SciCombinator

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Journal: Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc

144

Inflammatory bowel disease (IBD) and alimentary lymphoma (ALA) are common gastrointestinal diseases in cats. The very similar clinical signs and histopathologic features of these diseases make the distinction between them diagnostically challenging. We tested the use of supervised machine-learning algorithms to differentiate between the 2 diseases using data generated from noninvasive diagnostic tests. Three prediction models were developed using 3 machine-learning algorithms: naive Bayes, decision trees, and artificial neural networks. The models were trained and tested on data from complete blood count (CBC) and serum chemistry (SC) results for the following 3 groups of client-owned cats: normal, inflammatory bowel disease (IBD), or alimentary lymphoma (ALA). Naive Bayes and artificial neural networks achieved higher classification accuracy (sensitivities of 70.8% and 69.2%, respectively) than the decision tree algorithm (63%, p < 0.0001). The areas under the receiver-operating characteristic curve for classifying cases into the 3 categories was 83% by naive Bayes, 79% by decision tree, and 82% by artificial neural networks. Prediction models using machine learning provided a method for distinguishing between ALA-IBD, ALA-normal, and IBD-normal. The naive Bayes and artificial neural networks classifiers used 10 and 4 of the CBC and SC variables, respectively, to outperform the C4.5 decision tree, which used 5 CBC and SC variables in classifying cats into the 3 classes. These models can provide another noninvasive diagnostic tool to assist clinicians with differentiating between IBD and ALA, and between diseased and nondiseased cats.

Concepts: Gastroenterology, Artificial intelligence, Decision tree, Neural network, Supervised learning, Inflammatory bowel disease, Decision tree learning, Machine learning

23

Dogs with a 4-bp deletion in the MDR1 (or ABCB1) gene show intolerance to certain drugs routinely used in veterinary medicine, such as ivermectin, vincristine, and doxorubicin. The mutation leads to a dysfunctional P-glycoprotein drug transporter, which results in drug accumulation in the brain and severe neurotoxicity. A rapid and accurate in-house test to determine the genotype of patients in cases of acute neurotoxic signs or in tumor patients is desirable. We describe a cost-effective detection method with simple technical equipment for veterinary practice. Two allele-specific methods are presented, which allow discrimination of all genotypes, require little hands-on time, and show the results within ~1 h after DNA sampling. DNA from buccal swabs of 115 dogs with known genotype (no mutation, n = 54; heterozygous for the mutation, n = 37; homozygous for the mutation, n = 24) was extracted either by using a column-based extraction kit or by heating swabs in a simple NaOH-Tris buffer. Amplification was performed either by allele-specific fast polymerase chain reaction or by allele-specific loop-mediated isothermal amplification (LAMP). Analysis was done either on agarose gels, by simple endpoint visualization using ultraviolet light, or by measuring the increase of fluorescence and time to threshold crossing. Commercial master mixes reduced the preparation time and minimized sources of error in both methods. Both methods allowed the discrimination of all 3 genotypes, and the results of the new methods matched the results of the previous genotyping. The presented methods could be used for fast individual MDR1/ ABCB1 genotyping with less equipment than existing methods.

Concepts: Ultraviolet, Evolution, Agarose gel electrophoresis, Zygosity, Molecular biology, Polymerase chain reaction, Genetics, DNA

2

Respiratory diseases in pigs are mostly polymicrobial, and the involved pathogens can vary from farm to farm. The impact ofPneumocystis carinii(P. c.) f. sp.suison respiratory disorders has not been comprehensively appraised because tests were limited to lung tissue samples and, for this reason, it was not possible to detect the fungus in living animals. In the present study, bronchoalveolar lavage fluid (BALF) from 12 pigs and oral fluid samples from 9 pigs were tested for the presence ofPneumocystisby quantitative real-time polymerase chain reaction. The results from these 2 clinical specimens were compared withPneumocystisquantities in lung tissue samples.Pneumocystisquantities in BALF correlated significantly to those in lung tissue. BALF has proved to be an adequate specimen for detection of various respiratory pathogens in pigs, and the collection procedure directly on farms is also well established. In contrast to the BALF results, all oral fluid samples were negative. Thus, specimens from the lower respiratory tract should generally be preferred for the detection ofPneumocystis Additionally, under farm conditions, oral fluid is mainly collected in the form of collective samples per pen. In the present study, oral swab sampling of individual pigs was intended but failed in 3 of 12 pigs because they did not salivate sufficiently. As a conclusion, only BALF can be recommended as a useful tool forPneumocystisherd monitoring in vivo.

