MNBC: a multithreaded Minimizer-based Naïve Bayes Classifier for improved metagenomic sequence classification.

MOTIVATION: State-of-the-art tools for classifying metagenomic sequencing reads provide both rapid and accurate options, although the combination of both in a single tool is a constantly improving area of research. The machine learning-based Naïve Bayes Classifier (NBC) approach provides a theoretical basis for accurate classification of all reads in a sample. RESULTS: We developed the multithreaded Minimizer-based Naïve Bayes Classifier (MNBC) tool to improve the NBC approach by applying minimizers, as well as plurality voting for closely related classification scores. A standard reference- and test-sequence framework using simulated variable-length reads benchmarked MNBC with six other state-of-the-art tools: MetaMaps, Ganon, Kraken2, KrakenUniq, CLARK, and Centrifuge. We also applied MNBC to the "marine" and "strain-madness" short-read metagenomic datasets in the Critical Assessment of Metagenome Interpretation (CAMI) II challenge using a corresponding database from the time. MNBC efficiently identified reads from unknown microorganisms, and exhibited the highest species- and genus-level precision and recall on short reads, as well as the highest species-level precision on long reads. It also achieved the highest accuracy on the "strain-madness" dataset. AVAILABILITY AND IMPLEMENTATION: MNBC is freely available at: https://github.com/ComputationalPathogens/MNBC.

Brucellosis emergence in the Canadian Arctic.

Brucellosis is an important zoonotic disease affecting animals and subsistence harvesters in the circumarctic. We investigated recent trends (2015-2022) of brucellosis seropositivity in caribou (Rangifer tarandus) and muskoxen (Ovibos moschatus) in the Central Canadian Arctic by using data from community-based wildlife health surveillance programs. The overall sample prevalence of Brucella antibodies was 10.0% (n = 271) in muskoxen and 15.5% (n = 277) in caribou. Sample seroprevalence in muskoxen varied geographically with an increasing trend of exposure on NW Victoria Island (from 0% to 36.8% between 2016 and 2022; Kendall tau = 0.283, p = 0.001). The presence of Brucella suis biovar 4 was confirmed by culture from clinical cases in this area. Our results indicate that Brucella suis biovar 4 continues to circulate in the Central Canadian Arctic in caribou and muskoxen and may be now circulating in muskoxen independently from caribou. These findings highlight the need to better understand the ecology and drivers of brucellosis emergence in Arctic multi-host systems.

Is the gamma interferon assay in cattle influenced by multiple tuberculin injections?

Along with other developed countries, Canada is interested in adopting the gamma interferon (IFN-gamma) assay to test for bovine tuberculosis (TB). This study compared results of using the IFN-gamma assay in a large number of field-tested cattle in Manitoba, some previously tested with a caudal fold test (CFT) only, and others injected with tuberculins for both a CFT and a comparative cervical test (CCT). Parallel testing further compared the IFN-gamma assay and CCT results with the confirmed TB status of the animal (culture, histopathologic examination, polymerase chain reaction). Results from IFN-gamma assays did not differ following the CFT versus CFT and CCT injections. Parallel testing demonstrated an apparent higher prevalence of tuberculosis for the IFN-gamma assay versus CCT, which will assist in earlier removal of exposed animals and, ultimately, prevent populations from becoming infected.

HEALTH STATUS OF REINTRODUCED WOOD BISON ( BISON BISON ATHABASCAE): ASSESSING THE CONSERVATION VALUE OF AN ISOLATED POPULATION IN NORTHWESTERN CANADA.

A central goal for reintroduced populations of threatened wood bison ( Bison bison athabascae) is to maintain them free of diseases of concern, particularly bovine tuberculosis (caused by Mycobacterium bovis) and brucellosis (caused by Brucella abortus). A wood bison population in southwestern Yukon, Canada was reintroduced into the wild in 1988, but no health assessment has been done since then. To provide an initial assessment of the health status and, hence, the conservation value of this population, we serologically tested 31 wood bison (approximately 3% of the population) for pathogens of interest and obtained histopathology results for select tissues. We found no evidence of exposure to M. bovis or Brucella spp., but antibodies were present to bovine parainfluenza virus 3, bovine coronavirus, Leptospira interrogans, and Neospora caninum, with seroprevalences of 87, 7, 61, and 7% of the tested animals, respectively. Reintroduced wood bison in southwestern Yukon may be of high value for wood bison recovery because it is a large and geographically isolated population with no bacteriologic, histopathologic, or serologic evidence of exposure to Brucella spp. or M. bovis.

