which compose volatilome, whose analysis has been widely employed with success in different areas of animal science including animal health. The present study seeks to evaluate the combination of fecal volatilome analysis with chemometrics to detect field infections by bovine tuberculosis (Mycobacterium tuberculosis complex) in cattle. The good robust performance of discriminant models as well as the optimal data of sensitivity and specificity achieved highlight volatilome analysis as an innovative approach with huge potential.

Diagnostic accuracy of the Enferplex Bovine Tuberculosis antibody test in cattle sera

Bovine tuberculosis is a contagious bacterial disease of worldwide economic, zoonotic and welfare importance caused mainly by Mycobacterium bovis infection. Current regulatory diagnostic methods lack sensitivity and require improvement. We have developed a multiplex serological test for bovine tuberculosis and here we provide an estimate of the diagnostic accuracy of the test in cattle. Positive and negative reference serum samples were obtained from animals from Europe and the United States of America. The diagnostic specificity estimate was 98.4% and 99.7% using high sensitivity and high specificity settings of the test respectively. Tuberculin boosting did not affect the overall specificity estimate. The diagnostic sensitivity in samples from Mycobacterium bovis culture positive animals following tuberculin boosting was 93.9%.The relative sensitivity following boosting in tuberculin test positive, lesion positive animals and interferon gamma test positive, lesion positive animals was 97.2% and 96.9% respectively. In tuberculin test negative, lesion positive animals and in interferon gamma test negative, lesion positive animals, the relative sensitivity following tuberculin boosting was 88.2% and 83.6% respectively. The results show that the test has high diagnostic sensitivity and specificity and can detect infected animals that are missed by tuberculin and interferon gamma testing.

Molecular detection of Mycobacterium tuberculosis complex in a captive aguará popé (Procyon cancrivorus) with macroscopic tuberculosis like-lesions

Tuberculosis is a chronic and contagious infectious disease caused by multi-host species of the genus Mycobacterium grouped within the Mycobacterium tuberculosis complex. These pathogenic bacteria mainly affect mammals, including humans. The most recognized species is Mycobacterium bovis, the causative agent of bovine tuberculosis in livestock. Although livestock is the main host of M. bovis, this species is frequently isolated from wild animals. Wild native mammals from Central and South America, as the crab-eating raccoon or "aguará popé" (Procyon cancrivorus), may act as a source of tuberculosis and may represent a human health risk, especially in captive scenarios, due to closer animal-human interaction. However, the only presence of infection in wild animals is not enough to determine their epidemiological role in the disease. Here we identify tuberculosis in a captive aguará popé with clinical signs and lung macroscopic tuberculosis-like lesions during necropsy. We detected tuberculosis by polymerase chain reaction assay. DNA was extracted directly from lung tissue and the amplification target was the insertion sequence 6110. This study contributes to investigate the presence of the disease in wild native animals of Argentina and supports the knowledge that wild mammals may act as a source of TB for humans and domestic animals.

The Role of Histopathology as a Complementary Diagnostic Tool in the Monitoring of Bovine Tuberculosis

The diagnosis of bovine tuberculosis (bTB) is based on the single intradermal tuberculin test (SIT), interferon gamma, and compulsory slaughter of reactor animals. Culture and PCR from fresh tissue are regarded as gold standard techniques for post-mortem confirmation, with the former being time-consuming and presenting moderate to low sensitivity and the latter presenting promising results. Histopathology has the advantage to identify and categorize lesions in both reactor and non-reactor animals. Therefore, this study aims to highlight the role of histopathology in the systematic diagnosis of bTB to shorten the time to disclose positive animals. Blood (212) and lymph node (681) samples were collected for serological, bacteriological, and histopathological analyses from a total of 230 cattle subjected to the Spanish bTB eradication program. Seventy-one lymph nodes and 59 cattle yielded a positive result to bacteriology, with 59 lymph nodes and 48 cattle presenting a positive result in real-time PCR from fresh tissue. Roughly 19% (40/212) of sera samples gave a positive result to ELISA. Tuberculosis-like lesions (TBLs) were observed in 11.9% (81/681) of the lymph nodes and 30.9% (71/230) of cattle. Noteworthy, TBLs were evidenced in 18 out of 83 SIT⁻ and real-time PCR and bacteriology negative animals, with 11/18 disclosing a positive result to Ziehl-Neelsen technique and two of them to ddPCR from paraffin blocks targeting IS6110. Six out of these 11 ZN⁺ corresponded with mesenteric LN and were confirmed positive to paratuberculosis. Histopathology yielded a sensitivity of 91.3% (CI₉₅ 83.2–99.4%) and a specificity of 84.4% (CI₉₅ 78.6–89.3%) with good agreement (κ = 0.626) when compared with real-time PCR. Our results confirm that histopathology allows a rapid confirmation of real-time PCR and bacteriology, emphasizing its contribution to bTB control and monitoring.

Prevalence, Risk Factors, and Diagnostic Efficacy of Bovine Tuberculosis in Slaughtered Animals at the Chiang Mai Municipal Abattoir, Thailand

This study aimed to (1) investigate the prevalence of bovine tuberculosis (bTB) in slaughtered animals at the Chiang Mai Municipal abattoir in Chiang Mai, Thailand; (2) identify animal-level risk factors for bTB at the abattoir; and (3) evaluate the performance of techniques for bTB detection at the abattoir. From April 2020 to March 2021, 161 animals registered for slaughter were randomly selected for the study. Animal data including age, sex, species, body condition scores, and origins of the animals were collected. Meat inspection was performed by a trained meat inspector. Tissue samples of the lung, liver, and lymph nodes were collected for histopathological diagnosis and polymerase chain reaction (PCR) detection of Mycobacteria and specifically Mycobacterium bovis. The prevalence of bTB during meat inspection and PCR was calculated separately. Animal-level factors affecting bTB were determined using multivariate logistic regression analysis. The performance of meat inspection and PCR was evaluated using a Bayesian approach. The prevalence of bTB was 12.4% (20/161) and 34.8% (56/161) when the disease was diagnosed using meat inspection and PCR, respectively. Buffaloes had a significantly higher risk of being identified as bTB-positive using PCR compared to beef cattle (odds ratio = 2.19; confidence interval = 1.11–4.30). The median of posterior estimates of sensitivity (Se) and specificity (Sp) to detect bTB using meat inspection were 20.8% [95% posterior probability interval (PPI) = 9.1–36.5%] and 87.8% (95% PPI = 79.6–95.4%), respectively. The medians of the posterior estimates of Se and Sp for PCR were 88.6% (95% PPI = 70.5–98.3%) and 94.4% (95% PPI = 84.7–98.8%), respectively. These findings demonstrate that bTB is highly prevalent among slaughtered animals. PCR can be used as an ancillary test for bTB surveillance at abattoirs in Thailand.

Bayesian Estimation of Diagnostic Accuracy of Three Diagnostic Tests for Bovine Tuberculosis in Egyptian Dairy Cattle Using Latent Class Models

The aim of the present study was to calculate the sensitivity (Se) and specificity (Sp) of the single cervical tuberculin test (SCT), rapid lateral flow test (RLFT), and real-time polymerase chain reaction (RT-PCR) for the diagnosis of Mycobacterium bovis (M. bovis) infection in Egyptian dairy cattle herds within a Bayesian framework. The true M. bovis infection within-herd prevalence was assessed as a secondary objective. Data on the test results of SCT, RLFT, and RT-PCR for the detection of M. bovis were available from 245 cows in eleven herds in six major governorates in Egypt. A Bayesian latent class model was built for the estimation of the characteristics of the three tests. Our findings showed that Se of SCT (0.93 (95% Posterior credible interval (PCI): 0.89–0.93)) was higher than that of RT-PCR (0.83 (95% PCI: 0.28–0.93)) but was similar to the Se of RLFT (0.93 (95% PCI: 0.31–0.99)). On the contrary, SCT showed the lowest Sp estimate (0.60 (95% PCI: 0.59–0.65)), whereas Sp estimates of RT-PCR (0.99 (95% PCI: 0.95–1.00)) and RLFT (0.99 (95% PCI: 0.95–1.00)) were comparable. The true prevalence of M. bovis ranged between 0.07 and 0.71. In conclusion, overall, RT-PCR and RLFT registered superior performance to SCT, making them good candidates for routine use in the Egyptian bovine tuberculosis control program.