Concepts: Molecular biology, Enzyme, Upper respiratory tract, Respiratory system, Real-time polymerase chain reaction, Bronchoalveolar lavage, Polymerase chain reaction, Pulmonology

1

Bovine respiratory disease continues to be the most important ailment of feed yard cattle. While the disease is multifactorial in nature, therapy continues to target the primary bacterial pathogens, Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni. A survey of records from a single diagnostic laboratory was conducted to evaluate the percentage of M. haemolytica isolates that were resistant to multiple antimicrobials and if coresistance patterns could be detected. All susceptibility test results for M. haemolytica recovered from lung tissues of cattle were eligible for inclusion in the survey. There were no isolates over the course of the analysis that were resistant to all 6 antimicrobials, primarily due to a lack of resistance to ceftiofur. In 2009, just over 5% of isolates were resistant to 5 or more antimicrobials (pan-resistant). In 2011, more than 35% of the M. haemolytica isolates were characterized as pan-resistant. Significant antimicrobial coresistance patterns were only seen with oxytetracycline and tilmicosin; bacterial isolates that were resistant to either oxytetracycline or tilmicosin were more likely to be resistant to at least one other antimicrobial. The mechanisms by which M. haemolytica is developing multidrug resistance warrant investigation if antimicrobial utility in the therapy of bovine respiratory disease is to be preserved.

Concepts: Medicine, Infection, Cancer, Pulmonology, Antibiotic resistance, Pathogen, Pasteurella multocida, Microbiology

0

Method validation studies characterize the performance of new laboratory methods relative to established methods using quality guidelines in order to define the new method’s performance characteristics and to identify differences that could influence data interpretation. We investigated the performance of an in-clinic dry chemistry analyzer (Catalyst One, IDEXX) for measuring 19 routine plasma biochemistry analytes in dogs, cats, and horses. We analyzed 2 levels of quality control material (QCM) in duplicate twice daily for 5 d to determine the coefficient of variation (CV), percent bias, observed total error (TEobs), and sigma metric (σ) for each analyte at each level of QCM. We analyzed 82 canine, equine, and feline plasma samples with the in-clinic dry chemistry analyzer and a reference wet chemistry analyzer, and results were compared using correlation coefficients, Deming regression, and Bland-Altman analyses. CVs were <5% for 16 analytes and ⩾5% for 3 analytes. TEobs was less than allowable total error (TEa) for 9 analytes, and exceeded TEa for 10 analytes. Sigma metrics were >4 at both levels of QCM for 5 analytes, and at one level of QCM for 5 analytes; sigma metrics were <3 or could not be calculated at the remaining analyte concentrations. All analytes, except glucose, showed various magnitudes of bias compared to the wet chemistry analyzer. Based on these results, we recommend statistical (5 analytes) and non-statistical (14 analytes) QC measures and analyzer-specific reference intervals.

0

Carcinosarcomas are biphasic malignant tumors composed of 2 distinct neoplastic cell populations, epithelial cells and mesenchymal cells. A 13-y-old, female, mixed-breed goat was presented with a 1-wk history of anuria and lethargy. Transabdominal ultrasonography showed an irregular and heterogeneous structure in the region of the bladder and uterus and changes in the echogenicity of both kidneys. Given the poor prognosis, euthanasia was elected. Autopsy revealed a large mass within the uterine cervix and confirmed the changes in the urinary tract. Histopathology and immunohistochemistry revealed a mixed, anti-cytokeratin AE1/AE3-positive epithelial, and vimentin-positive mesenchymal neoplasm consistent with a homologous carcinosarcoma, also called malignant mixed Müllerian tumor, with areas of double-labeling. We highlight the complexity of the diagnosis of uterine neoplasms in domestic animals and in goats in particular.

0

We describe the clinicopathologic features of an ovine case of Krabbe disease (globoid cell leukodystrophy). Brain lesions, sometimes bilaterally distributed, were present in the cerebellar peduncles, cerebellar folia white matter, medulla, pons, and spinal cord and characterized by marked myelin loss and numerous large macrophages (globoid cells), which tended to aggregate perivascularly. Gemistocytic astrocytes were abundant, and their nuclei were frequently abnormal. The activity of the deficient enzyme, galactosylceramide β-galactosidase, was undetectable in this neurologic disorder compared to age- and breed-matched control brains, and levels of the neurotoxic substrate, psychosine, were markedly elevated.