Fluorescence polarization assay for the detection of antibodies to Mycobacterium bovis in bovine sera.

The performance of a fluorescence polarization assay (FPA) that detects antibodies to Mycobacterium bovis in bovine sera is described. The FPA reported here is a direct binding primary screening assay using a small polypeptide derived from the M. bovis MPB70 protein. A secondary inhibition assay confirms suspect or presumed positive samples. Specificity studies involved five different veterinary laboratories testing 4461 presumed negative bovine samples. FPA specificity was 99.9%. The FPA was used to identify herd status as either M. bovis infected or non-infected. Herd surveillance studies (nine herds) were performed in Mexico and South Africa. The FPA had a specificity of 100% (two negative herds), and correctly identified six of seven infected herds. Finally, sera from 105 slaughter animals that had gross lesions in lymph nodes similar to those seen with bovine tuberculosis were tested by the FPA. Thin sections from the associated formalin-fixed paraffin-embedded samples of lymph nodes were stained using hematoxylin and eosin (H&E) for morphologic examination and using the Ziehl-Neelsen (ZN) method for detection of acid-fast bacilli. Of the 105 animals, 78 were classified as TB suspect based on lesion morphology, 21 were positive by ZN, 9 were positive by FPA and 13 were positive by PCR for the tuberculosis group of Mycobacterium. Among the 21 ZN positives, 11 (52.4%) were PCR positive. Among the 9 FPA positives, 8 (88.9%) were PCR positive. For the 13 PCR positives, 8 (61.5%) were FPA positive and 11 (84.6%) were ZN positives. These results show that use of the FPA for detection of M. bovis infection of cattle has value for bovine disease surveillance programs.

Cervine (Cervus elaphus) cytokine mRNA quantification by real-time polymerase chain reaction.

It has been difficult to perform cytokine studies for many wildlife and nontraditional species because of a lack of immunologic reagents at the protein level. Recently, simple and rapid assays for quantifying mRNA expression by real-time reverse transcription-polymerase chain reaction (RT-PCR) have been used for analysis of cytokine profiles in humans and other mammalian species. This report describes the development and application of real time RT-PCR to measure the expression of several important elk (Cervus elaphus) cytokine mRNAs, including interleukin (IL)-2, IL-4, IL-10, IL-12p40, interferon-gamma, tumor necrosis factor (TNF)-alpha, and the enzyme-inducible nitric oxide synthase, all of which are involved in immune responses and regulation. For the broadest potential application of the assay, primers and probes were designed using consensus sequences from several species of interest. To obtain standardized quantitative results, external controls consisting of a DNA template for each target gene were used to generate linear standard curves over a 6 to 8 log range with detection of as few as 10 copies of amplicon per reaction. Sample-to-sample variation in the efficiency of the RT, as well as in the quantity and quality of the starting RNA, was compensated for by normalizing the results to the endogenous housekeeping gene beta(2)-microglobulin. The assay was evaluated by monitoring the kinetics of cytokine mRNA synthesis induced by mitogenic and antigenic stimulation of peripheral blood mononuclear cells (PBMCs) from Mycobacterium bovis-infected elk. Concanavalin A-stimulated PBMCs demonstrated a rapid but transient increase in cytokine mRNA expression following in vitro mitogenic activation with optimal mRNA induction observed after 4 to 16 hr. The PBMCs stimulated with the mycobacterial recall antigen, bovine-purified protein derivative (PPD-bovis), demonstrated variable mRNA induction kinetics for each cytokine. Whereas PPD-bovis optimally induced IL-2 mRNA after 8 hr of in vitro stimulation, longer in vitro stimulation times were necessary for the optimal induction of IL-4 and TNF-alpha mRNA (up to 48 hr). We demonstrate real-time RT-PCR to be a rapid, sensitive, and reproducible technique, which will make it a valuable tool in the study of immunologic responses and cytokine profiles of cervids and other nontraditional livestock and wildlife species.

Investigation of the cause of geographic disparities in IDEXX ELISA sensitivity in serum samples from Mycobacterium bovis-infected cattle.