The effectiveness of bovine tuberculosis surveillance in Dutch badgers

Countries survey wildlife for bovine tuberculosis (bTB) to ensure case detection or to ascertain a high probability of freedom from bTB in wildlife. The Eurasian badger (Meles meles) is a potential bTB reservoir host. Between 2008 and 2019, 282 badgers were examined post‐mortem in the context of general wildlife disease and targeted bTB surveillance programmes in the Netherlands, and no bTB cases were detected. However, it was unclear how effective this surveillance effort was to demonstrate freedom from Mycobacterium bovis infection in the badger population of ±6000 or to detect cases if present.

Therefore, surveillance effectiveness was assessed using scenario tree modelling. For lack of standards for wildlife, the models were run against three assumed levels of disease in the population called design prevalence P*: 0.1%, 0.5%, and 3%. A small risk of introduction (0.015/year) was applied, because the Netherlands are officially free from bTB in cattle, with rare import of bTB‐infected cattle and no bTB‐infected wildlife reported along the Belgian and German borders with the Netherlands. Surveillance more readily picks up bTB presence in badgers when case detection sensitivity tends towards 100% and demonstrates freedom best when the probability of freedom tends towards 100%.

For P* 0.1%, 0.5% and 3%, respectively, maximum case detection sensitivity during 2008–2019 was 8%, 35% and 94% and the probability of freedom in 2019 was 46%, 67%, and 95%. At P* = 3%, performing targeted surveillance on 300 badgers in a year would make it extremely unlikely to miss a case (case detection sensitivity > 99.9%); and if no cases are detected, the adjusted probability of freedom would then reach nearly 98.5%. Stakeholders should be made aware that at P* = 3%, one case detected implies around 3% infected badgers. Additional surveillance system components to assess bTB in wildlife and its economics are to be explored further.

Application of Volatilome Analysis to the Diagnosis of Mycobacteria Infection in Livestock

Volatile organic compounds (VOCs) are small molecular mass metabolites which compose the volatilome, whose analysis has been widely employed in different areas. This innovative approach has emerged in research as a diagnostic alternative to different diseases in human and veterinary medicine, which still present constraints regarding analytical and diagnostic sensitivity. Such is the case of the infection by mycobacteria responsible for tuberculosis and paratuberculosis in livestock. Although eradication and control programs have been partly managed with success in many countries worldwide, the often low sensitivity of the current diagnostic techniques against Mycobacterium bovis (as well as other mycobacteria from Mycobacterium tuberculosis complex) and Mycobacterium avium subsp. paratuberculosis together with other hurdles such as low mycobacteria loads in samples, a tedious process of microbiological culture, inhibition by many variables, or intermittent shedding of the mycobacteria highlight the importance of evaluating new techniques that open different options and complement the diagnostic paradigm. In this sense, volatilome analysis stands as a potential option because it fulfills part of the mycobacterial diagnosis requirements. The aim of the present review is to compile the information related to the diagnosis of tuberculosis and paratuberculosis in livestock through the analysis of VOCs by using different biological matrices. The analytical techniques used for the evaluation of VOCs are discussed focusing on the advantages and drawbacks offered compared with the routine diagnostic tools. In addition, the differences described in the literature among in vivo and in vitro assays, natural and experimental infections, and the use of specific VOCs (targeted analysis) and complete VOC pattern (non-targeted analysis) are highlighted. This review emphasizes how this methodology could be useful in the problematic diagnosis of tuberculosis and paratuberculosis in livestock and poses challenges to be addressed in future research.

Real-Time PCR Validation for Mycobacterium tuberculosis Complex Detection Targeting IS6110 Directly From Bovine Lymph Nodes

Rapid and accurate diagnostic tools, such as Real-Time PCR (qPCR), need to be implemented as a confirmatory test in the framework of bovine tuberculosis (bTB) surveillance and control programs, shortening the turnaround time to confirm bTB infection. The present study aimed to evaluate a direct qPCR from fresh tissue samples targeting the insertion sequence IS6110 using individually homogenized bovine lymph nodes compared with microbiological culture. Retropharyngeal, tracheobronchial, and mesenteric lymph nodes fresh tissue samples (n = 687) were collected from 230 different cattle carcasses at the slaughterhouse. Only 23 of the 230 examined animals showed tuberculosis-like lesions, with 62 of 230 considered as positive. Among these 62 animals, 61 resulted as culture-positive, whereas 48 were qPCR-positive. Thus, this qPCR targeting IS6110 showed an apparent diagnostic sensitivity and specificity values of 77.1% [95% confidence interval (CI): 66.5–87.6%] and 99.4% (95% CI: 98.3–100.6%), respectively, and a positive predictive value of 97.9% (95% CI: 93.9–102.0%) and negative predictive value of 92.3% (95% CI: 88.4–96.2%). Positive and negative likelihood ratios were 130.2 and 0.2, respectively, and the agreement between microbiological culture and this qPCR was almost perfect (κ = 0.82). These results highlight this qPCR targeting IS6110 as a suitable complementary method to confirm bTB in animals with either tuberculosis-like lesions or non-tuberculosis-like lesions, decreasing the number of samples subjected to microbiological culture and, hence, its overall associated costs and the turnaround time (under 48 h) to confirm bTB infection. Besides, sampling mesenteric lymph node, which is uncommonly sampled, together with tracheobronchial and retropharyngeal ones, is advisable during postmortem inspection in bTB surveillance programs at the slaughterhouse, especially in areas with a low bTB prevalence scenario.

Engineering Synthetic Lipopeptide Antigen for Specific Detection of Mycobacterium avium subsp. paratuberculosis Infection

Unlike other MAC members, Mycobacterium avium subsp. paratuberculosis (MAP) does not produce glycopeptidolipids (GPL) on the surface of the cell wall but a lipopentapeptide called L5P (also termed Lipopeptide-I or Para-LP-01) characterized in C-type (bovine) strains. This lipopeptide antigen contains a pentapeptide core, D-Phenylalanine-N-methyl-L-Valine-L-Isoleucine-L-Phenylalanine-L-Alanine, in which the N-terminal D-Phenylalanine is amido-linked with a fatty acid (C18–C20). The molecular and genetic characterization of this antigen demonstrated that L5P is unique to MAP. Knowledge of the structure of L5P enabled synthetic production of this lipopeptide in large quantities for immunological evaluation. Various studies described the immune response directed against L5P and confirmed its capability for detection of MAP infection. However, the hydrophobic nature of lipopeptide antigens make their handling and use in organic solvents unsuitable for industrial processes. The objectives of this study were to produce, by chemical synthesis, a water-soluble variant of L5P and to evaluate these compounds for the serological diagnosis of MAP using well-defined serum banks. The native L5P antigen and its hydrosoluble analog were synthesized on solid phase. The pure compounds were evaluated on collections of extensively characterized sera from infected and non-infected cattle. ROC analysis showed that L5P and also its water-soluble derivative are suitable for the development of a serological test for Johne's disease at a population level. However, these compounds used alone in ELISA have lower sensitivity (Se 82% for L5P and Se 62% for the water-soluble variant of L5P) compared to the Se 98% of a commercial test. Advantageously, these pure synthetic MAP specific antigens can be easily produced in non-limiting quantities at low cost and in standardized batches for robust studies. The fact that L5P has not been validated in the context of ovine paratuberculosis highlights the need to better characterize the antigens expressed from the different genetic lineages of MAP to discover new diagnostic antigens. In the context of infections due to other mycobacteria such as M. bovis or the more closely related species M. avium subsp. hominissuis, the L5P did not cross react and therefore may be a valuable antigen to solve ambiguous results in other tests.

