Bayesian latent class estimation of sensitivity and specificity parameters of diagnostic tests for bovine tuberculosis in chronically infected herds in Northern Ireland.

In the European Union, the recommended ante-mortem diagnostic methods for bovine tuberculosis (bTB) include the single intradermal cervical comparative tuberculin (SICCT) test and the interferon-gamma (IFN-γ) test as an ancillary test. The SICCT test has a moderate sensitivity (Se) and high specificity (Sp), while the IFN-γ test has good Se, but a lower Sp than the SICCT test. A retrospective Bayesian latent class analysis was conducted on 71,185 cattle from 806 herds chronically infected with bTB distributed across Northern Ireland (NI) to estimate the Se and Sp of the common ante-mortem tests and meat inspection. Analyses were also performed on data stratified by farming type and herd location to explore possible differences in test performance given the heterogeneity in the population. The mean estimates in chronically infected herds were: (1) 'standard' SICCT: Se 40.5-57.7%, Sp 96.3-99.7%; (2) 'severe' SICCT: Se 49.0%-60.6%, Sp 94.4-99.4%; (3) IFN-γ(bovine-avian) using a NI optical density (OD) cut-off difference of 0.05: IFN-γ(B-A)NI: Se 85.8-93.0%, Sp 75.6-96.2%; (4) IFN-γ(bovine-avian) using a standard 'commercial' OD cut-off difference of 0.1: IFN-γ(B-A)0.1: Se 83.1-92.1%, Sp 83.1-97.3%; and (5) meat inspection: Se 49.0-57.1% Se, Sp 99.1-100%. Se estimates were lower in cattle from dairy farms than from beef farms. There were no notable differences in estimates by location of herds. Certain population characteristics, such as production type, might influence the ability of bTB tests to disclose truly infected cases.

An analysis of effects of heterozygosity in dairy cattle for bovine tuberculosis resistance.

Genetic selection of cattle more resistant to bovine tuberculosis (bTB) may offer a complementary control strategy. Hypothesising underlying non-additive genetic variation, we present an approach using genome-wide high density markers to identify genomic loci with dominance effects on bTB resistance and to test previously published regions with heterozygote advantage in bTB. Our data comprised 1151 Holstein-Friesian cows from Northern Ireland, confirmed bTB cases and controls, genotyped with the 700K Illumina BeadChip. Genome-wide markers were tested for associations between heterozygosity and bTB status using marker-based relationships. Results were tested for robustness against genetic structure, and the genotypic frequencies of a significant locus were tested for departures from Hardy-Weinberg equilibrium. Genomic regions identified in our study and in previous publications were tested for dominance effects. Genotypic effects were estimated through ASReml mixed models. A SNP (rs43032684) on chromosome 6 was significant at the chromosome-wide level, explaining 1.7% of the phenotypic variance. In the controls, there were fewer heterozygotes for rs43032684 (P < 0.01) with the genotypic values suggesting that heterozygosity confers a heterozygote disadvantage. The region surrounding rs43032684 had a significant dominance effect (P < 0.01). SNP rs43032684 resides within a pseudogene with a parental gene involved in macrophage response to infection and within a copy-number-variation region previously associated with nematode resistance. No dominance effect was found for the region on chromosome 11, as indicated by a previous candidate region bTB study. These findings require further validation with large-scale data.

Fine-mapping host genetic variation underlying outcomes to Mycobacterium bovis infection in dairy cows.

BACKGROUND: Susceptibility to Mycobacterium bovis infection in cattle is governed in part by host genetics. However, cattle diagnosed as infected with M. bovis display varying signs of pathology. The variation in host response to infection could represent a continuum since time of exposure or distinct outcomes due to differing pathogen handling. The relationships between host genetics and variation in host response and pathological sequelae following M. bovis infection were explored by genotyping 1966 Holstein-Friesian dairy cows at 538,231 SNPs with three distinct phenotypes. These were: single intradermal cervical comparative tuberculin (SICCT) test positives with visible lesions (VLs), SICCT-positives with undetected visible lesions (NVLs) and matched controls SICCT-negative on multiple occasions. RESULTS: Regional heritability mapping identified three loci associated with the NVL phenotype on chromosomes 17, 22 and 23, distinct to the region on chromosome 13 associated with the VL phenotype. The region on chromosome 23 was at genome-wide significance and candidate genes overlapping the mapped window included members of the bovine leukocyte antigen class IIb region, a complex known for its role in immunity and disease resistance. Chromosome heritability analysis attributed variance to six and thirteen chromosomes for the VL and NVL phenotypes, respectively, and four of these chromosomes were found to explain a proportion of the phenotypic variation for both the VL and NVL phenotype. By grouping the M. bovis outcomes (VLs and NVLs) variance was attributed to nine chromosomes. When contrasting the two M. bovis infection outcomes (VLs vs NVLs) nine chromosomes were found to harbour heritable variation. Regardless of the case phenotype under investigation, chromosome heritability did not exceed 8% indicating that the genetic control of bTB resistance consists of variants of small to moderate effect situated across many chromosomes of the bovine genome. CONCLUSIONS: These findings suggest the host genetics of M. bovis infection outcomes is governed by distinct and overlapping genetic variants. Thus, variation in the pathology of M. bovis infected cattle may be partly genetically determined and indicative of different host responses or pathogen handling. There may be at least three distinct outcomes following M. bovis exposure in dairy cattle: resistance to infection, infection resulting in pathology or no detectable pathology.