Accurately identifying Mycobacterium bovis-infected cattle is critical for bovine tuberculosis prevention and control. One method for identifying infected cattle is an ELISA developed by IDEXX laboratories, which detects antibodies to two M. bovis proteins, MPB70 and MPB83. The assay's sensitivity varies by geographic region, with sensitivities of 77%, 45%, and 9% in bovine serum samples from the United Kingdom (n = 126), the United States (n = 146), and Mexico (n = 128), respectively. We hypothesized that geographically-biased sequence variation in mpb70 and mpb83, or in the genes that regulate their expression (sigK and rskA), may explain these differing sensitivities. This hypothesis was tested by comparing the sequences of these four genes in 455 M. bovis strains isolated from cattle in the aforementioned countries. For each gene, a single, common sequence was identified in most genomes of the M. bovis strains collected in all three countries. Twelve of the 455 strains were isolated from infected cattle for which the IDEXX ELISA was also performed. Five of the seven ELISA-positive genomes and three of the five ELISA-negative genomes contained the most common sequence of all four genes. Thus, sequence variation in mpb70, mpb83, sigK, and rskA does not explain the geographic disparities in IDEXX ELISA sensitivity.

Contagious Ecthyma, Rangiferine Brucellosis, and Lungworm Infection in a Muskox ( Ovibos moschatus ) from the Canadian Arctic, 2014.

An adult male muskox ( Ovibos moschatus ), harvested on 26 August 2014 on Victoria Island, Nunavut, in the Canadian Arctic, had proliferative dermatitis on the muzzle and fetlocks suggestive of contagious ecthyma or orf (Parapoxvirus). Histopathologic features of the lesions were consistent with this diagnosis. Orf virus DNA, phylogenetically similar to an isolate from a captive muskox of the Minnesota Zoo, US, was detected in the lesions by PCR using Parapoxvirus primers. Additionally, there was a metaphyseal abscess with a cortical fistula in the right metacarpus from which Brucella suis biovar 4 was isolated and identification supported by PCR. Brucella spp. antibodies were detected in serum. Finally, 212 nodules were dissected from the lungs. Fecal analysis and lung examination demonstrated co-infection with the lungworms Umingmakstrongylus pallikuukensis and Varestrongylus eleguneniensis. The zoonotic potential of orf and rangiferine brucellosis adds an important public health dimension to this case, particularly given that muskoxen are a valuable source of food for Arctic residents. Careful examination of these pathogens at a population level is needed as they may contribute to muskox population decline and potentially constitute a driver of food insecurity for local communities. This case underscores the importance of wildlife health surveillance as a management tool to conserve wildlife populations and maintain food security in subsistence-oriented communities.

Expression in Escherichia coli of flaB, the gene coding for a periplasmic flagellin of Leptospira interrogans serovar pomona.

A periplasmic flagellin gene, flaB, of Leptospira interrogans serovar pomona (strain Pomona) was expressed in Escherichia coli for the production and antigenic characterisation of the protein. The flaB structural gene, which was previously cloned into pUC118, was derived by PCR from the recombinant plasmid and used to generate an expression construct with the trc promoter-driven pProEx HT system. Under the conditions employed, the flaB was expressed as inclusion bodies formed within E. coli, yielding c. 120 mg of the recombinant protein/L of culture. A polyhistidine tag introduced at the amino-acid terminus of the FlaB protein allowed for the purification of the protein by nickel-chelate affinity chromatography. The expressed protein reacted with both mouse and bovine antisera to L. interrogans on Western blots, indicating that it could be of use in the diagnosis of leptospirosis. The recombinant leptospiral flagellin may also be of value in studying its role in the pathogenesis of leptospirosis.

A fluorescence polarization assay for the detection of antibodies to Mycobacterium bovis in cattle sera.

A fluorescence polarization assay (FPA) utilizing fluorescein-labelled MPB70 protein as the antigen was developed and evaluated for its ability to detect antibodies to Mycobacterium bovis in cattle sera. Three panels of sera were examined in this study. These included: (A) sera (n=28) obtained from cattle from which M. bovis was cultured; (B) sera (n=5666) from Canadian field cattle which were presumed to be free from M. bovis; (C) sera (n=10) from cattle infected with Mycobacterium paratuberculosis and known to contain antibodies to this organism. Receiver operating characteristic (ROC) curve analysis of the results of panels A and B yielded an area under the curve value of 0.975 (95% confidence interval=0.971-0.979), which indicated that this FPA is an accurate indicator of M. bovis infection. At the cut-off point recommended by the ROC curve analysis, the FPA sensitivity and specificity estimates were 92.9% (95% confidence interval=76.5-98.9%) and 98.3% (95% confidence interval=97.9-98.6%) respectively. The FPA results were compared to the results of the single intradermal (SID) test for the 28 infected cattle. Fifteen of these animals were scored positive with the SID test (sensitivity=53.6%). The FPA detected 15/15 (100%) of the SID test-positive animals and 11/13 (84.6%) of the SID test-negative animals. Two of the culture-positive cattle were not detected by either test. None of the sera that were obtained from the M. paratuberculosis-infected animals cross-reacted in this assay.