Engineering Synthetic Lipopeptide Antigen for Specific Detection of Mycobacterium avium subsp. paratuberculosis Infection

Unlike other MAC members, Mycobacterium avium subsp. paratuberculosis (MAP) does not produce glycopeptidolipids (GPL) on the surface of the cell wall but a lipopentapeptide called L5P (also termed Lipopeptide-I or Para-LP-01) characterized in C-type (bovine) strains. This lipopeptide antigen contains a pentapeptide core, D-Phenylalanine-N-methyl-L-Valine-L-Isoleucine-L-Phenylalanine-L-Alanine, in which the N-terminal D-Phenylalanine is amido-linked with a fatty acid (C18-C20). The molecular and genetic characterization of this antigen demonstrated that L5P is unique to MAP. Knowledge of the structure of L5P enabled synthetic production of this lipopeptide in large quantities for immunological evaluation. Various studies described the immune response directed against L5P and confirmed its capability for detection of MAP infection. However, the hydrophobic nature of lipopeptide antigens make their handling and use in organic solvents unsuitable for industrial processes. The objectives of this study were to produce, by chemical synthesis, a water-soluble variant of L5P and to evaluate these compounds for the serological diagnosis of MAP using well-defined serum banks. The native L5P antigen and its hydrosoluble analog were synthesized on solid phase. The pure compounds were evaluated on collections of extensively characterized sera from infected and non-infected cattle. ROC analysis showed that L5P and also its water-soluble derivative are suitable for the development of a serological test for Johne's disease at a population level. However, these compounds used alone in ELISA have lower sensitivity (Se 82% for L5P and Se 62% for the water-soluble variant of L5P) compared to the Se 98% of a commercial test. Advantageously, these pure synthetic MAP specific antigens can be easily produced in non-limiting quantities at low cost and in standardized batches for robust studies. The fact that L5P has not been validated in the context of ovine paratuberculosis highlights the need to better characterize the antigens expressed from the different genetic lineages of MAP to discover new diagnostic antigens. In the context of infections due to other mycobacteria such as M. bovis or the more closely related species M. avium subsp. hominissuis, the L5P did not cross react and therefore may be a valuable antigen to solve ambiguous results in other tests.

Evaluation of histopathology, PCR, and qPCR to detect Mikrocytos mackini in oysters Crassostrea gigas using Bayesian latent class analysis

Latent class analysis (LCA) is a common method to evaluate the diagnostic sensitivity (DSe) and specificity (DSp) for pathogen detection assays in the absence of a perfect reference standard. Here we used LCA to evaluate the diagnostic accuracy of 3 tests for the detection of Mikrocytos mackini in Pacific oysters Crassostrea gigas: conventional polymerase chain reaction (PCR), real-time quantitative PCR (qPCR), and histopathology. A total of 802 Pacific oysters collected over 12 sampling events from 9 locations were assessed. Preliminary investigations indicated that standard LCA assumptions of test independence and constant detection accuracy across locations were likely unrealistic. This was mitigated by restructuring the LCA in a Bayesian framework to include test-derived knowledge about pathogen prevalence and load for categorizing populations into 2 classes of infection severity (low or high) and assessing separate DSe and DSp estimates for each class. Median DSp estimates were high (>96%) for all 3 tests in both population classes. DSe estimates varied between tests and population classes but were consistently highest for qPCR (87-99%) and lowest for histopathology (21-51%). Acknowledging that detection of M. mackini may be fitted to multiple diagnostic and management purposes, qPCR had the highest DSe while maintaining similar DSp to both conventional PCR and histopathology and thus is generally well-suited to most applications.

Direct PCR on Tissue Samples To Detect Mycobacterium tuberculosis Complex: an Alternative to the Bacteriological Culture

Bovine tuberculosis (bTB) is an ongoing issue in several countries within the European Union. Microbiological culture is the official confirmation technique for the presence of Mycobacterium tuberculosis complex (MTBC) members in bovine tissues, but several methodological issues, such as moderate sensitivity and long incubation times, require the development of more sensitive and rapid techniques. This study evaluates the analytical and diagnostic performance, comparative to culture, of a real-time PCR targeting the MTBC-specific IS6110 transposon using a panel of bovine tissue samples sourced from the Spanish bTB eradication campaign. Robustness and repeatability were evaluated in an interlaboratory trial between European Union National Reference Laboratories. The limit of detection with 95% confidence was established at 65 fg/reaction of purified genomic equivalents. Diagnostic sensitivity (Se) and specificity (Sp) were, respectively, 96.45% and 93.66%, and the overall agreement (κ) was 0.88. Cross-reactivity was detected against two mycobacterial isolates identified as Mycobacterium marinum and "Mycobacterium avium subsp. hominissuis," and whole-genome sequencing (WGS) analysis of the latter isolate revealed an IS6110-like sequence with 83% identity. An identical IS-like element was found in other Mycobacterium avium complex species in the NCBI nucleotide and WGS databases. Despite this finding, this methodology is considered a valuable alternative to culture, and the strategy of use should be defined depending on the control or eradication programs.

Engineering Synthetic Lipopeptide Antigen for Specific Detection of Mycobacterium avium subsp. paratuberculosis Infection

Unlike other MAC members, Mycobacterium avium subsp. paratuberculosis (MAP) does not produce glycopeptidolipids (GPL) on the surface of the cell wall but a lipopentapeptide called L5P (also termed Lipopeptide-I or Para-LP-01) characterized in C-type (bovine) strains. This lipopeptide antigen contains a pentapeptide core, D-Phenylalanine-N-methyl-L-Valine-L-Isoleucine-L-Phenylalanine-L-Alanine, in which the N-terminal D-Phenylalanine is amido-linked with a fatty acid (C18-C20). The molecular and genetic characterization of this antigen demonstrated that L5P is unique to MAP. Knowledge of the structure of L5P enabled synthetic production of this lipopeptide in large quantities for immunological evaluation. Various studies described the immune response directed against L5P and confirmed its capability for detection of MAP infection. However, the hydrophobic nature of lipopeptide antigens make their handling and use in organic solvents unsuitable for industrial processes. The objectives of this study were to produce, by chemical synthesis, a water-soluble variant of L5P and to evaluate these compounds for the serological diagnosis of MAP using well-defined serum banks. The native L5P antigen and its hydrosoluble analog were synthesized on solid phase. The pure compounds were evaluated on collections of extensively characterized sera from infected and non-infected cattle. ROC analysis showed that L5P and also its water-soluble derivative are suitable for the development of a serological test for Johne's disease at a population level. However, these compounds used alone in ELISA have lower sensitivity (Se 82% for L5P and Se 62% for the water-soluble variant of L5P) compared to the Se 98% of a commercial test. Advantageously, these pure synthetic MAP specific antigens can be easily produced in non-limiting quantities at low cost and in standardized batches for robust studies. The fact that L5P has not been validated in the context of ovine paratuberculosis highlights the need to better characterize the antigens expressed from the different genetic lineages of MAP to discover new diagnostic antigens. In the context of infections due to other mycobacteria such as M. bovis or the more closely related species M. avium subsp. hominissuis, the L5P did not cross react and therefore may be a valuable antigen to solve ambiguous results in other tests.