0

We conducted a nested, case-control study of pre-weaned dairy calves ( n = 477; 4 California dairy farms) to assess the association between bovine respiratory disease (BRD) and hematologic biomarkers, including plasma haptoglobin (Hp) and plasma bactericide (PB). At each location, heifer or bull dairy calves were observed 2-4 times per week until confirmed as BRD-positive using parallel interpretation of thoracic ultrasound examination and auscultation. In addition, control calves were enrolled after being confirmed as BRD-negative using ultrasound and auscultation. Complete blood counts (CBC), PB, and Hp concentrations were measured. Hp values were higher in calves with confirmed BRD than in controls ( p < 0.01). The area under the curve (AUC) for the various biomarkers was obtained from the corresponding receiver operating characteristic curves. The AUC for Hp was 0.68, a value greater than those for PB or the remaining CBC parameters, indicating that Hp may be the most useful biomarker of BRD in pre-weaned dairy calves. The cutoff value for Hp was 0.195 g/L.

0

We evaluated effects of handling procedures on detection of porcine reproductive and respiratory syndrome virus (PRRSV) in oral fluids (OFs) by reverse-transcription real-time PCR (RT-rtPCR). The experiments were conducted using a composite sample of PRRSV-positive OF collected from 5-wk-old pigs vaccinated 15 d earlier with a modified-live PRRSV vaccine. Five pre-extraction sample-handling steps and all combinations thereof were evaluated: 1) thaw temperature (4°C or 25°C); 2) sample diluent (1:1 dilution with nuclease-free water or guanidinium thiocyanate-phenol); 3a) sonication of the sample (yes or no); 3b) temperature (4°C or 25°C) at which step 3a was conducted; and 4) temperature at which the sample was maintained after step 3b and until RNA extraction was initiated (4°C or 25°C). All combinations of the 5 sample-handling steps (i.e., 32 unique treatments) were tested in a completely randomized factorial design with 4 replicates and 1 negative control for each treatment. The entire experiment was repeated on 5 separate days to produce a total of 800 PRRSV RT-rtPCR results. Binary (positive or negative) data were analyzed by logistic regression and results (Ct) were analyzed using a generalized linear model. Overall, 1 false-positive result was observed among 160 negative controls (99.4% specificity), and 85 false-negative results were observed among the 640 known-positive samples (86.7% sensitivity). The most significant factor affecting test outcome was thaw temperature (4°C or 25°C); samples thawed at 4°C had higher positivity rate (94% vs. 80%, p < 0.0001) and lower Ct (36.2 vs. 37.5, p < 0.0001).

0

We compared 3 major cross-match (XM) tests to identify dog erythrocyte antigen (DEA) 7 blood incompatibilities in dogs as a result of anti-DEA 7 antibodies: gel (GEL), standard tube (TUBE) agglutination, and immunochromatography strips (STRIP). Blood samples from 42 dogs were typed for DEA 7; 2 tested DEA 7-positive (DEA 7+). The 40 DEA 7-negative (DEA 7-) plasma samples were cross-matched against the 2 DEA 7+ and 3 DEA 7- red blood cell (RBC) samples by GEL to identify samples with anti-DEA 7 antibodies. Twenty DEA 7- plasma samples without and with anti-DEA 7 antibodies were cross-matched with samples of the 2 DEA 7+ RBCs in a double-blind fashion using the TUBE and STRIP XM methods. GEL results were used as the reference method for comparison. To determine relationships between results, 2 × 2 tables were used. Cohen kappa coefficient (κ) was calculated between results of GEL and the other 2 methods. With GEL, 21 of 40 XM tests were positive and 19 of 40 negative for anti-DEA 7 antibodies. The same results were obtained by TUBE, whereas only 1 of 40 XM tests was positive by STRIP. There was a statistically significant relationship between results of GEL and TUBE ( p < 0.000) with perfect agreement (κ = 1.000), but not between GEL and STRIP results ( p = 1.000) in which agreement was equivalent to chance (κ = 0.0453). The GEL and TUBE XM tests, but not STRIP, are useful methods for identification of DEA 7 incompatibilities caused by anti-DEA 7 antibodies.