An indirect enzyme linked immunosorbent assay for the detection of bovine antibodies to multiple Leptospira serovars.

An indirect enzyme linked immunosorbent assay was developed for the detection of bovine antibodies to multiple pathogenic Leptospira serovars, including canicola, copenhageni (represents icterohaemorrhagiae), grippotyphosa, hardjobovis, pomona, and sejroe. The antigen utilized in this assay was a sonicated mixture of equal parts of killed whole cells of each of the 6 serovars named above. A mouse monoclonal antibody against bovine immunoglobulin (Ig)G1 that was conjugated with horseradish peroxidase was used for detection of bound antibodies. This assay was evaluated with sera (n = 3107) that were microscopic agglutination test (MAT)-negative (at a 1:100 dilution) for each of the 6 serovars listed above and sera (n = 601) that were MAT-positive (at a 1:100 dilution) for 1, or any combination of the 6 listed serovars. In addition, sera from serial weekly bleedings of cows, which were individually experimentally infected with serovars hardjobovis, copenhageni, grippotyphosa, or canicola, were also tested in this assay. At an optimal cut-off point determined by receiver operating characteristic (ROC) curve analysis, the relative sensitivity and specificity of the assay were 93.5% (95% confidence interval = 91.2% to 95.3%) and 94.7% (95% confidence interval = 93.9% to 95.5%), respectively. This assay was able to detect antibody in the sera of animals experimentally infected with serovar hardjobovis as early as 1 week postinoculation.

Field evaluation of three blood-based assays for elk (Cervus canadensis) naturally infected with Mycobacterium bovis.

Diagnosis of Mycobacterium bovis in wild populations is very challenging due to complications imposed by the use of traditional skin tests, poor sensitivity of gold standard tests which rely on culture of M. bovis from tissues and wide variations in severity of disease. Various combinations of a lymphocyte stimulation test (LST), fluorescence polarization assay (FPA) and the Cervid TB Stat-Pak were evaluated using two different validation approaches: a latent class analysis and classical statistical approach using culture as a gold standard. A validation subsample consisting of animals culled for population control and mortalities from capture provided an unbiased estimate of test performance for comparison. The sensitivity of the LST (0.83, 95% CI: [0.70-0.97] as a single test was similar to existing tuberculin skin tests, but the sensitivity of the FPA (0.40, 95% CI: [0.22-0.58]) and Cervid TB Stat-Pak (0.62, 95% CI: [0.41-0.83]) were lower in this population. Test performance of the LST and Cervid TB Stat-Pak in parallel was similar to the use of all three tests in parallel and inclusion of the FPA did not greatly enhance test performance. Prevalence of M. bovis in elk varied substantially between the high risk area of southern Manitoba (9.1%, 95% CI: [6.09-12.1%]) and lower risk areas outside this zone (0.76%, 95% CI: [0-2.26%]). Bayesian latent class analysis indicated lack of covariance between the two antibody tests (FPA and Cervid TB Stat-Pak) while the classical two-stage analysis indicated there was conditional dependence between the tests. All three tests when used in parallel resulted in 100% NPV using all three validation methods, indicating few elk were misclassified as false negative by post mortem culture. Similar to previous studies, this study found that combinations of blood tests that utilize cell mediated responses along with humoral antibody responses maximize the sensitivity of tests for diagnosis of M. bovis in wild cervid populations.

European 1: a globally important clonal complex of Mycobacterium bovis.

We have identified a globally important clonal complex of Mycobacterium bovis by deletion analysis of over one thousand strains from over 30 countries. We initially show that over 99% of the strains of M. bovis, the cause of bovine tuberculosis, isolated from cattle in the Republic of Ireland and the UK are closely related and are members of a single clonal complex marked by the deletion of chromosomal region RDEu1 and we named this clonal complex European 1 (Eu1). Eu1 strains were present at less than 14% of French, Portuguese and Spanish isolates of M. bovis but are rare in other mainland European countries and Iran. However, strains of the Eu1 clonal complex were found at high frequency in former trading partners of the UK (USA, South Africa, New Zealand, Australia and Canada). The Americas, with the exception of Brazil, are dominated by the Eu1 clonal complex which was at high frequency in Argentina, Chile, Ecuador and Mexico as well as North America. Eu1 was rare or absent in the African countries surveyed except South Africa. A small sample of strains from Taiwan were non-Eu1 but, surprisingly, isolates from Korea and Kazakhstan were members of the Eu1 clonal complex. The simplest explanation for much of the current distribution of the Eu1 clonal complex is that it was spread in infected cattle, such as Herefords, from the UK to former trading partners, although there is evidence of secondary dispersion since. This is the first identification of a globally dispersed clonal complex M. bovis and indicates that much of the current global distribution of this important veterinary pathogen has resulted from relatively recent International trade in cattle.