Latent transition analysis of cardiac arrest patients treated in the intensive care unit

BACKGROUND AND OBJECTIVE

Post-cardiac arrest (CA) syndrome is heterogenous in their clinical presentations and outcomes. This study aimed to explore the transition and stability of subphenotypes (profiles) of CA treated in the intensive care unit (ICU).

PATIENTS AND METHODS

Clinical features of CA patients on day 1 and 3 after ICU admission were modeled by latent transition analysis (LTA) to explore the transition between subphenotypes over time. The association between different transition patterns and mortality outcome was explored using multivariable logistic regression.

RESULTS

We identified 848 eligible patients from the database. The LPA identified three distinct subphenotypes: Profile 1 accounted for the largest proportion (73%) and was considered as the baseline subphenotype. Profile 2 (13%) was characterized by brain injury and profile 3 (14%) was characterized by multiple organ dysfunctions. The same three subphenotypes were identified on day 3. The LTA showed consistent subphenotypes. A majority of patients in profile 2 (72%) and 3 (82%) on day 1 switched to profile 1 on day 3. In the logistic regression model, patients in profile 1 on day 1 transitioned to profile 3 had worse survival outcome than those continue to remain in profile 1 (OR: 20.64; 95% CI: 6.01 to 70.94; p < 0.001) and transitioned to profile 2 (OR: 8.42; 95% CI: 2.22 to 31.97; p = 0.002) on day 3.

CONCLUSION

The study identified three subphenotypes of CA, which was consistent on day 1 and 3 after ICU admission. Patients who transitioned to profile 3 on day 3 had significantly worse survival outcome than those remained in profile 1 or 2.

Intra-vitam Diagnosis of Tuberculosis in Pigs: Concordance Between Interferon-Gamma Release Assay and Comparative Tuberculin Skin Test

The role of pigs in the maintenance of bovine tuberculosis caused by Mycobacterium bovis has been demonstrated in many settings; however, the current control programs usually do not state any intra-vitam diagnostic procedure in this species, as for the cattle. Carcass inspection has shown to be insufficient to detect infection in swine; thus, the assessment of intradermal tuberculin test and interferon-gamma release assay (IGRA) in this species is mandatory. The current study compares the performances of the single intradermal comparative cervical tuberculin (SICCT) test and IGRA. A total of 628 Nebrodi Black pigs raised in free-roaming farms were subjected to the two tests simultaneously. Besides, 124 animals underwent postmortem examination for the detection of tuberculous lesions and isolation of mycobacteria from target organs. The two tests showed a concordance of 94.42% with a Cohen's k coefficient of 0.786 and McNemar chi-square of 4.83 (P = 0.03). Slightly lower levels of concordance (90.32%) between SICCT and IGRA were obtained in the group of 124 animals, with a Cohen's k = 0.797 and McNemar chi-squared value of 0.69 with a non-significant P = 0.41. Moreover, the results showed how IGRA tends to result positive in higher rates, mostly when non-tuberculous mycobacteria (NTM) were isolated, suggesting a possible impairment of specificity in the event of coinfections in the swine. In conclusion, the results obtained support the possibility of the strategic use of IGRA or SICCT in combination or alternatively one to the other, particularly IGRA which showed lower specificity but has evident advantages over SICCT.

Mycobacterium uberis Infection in the Subcutaneous Tissue of the Radius/Ulna Area of a Cow

Mycobacterium uberis (M. uberis) is a recently described non-tuberculous mycobacterium phylogenetically close to Mycobacterium leprae (M. leprae) and Mycobacterium lepromatosis (M. lepromatosis). This pathogen classically causes nodular thelitis in cattle and goats. Here, we discuss what seems to be the first described case of M. uberis infection in a novel anatomical site, in the proximal or distal position (information not available) of the radius/ulna area of a cow. As this case was discovered in the framework of bovine tuberculosis (bTB) surveillance program in France, this type of infection could interfere with the screening and diagnostic tools employed for bTB.

Accuracy of tuberculosis diagnostic tests in small ruminants: A systematic review and meta-analysis

Tuberculosis (TB) in small ruminants is a neglected disease despite its major impact on goat and sheep production and the global public health. The awareness of the role of small ruminants in the epidemiology of animal TB has increased in the last two decades, however, there is a lack of standardization of procedures and robust quantitative estimates on the accuracy of diagnostic TB tests in the scientific literature. To address this knowledge gap, all the available information regarding the use of ante-mortem diagnostic techniques in small ruminants was collected and summarized through a systematic review process. Furthermore, a random-effects meta-analysis was conducted to separately estimate the sensitivity (Se) and specificity (Sp) of cell-based tests among the retrieved studies in goats. Studies included in the meta-analysis were also evaluated using the Quality Assessment of Diagnostic Accuracy Studies included in systematic reviews adapted for animal diagnostic tests (VETQUADAS). Median pooled Se estimates of the single intradermal tuberculin (SIT) test (ranged from 0.51 to 0.59), the comparative intradermal tuberculin (CIT) test (ranged from 0.30 to 0.50) and the interferon-gamma (IFN-γ) release assay (IGRA) (ranged from 0.66 to 0.72) were lower than that reported previously in cattle, regardless the interpretation criteria and the reporting of MAP infection or vaccination. However, the specificity was adequate for all the tests (ranged from 0.95 to 0.99), except for the SIT test in MAP vaccinated herds (ranged from 0.78 to 0.90). This study provides an overview of the accuracy of diagnostic tests for TB in goats, however, the considerable between-study heterogeneity found hampered the conclusive interpretation of the pooled Se and Sp estimates. Therefore, further studies in small ruminants are necessary to optimize the diagnostic Se, which could help to design effective control strategies, accelerate the eradication of TB in these species and harmonize test procedures.

The VetMAX™ M. tuberculosis complex PCR kit detects MTBC DNA in antemortem and postmortem samples from white rhinoceros (Ceratotherium simum), African elephants (Loxodonta africana) and African buffaloes (Syncerus caffer)

BACKGROUND

Bovine tuberculosis and tuberculosis are chronic infectious diseases caused by the Mycobacterium tuberculosis complex members, Mycobacterium bovis and Mycobacterium tuberculosis, respectively. Infection with M. bovis and M. tuberculosis have significant implications for wildlife species management, public health, veterinary disease control, and conservation endeavours.

RESULTS

Here we describe the first use of the VetMAX™ Mycobacterium tuberculosis complex (MTBC) DNA quantitative real-time polymerase chain reaction (qPCR) detection kit for African wildlife samples. DNA was extracted from tissues harvested from 48 African buffaloes and MTBC DNA was detected (test-positive) in all 26 M. bovis culture-confirmed animals with an additional 12 PCR-positive results in culture-negative buffaloes (originating from an exposed population). Of six MTBC-infected African rhinoceros tested, MTBC DNA was detected in antemortem and postmortem samples from five animals. The PCR was also able to detect MTBC DNA in samples from two African elephants confirmed to have M. bovis and M. tuberculosis infections (one each). Culture-confirmed uninfected rhinoceros and elephants' samples tested negative in the PCR assay.

CONCLUSIONS

These results suggest this new detection kit is a sensitive screening test for the detection of MTBC-infected African buffaloes, African elephants and white rhinoceros.

