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.

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 () and muskoxen () in the Central Canadian Arctic by using data from community-based wildlife health surveillance programs. The overall sample prevalence of a antibodies was 10.

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.

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.

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.

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.

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).

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.

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.

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).

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.

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.

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.

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.

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.

Risk of transmission of Mycobacterium avium ssp. paratuberculosis by embryo transfer of in vivo and in vitro fertilized bovine embryos.

Over a 5-year interval, experiments were conducted to determine if Mycobacterium avium ssp. paratuberculosis (Map) is associated with in vivo and in vitro fertilized (IVF) embryos and whether it can be transmitted by embryo transfer. The present studies included: collection of embryos from five asymptomatic, naturally infected donors and transfer to uninfected recipients; collection of oocytes from two naturally infected donors with overt clinical signs; exposure of in vivo and IVF embryos to Map and transfer to uninfected recipients; and the inoculation (transfer) of "clean" IVF embryos to the uterine lumen of infected cows.

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.

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.

Competitive enzyme-linked immunosorbent assay for detection of Leptospira interrogans serovar pomona antibodies in bovine sera.

A competitive enzyme-linked immunosorbent assay (ELISA) using a specific monoclonal antibody (M898) was developed for detection of bovine antibodies to Leptospira interrogans serovar pomona. This assay was evaluated using field sera (n = 190) with serovar pomona microscopic agglutination test (MAT) titers of > or =100 as the positive population (group A); field sera (n = 1,445) which were negative in the MAT (1:100 dilution) for serovar pomona (group B); and sera (from a specific-pathogen-free cattle herd [n = 210]) which were negative in the MAT (1:100 dilution) for serovars canicola, copenhageni, grippotyphosa, hardjo, pomona, and sejroe (group C). At the cutoff point recommended by receiver operating characteristic (ROC) curve analysis of the combined ELISA results of serum groups A, B, and C, the sensitivity and specificity values were 93.

Monoclonal antibodies suitable for incorporation into a competitive enzyme-linked immunosorbent assay (ELISA) for detection of specific antibodies to Leptospira interrogans serovar pomona.

Monoclonal antibodies (mAb) were produced by fusing Sp2/0-Ag14 myeloma cells with spleen cells from BALB/c and ND4 mice that were immunized with killed Leptospira interrogans serovar pomona whole cells. Thirty hybridomas which produced antibodies (of the IgG1, IgG2a, IgG2b, or IgG3 isotype) that bound to epitopes on the serovar pomona whole cell antigen were identified by an indirect enzyme-linked immunosorbent assay (ELISA). Twenty-eight of these 30 mAbs cross-reacted in the indirect ELISA with at least one whole cell antigen prepared from 12 other pathogenic Leptospira serovars, and/or with whole cell antigen from the non-pathogenic Leptospira biflexa serovar patoc.

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.

Use of recombinant flagellin protein as a tracer antigen in a fluorescence polarization assay for diagnosis of leptospirosis.

The objective of the present study was to investigate the usefulness of a recombinant flagellar protein, FlaB, of Leptospira interrogans serovar pomona in the serodiagnosis of leptospirosis by the fluorescence polarization assay (FPA). The recombinant protein FlaB was purified to homogeneity by a combination of nickel-nitriloacetic acid agarose chromatography, electrophoresis, and electroelution. Purified FlaB was labeled with fluorescein isothiocyanate (FITC).

Production and characterization of monoclonal antibodies specific for Leptospira borgpetersenii serovar hardjo type hardjobovis and Leptospira interrogans serovar hardjo type hardjoprajitno.

Murine monoclonal antibodies were produced by immunizing BALB/c mice with a killed whole-cell antigen prepared from Leptospira borgpetersenii serovar hardjo type hardjobovis. Six of these antibodies recognized epitopes on the homologous antigen and on whole-cell antigen prepared from Leptospira interrogans serovar hardjo type hardjoprajitno. These antibodies did not cross-react with whole-cell antigens prepared from L.

Sanitary status of oocytes and embryos collected from heifers experimentally exposed to Leptospira borgpetersenii serovar hardjobovis.

In a preliminary trial and three experiments, a total of 30 Holstein heifers were experimentally infected with a culture of Leptospira borgpetersenii serovar hardjobovis via one or more routes (uterine, cervical supraconjunctival, intranasal) and oviductal and uterine fluids recovered post-mortem or in vivo following superovulation with FSH. All routes of administration were effective in establishing Leptospira infection in the reproductive tract and Leptospira were identified in the oviductal and uterine fluids of all 30 heifers by microscopy. The incidence of infection was confirmed by positive identification of serum antibodies by the microscopic agglutination test (MAT).

Leptospira borgpetersenii serovar hardjo type hardjobovis in bovine embryos fertilized in vitro.

The association of Leptospira borgpetersenii serovar hardjo type hardjobovis with bovine embryos produced by in vitro fertilization was examined by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Morula stage embryos with an intact zona pellucida (ZP) were exposed to this spirochete for 24 h in culture medium, washed by the standard washing procedure as recommended by the International Embryo Transfer Society, and then examined. SEM showed typical helicoid leptospires on the surface and in the pores of the ZP.