Comparison of test performance and evaluation of novel immunoassays for tuberculosis in a captive herd of wood bison naturally infected with Mycobacterium bovis.

In 1996, the Hook Lake Wood Bison Recovery Project was initiated to establish a small, disease-free, captive, bison-breeding herd. Founders originated from wild bison herds in the Slave River Lowlands in northern Canada, which, like other bison herds in and around Wood Buffalo National Park, are endemically infected with bovine tuberculosis (caused by Mycobacterium bovis) and brucellosis (caused by Brucella abortus). After 9 yr of apparent disease freedom, tuberculosis was detected within the captive herd, leading to complete depopulation. This study examined the performance of antemortem tuberculosis diagnostic tests used during the project. Performances of the caudal-fold test, fluorescent polarization assay, multiantigen print immunoassay (MAPIA), and the rapid test (RT) were assessed by estimating sensitivity, specificity, positive predictive value, and negative predictive value for each test. Kappa values measuring agreement between tests were calculated. Overall, the tests did not differ with respect to sensitivities and specificities, which ranged from 50% to 92% and from 34% to 100%, respectively. The MAPIA tended to show high sensitivity, and there was significant agreement only between the MAPIA and RT. Serum collected from infected animals at slaughter produced highly variable results on the different assays, and one infected bison was negative on all antemortem tests. The results of this analysis suggest use of multiple antemortem tests in parallel, particularly those incorporating multiple antigens, to optimize sensitivity in detecting bovine tuberculosis in bison. However, as demonstrated in this herd, even a seemingly optimal antemortem testing regimen can fail to detect M. bovis-infected individuals.

Sensitive diagnosis of bovine tuberculosis in a farmed cervid herd with use of an MPB70 protein fluorescence polarization assay.

After histopathological examination of a lesion found in a herd member returned a diagnosis of mycobacteriosis, a farmed herd (n = 47) of elk (Cervus elaphus nelsoni) and red deer (C. elaphus elaphus) was investigated for bovine tuberculosis with a battery of antemortem and postmortem diagnostic tests. Every animal was tested with the mid-cervical tuberculin skin test; all 47 had negative results. All of the 16 adult animals and 15 of the 31 calves (approximately 2-years-old) were blood-tested with a lymphocyte stimulation test (LST) and a fluorescence polarization assay (FPA), which detects antibody to the MPB70 protein antigen. At necropsy of the 31 blood-tested animals, tissues were harvested for histopathological examination and culture of mycobacteria. Mycobacterium bovis was isolated from 16 of the 31 animals, and a scotochromogen was also isolated from 1 of the 16 whose tissues yielded M. bovis. Each of these 16 animals, 15 of which were calves, also received a histopathological diagnosis of mycobacteriosis. Other species of mycobacteria, including those belonging to the M. avium and M. terrae complexes, were isolated from an additional 7 animals. The FPA was scored "positive" or "suspect" for 16 animals, 13 (81%) of which were culture-positive for M. bovis. The other 3 animals that were culture-positive for M. bovis had negative FPA results. Of the 3 FPA-positive or FPA-suspect animals that were culture-negative, 2 were suspected to have mycobacteriosis on the basis of the histopathological examination. The 7 animals from which Mycobacterium species other than M. bovis were cultured were all FPA-negative. The only animal with positive LST results was also FPA-positive and culture-positive for M. bovis. The M. bovis isolates had an identical spoligotype pattern, with an octal code of 664073777777600. This is the first report of the isolation and identification of this strain type in Canada.

Comparative assessment of fluorescence polarization and tuberculin skin testing for the diagnosis of bovine tuberculosis in Chadian cattle.