Post-mortem surveillance of bovine tuberculosis in Ireland: herd-level variation in the probability of herds disclosed with lesions at routine slaughter to have skin test reactors at follow-up test

Post-mortem surveillance in Ireland discloses skin-test negative cattle with presumptive evidence of infection of Mycobacterium bovis (lesions at routine slaughter (LRS)), the causative agent of bovine tuberculosis (bTB). Laboratory confirmation of lesions has impacts on trade restrictions for herds, therefore if laboratory capacity was diminished, how herds are treated would require an informed risk policy. Here we report the proportion of herds with subsequent evidence of within-herd transmission, based on skin-test results. We assess how herd-size, herd-type, and bTB-history affect the probability of additional reactors at follow-up test using univariable and multivariable random-effects models. The study represents a rapid response to developing an evidential base for policy demands during an extraordinary event, the COVID-19 epidemic in Ireland. A dataset from 2005 to 2019 of breakdowns were collated. Overall, 20,116 breakdowns were initiated by LRS cases. During the index tests of these breakdowns, 3931 revealed ≥1 skin-test reactor animals (19.54%; ≥1 standard reactors: 3827; 19.02%). Increasing herd-size was associated with reactor disclosure on follow-up. For small herds (<33 animals), 11.74% of follow-up tests disclosed ≥1 reactor; 24.63% of follow-up tests from very large herds (>137) disclosed ≥1 reactors. Beef (13.87%) and “other” (13%) herd production types had lower proportion of index tests with reactors in comparison with dairy (28.27%) or suckler (20.48%) herds. Historic breakdown size during the previous 3-years was associated reactor disclosure risk on follow-up. Our results are useful for rapid tailored policy development aimed at identifying higher risk herds.

Accuracy of PCR, mycobacterial culture and interferon-γ assays for detection of Mycobacterium bovis in blood and milk samples from Egyptian dairy cows using Bayesian modelling

The number of bovine tuberculosis (bTB) infected dairy herds in Egypt is growing and this calls for accurate and reliable diagnostic methods at cow level for cost-effective bTB eradication as culling of the whole herd is not economically sustainable. The present study aimed to estimate the sensitivity (Se) and specificity (Sp) of PCR, mycobacterial culture and interferon-γ (IFN-γ) assays for Mycobacterium bovis (M. bovis) detection in blood and milk samples from dairy cows in Egyptian dairy herds within a Bayesian framework. As a secondary objective, the distribution of true within-herd prevalence of M. bovis infection was estimated. Blood and milk samples were collected from 245 Holstein dairy cows in 11 Egyptian dairy herds and subjected to PCR, mycobacterial culture and IFN-γ testing. With respect to the detection of M. bovis in blood, IFN-γ recorded higher Se [0.97 (95% Posterior Credible Interval (PCI): 0.87-1.00)] than PCR [0.68 (95% PCI: 0.53-0.95)] and culture [0.22 (95% PCI: 0.13-0.37)]. However, Sp estimates of PCR [0.98 (95% PCI: 0.95-1.00)], culture [0.99 (95% PCI: 0.98-1.00)] and IFN-γ [0.97 (95% PCI: 0.88-1.00)] were comparable. As for milk samples, Se estimate of PCR [0.29 (95% PCI: 0.01-0.60)] was higher than that of culture [0.08 (95% PCI: 0.001-0.23)]. However, the Sp estimates of both tests were statistically similar. The estimated true within-herd prevalences of M. bovis varied across the tested bovine subpopulations and ranged between 0.06 and 0.66. In conclusion, IFN-γ registered a similar overall performance to PCR but was superior to mycobacterial culture. With its good accuracy and wide applicability, IFN-γ lends itself to use in the Egyptian bTB eradication program.

Assessment of the sensitivity of the bovine tuberculosis eradication program in a high prevalence region of Spain using scenario tree modeling

In spite of the efforts invested to eradicate bovine tuberculosis (bTB) in cattle, the disease is still present in several developed countries, including Spain. Among the factors related with disease persistence in high prevalence areas, the lack of sensitivity of the screening test for detection of infected herds [single intradermal tuberculin (SIT) test] can play a major role. Here, a scenario tree model mimicking the diagnostic test scheme in place in the region of Castilla y Leon (Spain) was developed to estimate the probability of detecting bTB in an infected-non detected officially tuberculosis free (OTF) herd (herd sensitivity, HSe). In order to do so the probability of detecting at least one positive animal in the SIT test with/without post-mortem (detection of lesions and culture) confirmation in an infected herd was estimated using Monte Carlo simulation through @RISK (Palisade Co, NY, USA). Uncertainty on the accuracy of the diagnostic tests was introduced in the model using distributions based on the literature. The performance of the model was evaluated by comparing the predicted number of SIT/post-mortem positive animals in infected herds with those observed in newly detected bTB-infected herds in the region in 2011-2015. The estimated HSe of the SIT test was 76.2% (95% probability interval: 19.8-97.6). According to the model, bTB infection would be then confirmed through culture in 65.3% (95% PI: 50.0-82.3) of the herds detected through the SIT test, so that overall the proportion of infected-non detected OTF herds in which the infection could be confirmed after the initial SIT test was 49.6% (95% PI: 9.75-80.3). The predicted HSe of both SIT test and culture was directly correlated with herd size. Results from the model suggest a moderate but highly variable HSe of the current surveillance system in place for bTB detection in OTF herds located in high prevalence areas, that could be maximized by performing multiple tests within a year as indicated in the Spanish eradication program (with a median SIT HSe of 87% when two consecutive tests were considered). In addition, these results highlight the usefulness of performing subsequent SIT tests to rule out infection in SIT-positive herds even when the causative agent cannot be isolated.

Tuberculosis in the wild boar: Frequentist and Bayesian estimations of diagnostic test parameters when Mycobacterium bovis is present in wild boars but at low prevalence

The Eurasian wild boar (Sus scrofa) is increasingly considered as a relevant actor in the epidemiology of animal tuberculosis (TB). Therefore, monitoring TB in this species is key when establishing comprehensive control schemes for this disease still present in Europe. No data are available on direct and indirect TB diagnostic methods in wild boars in epidemiological contexts where TB is endemic in cattle and detected in wild boars at low prevalence. We aimed to estimate and compare sensitivity and specificity values for bacterial culture, PCR and three commercial ELISAs, i.e. the TB ELISA-VK (using the bPPD antigen), INgezim TB Porcine and IDEXX M. bovis Ab Test (both using the MPB83 and MPB70 antigens), under field conditions in France. We used frequentist methods, with bacteriology as the gold standard, and a Bayesian formulation of the latent class analysis (LCA), without using a gold standard. Submandibular lymph nodes and sera from 495 wild boars hunter-harvested in three endemic areas (Aquitaine region, Côte d’Or region, and Corsica region) were collected between 2014 and 2016. Only eight individuals were positive for M. bovis by bacteriology (1.61%; CI_95% 0.70–3.51%). The LCA method provided high specificities (99.2%; CI_95% 98.2–99.8% for INgezim TB Porcine and 99.7%; CI_95% 98.8–100% for IDEXX M. bovis Ab Test) and sensitivities (78.5%; CI_95% 65.1–88.8% for INgezim TB Porcine and 83.9%; CI_95% 58.9–97.2% for IDEXX M. bovis Ab Test) for both ELISAs using the MPB83 and MPB70 antigens. Bacterial culture showed limited sensitivity (42.8%; CI_95% 19.0–70.6%), estimated as the probability of a positive result in an animal exposed to M. bovis. PCR and ELISA using the bPPD antigens demonstrated high specificities, and sensitivities intermediates between culture and the ELISAs using the MPB83 and MPB70 antigens. These results suggest that ELISA tests using the MPB83 and MPB70 antigens are useful to detect and monitor TB exposure of wild boar populations in field conditions in France.

Bayesian Assessment of the Accuracy of a PCR-Based Rapid Diagnostic Test for Bovine Tuberculosis in Swine

Infection with the Mycobacterium bovis (M. bovis) causes a disease referred to as bovine tuberculosis (bTB), which affects a wide range of mammal hosts. Many countries have implemented control and eradication plans that have resulted in variable levels of efficacy and success. Although bTB is a notifiable disease in Argentina, and a control plan that targets cattle herds has been in place for decades, M. bovis is still prevalent in cattle, swine, and certain wild species. The aim of the paper here was to assess the sensitivity (Se), specificity (Sp), and positive and negative predictive values (PPV and NPV) of PCR from tissue, which is a test for rapid M. bovis detection in swine. Bacteriological culture was also performed for comparison purposes. A Bayesian approach was applied to estimate the accuracy of the diagnostic tests, PCR and bacteriological culture, in 266 swine samples with bTB-like lesions recovered during routine official inspections at slaughterhouses. A one-population model, assuming conditional dependence between test results, and incorporating prior information on the performance of the tests obtained from the literature, was used to estimate the tests Se and Sp. The accuracy of the combined (in parallel) application of both tests was also estimated. The Se of the PCR (82.9%) was higher than the Se of the bacteriological culture (79.9%), whereas the Sp of both tests was similar (88.5 and 89.0%, respectively). Furthermore, when both techniques were assessed in parallel, the Se of the diagnostic system increased substantially (Se = 96.6%) with a moderate Sp loss (Sp = 78.8%; PPV = 92.8%; NPV = 89%). Results suggest that the PCR, or the combined application of bacteriological culture and PCR, may serve as an accurate diagnostic tool to confirm bTB in swine samples. Results here will help the design and implementation of effective surveillance strategies for the disease in swine of Argentina and other settings in which the disease is prevalent.

Evaluation of post-mortem diagnostic tests' sensitivity and specificity for bovine tuberculosis using Bayesian latent class analysis

This study aimed to evaluate the performance of real-time PCR (qPCR), ELISA IDEXX™, and bacterial isolation as post-mortem diagnostic tests in animals with lesions compatible with bovine tuberculosis detected by Brazilian Federal Inspection Service as part of the bovine tuberculosis active surveillance. Bayesian latent class models were used to estimate diagnostic tests' sensitivity, specificity, correlations, predictive values and frequency of infected animals. Samples of tuberculosis-suggestive lesions collected by FIS sanitary inspection routine in slaughterhouses from 11 Brazilian states were analyzed. Isolation was the most sensitive technique, 94.54% (95% Credible Interval (CrI) 90.09%-97.65%), qPCR was 64.69% (95% CrI 54.41%-74.15%) sensitive and ELISA IDEXX™ 26.74% (95% CrI 22.82%-30.97%). Tests' specificities were 98.19% (95% CrI 95.75%-99.45%), 93.49% (95% CrI 79.28%-99.66%), 95.53% (95% CrI 91.71%-98.02%) respectively. Despite its low sensitivity, ELISA IDEXX™ was able to identify positive samples that were not detected by the other techniques. These samples had high probability to be true positives given ELISA's positive predictive value. The correlations between qPCR and isolation were neither biologically nor statistically significant. The low sensitivity of the qPCR is a limiting factor to its use as a post-mortem diagnosis in bovine tuberculosis suggestive lesions. Its use could be recommended in situations of high prevalence, or in parallel association with other tests, such as ELISA IDEXX™. ELISA IDDEX™ should not be used as a unique test, or in substitution of the other tests, for the post-mortem diagnosis of bovine tuberculosis due to its sensitivity.

Assessment of the specificity of a gamma-interferon test performed with specific antigens to detect bovine tuberculosis, after non-negative results to intradermal tuberculin testing

In cattle herds in France, cervical skin tests (STs) using simple intradermal tuberculin (SIT) are performed to detect bovine tuberculosis (bTB). When positive results are found on ST screening, the herd is considered to be ‘under suspicion’ and confined, raising economic issues. The suspicion can be lifted by carrying out a single intradermal cervical comparative test (SICCT) at least six weeks later.The authors conducted an experimental study in France between 2013 and 2015 to assess the accuracy of the gamma-interferon test (IFN-γ), used in series after a non-negative result to ST screening, and to study the possibility of replacing the SICCT performed six weeks later by an IFN performed within a few days. Data were collected concerning 40 infected and 1825 bTB-free animals from herds with non-negative results to ST screening. This study showed that the IFN-γ test based on specific antigens and performed within a few days of a non-negative result to the ST has higher sensitivity than the SICCT performed six weeks later and equal specificity. The IFN test is more convenient to perform; however, it is more expensive. The IFN-γ test based on MIX antigens may be a useful alternative to the SICCT, to shorten the confinement period of suspect herds without underdetecting bTB.

Cost-effectiveness assessment of three components of the bovine tuberculosis surveillance system by intradermal tuberculin testing in French cattle farms by a scenario tree approach

In most officially bovine tuberculosis (bTB)-free countries, bTB has not been fully eradicated. Costly and time-consuming surveillance and control measures are therefore still in place to control this infection. An officially bTB-free status, both at the national and at the herd level, influences whether and when animals can be sold. Thus, this infection is still an economic issue, justifying measures towards its eradication. An evaluation of the cost-effectiveness of such measures would be highly useful, especially to optimise the costs of control measures and their adaptation to a local epidemiological context. We evaluated the cost-effectiveness of three mandatory surveillance protocols currently used in France by herd type (type of production, size, and turnover of the herd) under French field conditions. The first protocol ("strict") implies the direct slaughter and post-mortem analyses of any intradermal cervical tuberculin test (ICT) reactor, and negative results to a second intradermal cervical comparative tuberculin test (ICCT) to regain bTB-free status of the herd. In the second protocol ("compliant quick-path") bTB-free status can be regain if post-mortem analyses of reactors to the first ICT are negative. In the third protocol ("compliant slow-path"), ICCT-reactive animals are tested using the interferon gamma assay; the results of this test influence the path of further investigation. We built scenario trees for each of these protocols at the animal level. They allowed us to estimate herd sensitivity and the total cost of each protocol by herd type. The protocols could be ordered by decreasing herd sensitivity and cost, regardless of the herd type, as follows: strict protocol, compliant quick-path protocol, and compliant slow-path protocol. We calculated a cost-effectiveness index to evaluate the cost-effectiveness of each protocol. The strict protocol was never the most cost-effective, regardless of herd type, due to higher costs relative to the other protocols, despite better herd sensitivity. We found the compliant quick-path to be the most cost-effective protocol for big beef, big dairy, and mixed herds. The compliant slow-path was the most cost-effective for small-scale beef and dairy herds. All differences were significant. This comparison of the cost-effectiveness of the protocols by herd type could help authorities to choose the most suitable protocol in the investigation of suspected cases, depending on the herd type, but could be improved by accounting for important sociological data, such as the acceptability of the protocols.