Effective surveillance of bovine tuberculosis (BTB) in developing countries where reliable data on disease prevalence is scarce or absent is a precondition for considering potential control options. We conducted a slaughterhouse survey to assess for the first time the burden of BTB in Southern Chad. Altogether, 954 slaughter animals were consecutively sampled and tested using the single intra-dermal comparative cervical tuberculin (SICCT) test, a recently developed fluorescence polarization assay (FPA) and routine abattoir meat inspection after slaughter. Gross visible lesions were detected in 11.3% (CI: 9.4-13.5%) of the animals examined and they were mostly located in the lymph nodes and the lung. Significantly more Mbororo zebus (15.0%) were affected by lesions than Arab zebus (9.9%; OR=2.20, CI: 1.41-3.41%; p<0.001). Of all animals tested, 7.7% (CI: 6.2-9.6%) reacted positively to SICCT if OIE guidelines were applied. However, receiver operating characteristic (ROC) analysis using Mycobacterium tuberculosis complex (MTBC) infected animals as the positive population and lesion negative animals as the negative population, revealed a better SICCT performance if the cut-off value was decreased to >2mm. SICCT reactor prevalence rose to 15.5% (CI: 13.3-18.0%) and FPA did not perform better than SICCT, when this setting adapted cut-off was applied.

Antibody responses of cervids (Cervus elaphus) following experimental Mycobacterium bovis infection and the implications for immunodiagnosis.

Captive and free-ranging wildlife animals are implicated in the maintenance and transmission of bovine tuberculosis and therefore pose a significant obstacle to eradication of the disease from domestic livestock. The current antemortem diagnostic method, the intradermal tuberculin skin test, is impractical for routine use with many wild animals. Antibody-based assays are particularly attractive because the animals are handled only once and immediate processing of the sample is not required. This report characterizes the antibody responses of red deer-elk hybrids (Cervus elaphus) against Mycobacterium bovis and subsequently evaluates the diagnostic performance of select antigens in a rapid-test format. Sequential serum samples were collected from 10 animals experimentally infected with M. bovis and 5 noninfected animals over a 7-month period postinfection (p.i.). Samples were evaluated by enzyme-linked immunosorbent assays, immunoblot analyses, and multiantigen print immunoassays for seroreactivity to mycobacterial antigens. Although all infected animals produced antibodies to M. bovis protein antigens, there was significant animal-to-animal variation in the kinetics and magnitudes of responses and the antigens recognized. The most frequently recognized antigens included MPB83, ESAT-6, CFP10, and MPB70. Responses to some antigens, such as MPB83, were consistently detected as early as 4 weeks after inoculation, whereas other antigens were detected only much later (>140 days p.i.). Antibody responses were boosted by injection of tuberculin for intradermal tuberculin skin testing. Comparison of single-antigen (fluorescence polarization assay) with multiantigen (CervidTB STAT-PAK) rapid tests demonstrated that a highly sensitive and specific serodiagnostic test for tuberculosis in cervids will require multiple and carefully selected seroreactive antigens covering a broad spectrum of antibody specificities.

Development and evaluation of a real-time reverse transcription-PCR assay for quantification of gamma interferon mRNA to diagnose tuberculosis in multiple animal species.

Tuberculosis of free-ranging and captive wildlife, including species implicated in the maintenance and transmission of Mycobacterium bovis, is a difficult disease to diagnose and control. Historically, diagnosis of tuberculosis has relied largely upon assays of cell-mediated immunity (CMI), such as tuberculin skin testing. This approach, however, is problematic or impractical for use with many wildlife species. Increasingly, in vitro diagnostic tests, including gamma interferon (IFN-gamma)-based assays, are replacing or complementing skin testing of cattle and humans. Analogous assays are unavailable for most wildlife because of a lack of species-specific immunological reagents. This report describes the development and validation of a whole-blood assay to quantify antigen-specific IFN-gamma mRNA expression by quantitative real-time reverse transcription-PCR. Oligonucleotide primers and probes were designed and tested for reactivity towards several susceptible species of interest with respect to tuberculosis infection. The assay was subsequently optimized to quantify the IFN-gamma mRNA expression in elk and red deer (Cervus elaphus) and was evaluated for its ability to detect mycobacterial antigen-specific responses of experimentally tuberculosis-infected animals. The assay was a simple, rapid, and sensitive measure of antigen-specific CMI. The IFN-gamma mRNA responses correlated well with IFN-gamma protein production and showed performance in determining an animal's infection status superior to that of either lymphocyte proliferation or IFN-gamma protein enzyme-linked immunosorbent assay methods. An additional advantage is the ease with which the assay can be modified to reliably quantify IFN-gamma expression by using consensus sequences of closely related species or of other species for which IFN-gamma sequence information is available.