Validation of a Real-Time PCR for the Detection of Mycobacterium tuberculosis Complex Members in Bovine Tissue Samples

Although the post-mortem diagnosis of bovine tuberculosis is mainly achieved through microbiological culture, the development of other techniques to detect Mycobacterium tuberculosis complex (MTBC) members directly from tissue samples has been pursued. The present study describes the development, optimization and validation of a Real-Time PCR based on the mpb70 gene to detect MTBC members in clinical tissue samples from cattle. Specific primers and a hybridization probe were used to amplify MTBC-specific sequences in order to avoid cross-reaction with non-MTBC species. An Internal Amplification Control (IAC) was included in order to assess the presence of PCR inhibitors in the samples. The PCR was optimized to achieve maximum efficiency, and the limit of detection, limit of quantification and dynamic range of the reaction were determined. The specificity of the reaction was tested against 34 mycobacterial and non-mycobacterial species. The diagnostic sensitivity, specificity and positive and negative predictive values (PPV and NPV) of the method were assessed on 200 bovine tissue samples in relation to bacteriological culture. The dynamic range of the reaction spanned from 5 ng/reaction (10⁶ genome equivalents) to 50 fg/reaction (10 genome equivalents). The efficiency of the reaction was 102.6% and the achieved R² was 0.999. The limit of detection with 95% confidence was 10 genome equivalents/reaction. No cross-reactions with non-MTBC species were observed. The diagnostic sensitivity and specificity values of the mpb70 specific Real-Time PCR respect to culture were 94.59% (95% CI: 86.73–98.51%) and 96.03% (95% CI: 90.98–98.70%), respectively, with a PPV of 93.33% (95% CI: 85.55–97.07%) and a NPV of 96.80% (95% CI: 92.10–98.74%). The concordance of the Real-Time PCR based on mpb70 is comparable to that of culture (K = 0.904) showing a great potential for the detection of members of the MTBC in animal tissues.

Identification of Mycobacterium genavense natural infection in a domestic ferret

A 6-y-old neutered male ferret ( Mustela putorius furo) was presented because of a 1-mo history of progressive weight loss, chronic cough, and hair loss. On clinical examination, the animal was coughing, slightly depressed, moderately hypothermic, and had bilateral epiphora. Thoracic radiography was suggestive of severe multinodular interstitial pneumonia. Abdominal ultrasound examination revealed hepatosplenomegaly and mesenteric and pancreaticoduodenal lymphadenopathy. Fine-needle aspiration of the pancreaticoduodenal lymph node, followed by routine Romanowsky and Ziehl-Neelsen stains, revealed numerous macrophages containing myriad acid-fast bacilli, leading to identification of mycobacteriosis. Autopsy and histologic examination confirmed the presence of disseminated, poorly defined, acid-fast, bacilli-rich granulomas in the pancreaticoduodenal and mesenteric lymph nodes, intestines, and lungs. Destaining of May-Grünwald/Giemsa-stained slides with alcohol, and then restaining with Ziehl-Neelsen, revealed acid-fast rods and avoided repeat tissue sampling without affecting the Ziehl-Neelsen stain quality and cytologic features. Tissue samples were submitted for a PCR assay targeting the heat shock protein gene ( hsp65) and revealed 100% homology with Mycobacterium genavense. We emphasize the use of special stains and PCR for identification of this potential zoonotic agent.

Second line molecular diagnosis for bovine tuberculosis to improve diagnostic schemes

Surveillance of bovine tuberculosis (bTB) is partly based on the sanitary inspection of carcasses at the abattoir to detect bTB-like lesions which, in compliance with EU recommendations, are analysed by bacteriology and histopathology to disclose Mycobacterium bovis (or M. caprae) infection. Moreover, since 2012, a PCR method with similar sensitivity and specificity values of histopathology and bacteriology respectively is additionally employed in France, partially compensating for the weaknesses of classical diagnostic methods. We analysed a collection of bTB-like lesions from cattle presenting positive histological results albeit with negative PCR results. We present here the results of these samples, recovered from 292 animals culled between 2013 and 2016, analysed with a second line molecular diagnosis approach that consists in a combination of PCRs targeting the M. tuberculosis-M. avium complexes as well as the Mycobacterium genus and sequencing of hsp65 gene. These molecular analyses disclosed to identify the presence of non-tuberculous bacteria which could be responsible for most of these non-specific TB lesions: non tuberculous mycobacteria (24%) or Actinomycetales (56%) such as Rhodococcus equi (53%); 24% of the samples were negative. M. bovis -or any other MTBC members- was neither detected by molecular methods nor isolated in any of them at the end of the 3 months of culture. In conclusion, these results highlight the lack of specificity of histopathology and the usefulness of a first line PCR with a second line molecular diagnostic test to circumvent it. This diagnostic strategy makes it possible to reduce the number of suspect bTB cases raised at the abattoir or shortening their lock-up periods. By simplifying diagnostic schemes, the use of this tool could improve bTB surveillance and make eradication programs more efficient in the future.

Infection of Wildlife by Mycobacterium bovis in France Assessment Through a National Surveillance System, Sylvatub

Mycobacterium bovis infection was first described in free-ranging wildlife in France in 2001, with subsequent detection in hunter-harvested ungulates and badgers in areas where outbreaks of bovine tuberculosis (TB) were also detected in cattle. Increasing concerns regarding TB in wildlife led the French General Directorate for Food (DGAL) and the main institutions involved in animal health and wildlife management, to establish a national surveillance system for TB in free-ranging wildlife. This surveillance system is known as “Sylvatub.” The system coordinates the activities of various national and local partners. The main goal of Sylvatub is to detect and monitor M. bovis infection in wildlife through a combination of passive and active surveillance protocols adapted to the estimated risk level in each area of the country. Event-base surveillance relies on M. bovis identification (molecular detection) (i) in gross lesions detected in hunter-harvested ungulates, (ii) in ungulates that are found dead or dying, and (iii) in road-killed badgers. Additional targeted surveillance in badgers, wild boars and red deer is implemented on samples from trapped or hunted animals in at-risk areas. With the exception of one unexplained case in a wild boar, M. bovis infection in free-living wildlife has always been detected in the vicinity of cattle TB outbreaks with the same genotype of the infectious M. bovis strains. Since 2012, M. bovis was actively monitored in these infected areas and detected mainly in badgers and wild boars with apparent infection rates of 4.57–5.14% and 2.37–3.04%, respectively depending of the diagnostic test used (culture or PCR), the period and according to areas. Sporadic infection has also been detected in red deer and roe deer. This surveillance has demonstrated that M. bovis infection, in different areas of France, involves a multi-host system including cattle and wildlife. However, infection rates are lower than those observed in badgers in the United Kingdom or in wild boars in Spain.

Evaluating accuracy of diagnostic tests without conditional independence assumption

Evaluating the accuracy (ie, estimating the sensitivity and specificity) of new diagnostic tests without the presence of a gold standard is of practical meaning and has been the subject of intensive study for several decades. Existing methods use 2 or more diagnostic tests under several basic assumptions and then estimate the accuracy parameters via the maximum likelihood estimation. One of the basic assumptions is the conditional independence of the tests given the disease status. This assumption is impractical in many real applications in veterinary research. Several methods have been proposed with various dependence models to relax this assumption. However, these methods impose subjective dependence structures, which may not be practical and may introduce additional nuisance parameters. In this article, we propose a simple method for addressing this problem without the conditional independence assumption, using an empirical conditioning approach. The proposed method reduces to the popular Hui-Walter model in the case of conditional independence. Also, our likelihood function is of order-2 polynomial in parameters, while that of Hui-Walter is of order-3. The reduced model complexity increases the stability in estimation. Simulation studies are conducted to evaluate the performance of the proposed method, which shows overall smaller biases in estimation and is more stable than the existing method, especially when tests are conditionally dependent. Two real data examples are used to illustrate the proposed method.

Successful Application of the Gamma-Interferon Assay in a Bovine Tuberculosis Eradication Program: The French Bullfighting Herd Experience

In the French Camargue region, where bovine tuberculosis had been enzootic for several years in bullfighting cattle herds, the gamma-interferon (IFN) assay was used since 2003 in parallel with the intradermal test in order to increase overall disease detection sensitivity in infected herds. This study presents the results of a field-evaluation of the assay during a 10-year period (2004–2014) of disease control and surveillance program and explores the particular pattern of IFN assay results in bullfight herds in comparison to cattle from other regions of France. The low sensitivity [59.2% (50.6; 67.3)] of IFN assay using the tuberculin stimulation could be related to the poor gamma-IFN production from bullfight cattle blood cells which is significantly lower than in animals of conventional breeds. The characteristics of the assay were progressively adapted to the epidemiological situation and the desired strategic applications. Data analysis with a receiver operating characteristic curve based on a simple S/P value algorithm allowed for the determination of a new cutoff adapted for a global screening, giving a high specificity of 99.9% results and a high accuracy of the assay. Having regularly risen to above 5% since 2005, with a peak around 10% in 2010, the annual incidence dropped to under 1% in 2014. The positive predictive value relative to the bacteriological confirmation evolved during the years, from 33% in 2009 to 12% during the last screening period, a normal trend in a context of decreasing prevalence. The estimated rate of false-positive reactions during screening campaigns was 0.67%, confirming the high specificity of the test, measured in bTB negative herds, in this epidemiological context. The proportion of false-positive reactions decreased with the age and was higher in males than in females. Although these results indicate that the IFN assay is accurate in the field, it also emphasizes great differences between interferon quantities produced by bullfight cattle blood samples compared to those of classical bovine breeds, which underlines the necessity to adapt the algorithms and combinations of the assay according to local epidemiological contexts.

Multilaboratory Evaluation of a Novel Lateral Flow Immunochromatographic Assay for Confirming Isolation of Mycobacterium bovis from Veterinary Diagnostic Specimens

A novel lateral flow immunochromatographic device (LFD) was evaluated in several veterinary diagnostic laboratories. It was confirmed to be specific for Mycobacterium bovis and M.caprae cells. The performance of the novel LFD was assessed relative to the confirmatory tests routinely applied after culture (spoligotyping or quantitative PCR [qPCR]) in each laboratory; liquid (MGIT or BacT/Alert) and/or solid (Stonebrink, Coletsos, or Lowenstein-Jensen) cultures were tested. In comparison to spoligotyping of acid-fast-positive MGIT cultures, percent agreement between positive LFD and spoligotyping results was excellent in two United Kingdom laboratories (97.7 to 100%) but lower in the Spanish context (76%), where spoligotyping was applied to MGIT cultures previously confirmed to be positive for M. tuberculosis complex (MTBC) by qPCR. Certain spoligotypes of M. bovis and M. caprae were not detected by the LFD in Spanish MGIT cultures. Compared to qPCR confirmation, the agreement between positive LFD and qPCR results was 42.3% and 50% for BacT/Alert and MGIT liquid cultures, respectively, and for solid cultures, it ranged from 11.1 to 89.2%, depending on the solid medium employed (Coletsos, 11.1%; Lowenstein-Jensen, 55.6%; Stonebrinks, 89.2%). Correlation between the novel LFD and BD MGIT TBc Identification test results was excellent when 190 MGIT cultures were tested (r = 0.9791; P < 0.0001), with the added benefit that M. bovis was differentiated from another MTBC species in one MGIT culture by the novel LFD. This multilaboratory evaluation demonstrated the novel LFD's potential utility as a rapid test to confirm isolation of M. bovis and M. caprae from veterinary specimens following culture.

Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation (EU) No 2016/429): bovine tuberculosis

Bovine tuberculosis has been assessed according to the criteria of the Animal Health Law (AHL), in particular criteria of Article 7 on disease profile and impacts, Article 5 on the eligibility of bovine tuberculosis to be listed, Article 9 for the categorisation of bovine tuberculosis according to disease prevention and control rules as in Annex IV and Article 8 on the list of animal species related to bovine tuberculosis. The assessment has been performed following a methodology composed of information collection and compilation, expert judgement on each criterion at individual and, if no consensus was reached before, also at collective level. The output is composed of the categorical answer, and for the questions where no consensus was reached, the different supporting views are reported. Details on the methodology used for this assessment are explained in a separate opinion. According to the assessment performed, bovine tuberculosis can be considered eligible to be listed for Union intervention as laid down in Article 5(3) of the AHL. The disease would comply with the criteria as in Sections 2, 3, 4 and 5 of Annex IV of the AHL, for the application of the disease prevention and control rules referred to in points (b), (c), (d) and (e) of Article 9(1). The main animal species to be listed for bovine tuberculosis according to Article 8(3) criteria are several mammal species, as indicated in the present opinion.

Matrixlysis, an improved sample preparation method for recovery of Mycobacteria from animal tissue material

Mycobacterium caprae, a member of the Mycobacterium tuberculosis complex, is the main causative agent of bovine tuberculosis in alpine regions. Bacterial culture is the gold standard in bovine tuberculosis diagnostic but takes up to twelve weeks. This increases the time and costs for stocks affected with bovine tuberculosis. Hence this study focused on the implementation of a fast and precise mycobacterial detection method and compared it with currently used methods. Matrix lysis is a chemical lysis using high concentrations of urea to solubilize bovine and red deer tissue and was used to detect even smallest amounts or non-visible lesions of mycobacteria. A total of 64 samples collected from 44 animals (37 red deer and 7 cattle) were tested by Matrix lysis. Forty-three of these samples were used for Mycobacterium tuberculosis complex detection by quantitative PCR and other 21 for subtyping the genetically different variants of M. caprae. Furthermore, three Matrix lysis samples were used for Next Generation Sequencing. Our results confirm that Matrix lysis is a fast and precise method for detecting Mycobacterium tuberculosis complex in native tissue samples. However, at the moment it reaches its limits when the samples were analyzed by Next Generation Sequencing and RD4 subtyping.

Evaluating diagnostic tests for bovine tuberculosis in the southern part of Germany: A latent class analysis

Germany has been officially free of bovine tuberculosis since 1996. However, in the last years there has been an increase of bovine tuberculosis cases, particularly in the southern part of Germany, in the Allgäu region. As a consequence a one-time tuberculosis surveillance program was revisited with different premortal and postmortal tests. The aim of this paper was to estimate diagnostic sensitivities and specificities of the different tests used within this surveillance program. In the absence of a perfect test with 100% sensitivity and 100% specificity, thus in the absence of a gold standard, a Bayesian latent class approach with two different datasets was performed. The first dataset included 389 animals, tested with single intra-dermal comparative cervical tuberculin (SICCT) test, PCR and pathology; the second dataset contained 175 animals, tested with single intra-dermal cervical tuberculin (SICT) test, Bovigam® assay, pathology and culture. Two-way conditional dependencies were considered within the models. Additionally, inter-laboratory agreement (five officially approved laboratories) of the Bovigam® assay was assessed with Cohen's kappa test (21 blood samples). The results are given in posterior means and 95% credibility intervals. The specificities of the SICT test, SICCT test, PCR and pathology ranged between 75.8% [68.8-82.2%] and 99.0% [96.8-100%]. The Bovigam® assay stood out with a very low specificity (6.9% [3.6-11.1%]), though it had the highest sensitivity (95.7% [91.3-99.2%]). The sensitivities of the SICCT test, PCR, SICT test, pathology and culture varied from 57.8% [48.0-67.6%] to 88.9% [65.5-99.7%]. The prevalences were 19.8% [14.6-26.5%] (three-test dataset) and 7.7% [4.2-12.3%] (four-test dataset). Among all pairwise comparisons the highest agreement was 0.62 [0.15-1]). In conclusion, the specificity of the Bovigam® assay and the inter-laboratory agreement were lower than expected.