Genome-wide association study identifies novel loci associated with resistance to bovine tuberculosis.

Tuberculosis (TB) caused by Mycobacterium bovis is a re-emerging disease of livestock that is of major economic importance worldwide, as well as being a zoonotic risk. There is significant heritability for host resistance to bovine TB (bTB) in dairy cattle. To identify resistance loci for bTB, we undertook a genome-wide association study in female Holstein-Friesian cattle with 592 cases and 559 age-matched controls from case herds. Cases and controls were categorised into distinct phenotypes: skin test and lesion positive vs skin test negative on multiple occasions, respectively. These animals were genotyped with the Illumina BovineHD 700K BeadChip. Genome-wide rapid association using linear and logistic mixed models and regression (GRAMMAR), regional heritability mapping (RHM) and haplotype-sharing analysis identified two novel resistance loci that attained chromosome-wise significance, protein tyrosine phosphatase receptor T (PTPRT; P=4.8 × 10(-7)) and myosin IIIB (MYO3B; P=5.4 × 10(-6)). We estimated that 21% of the phenotypic variance in TB resistance could be explained by all of the informative single-nucleotide polymorphisms, of which the region encompassing the PTPRT gene accounted for 6.2% of the variance and a further 3.6% was associated with a putative copy number variant in MYO3B. The results from this study add to our understanding of variation in host control of infection and suggest that genetic marker-based selection for resistance to bTB has the potential to make a significant contribution to bTB control.

Mycobacterium bovis genotypes in Northern Ireland: herd-level surveillance (2003 to 2008).

Surveillance genotyping (variable number tandem repeat profiling and spoligotyping) of Mycobacterium bovis isolates from culture-confirmed bovine tuberculosis (TB)-affected herds in Northern Ireland is presented for the years 2003 to 2008 inclusive. A total of 175 M bovis genotypes were identified in 8630 isolates from 6609 herds. On average, 73 genotypes were identified each year, with 29 genotypes present in all six years. Highly significant differences (P<0.0001) were observed between the relative frequency of some genotypes in the years 2003 to 2008. The spatial distribution of M bovis genotypes was not random (P<0.0001). Significant geographical localisation of M bovis genotypes was evident, suggesting that sources tended to be local. Despite regions being dominated by geographically localised genotypes, substantial and exploitable local diversity was still evident. Genotypes were also translocated significant distances from their normal geographical location.

Campylobacter spp. in conventional broiler flocks in Northern Ireland: epidemiology and risk factors.

Risk factors for Campylobacter infection in conventional broiler flocks in the time period up to the first removal of birds to slaughter were investigated over a maximum of five consecutive production cycles in a cohort of 88 broiler farms in Northern Ireland. Samples for Campylobacter culture, which consisted of 14 cloacal swabs per flock, were collected from one house on each farm prior to the first depopulation of birds. In total 388 flocks were sampled, of which 163 tested positive for Campylobacter spp. (42.0%; 95% CI 35.1-48.9%). Data on farm and flock variables were obtained from questionnaires and random-effects logistic regression modelling used to investigate the association between these and the Campylobacter status of flocks. Six variables, all of which were significant at p<0.05, were included in the final multivariable model. These included a combined variable on the presence of rodents on farms, which showed an increased odds of infection in flocks where the farmer reported having observed rodents during the production cycle (OR=2.1) and/or where rodent droppings were observed at the sampling visit (OR=2.9). Other variables that were significantly associated with an increased odds of infection included the age of the birds at sampling (odds ratio for its linear effect=1.16 for each day of increase in age), season (summer versus other seasons OR=2.0), farms with three or more broiler houses (OR=2.9 compared to those with one house), the frequency of footbath disinfectant changes (OR=2.5 for once weekly and OR=4.0 for less than once weekly compared to twice weekly changes) and a categorical variable on the standard of tidiness and cleanliness of the broiler house ante-room (OR=2.0 and OR=4.9 for flocks from houses with poorer standards). There was no significant evidence of direct carry-over of infection from one production cycle to the next, neither was there evidence of other farm species acting as a source of infection.

Discrimination of isolates of Mycobacterium bovis in Northern Ireland on the basis of variable numbers of tandem repeats (VNTRs).

The ability to reproducibly discriminate Mycobacterium bovis isolates and trace their transmission has the potential to clarify sources of infection and major routes of transmission for bovine tuberculosis (TB). A PCR-based genotyping assay has been developed to discriminate between strains of M bovis by examining multiple sites in its genome that consist of variable numbers of tandem repeats (VNTRS). The discriminatory power and reproducibility of this VNTR typing has been compared with that of the established PCR-based spoligotyping technique by using a panel of 461 isolates of M bovis prevalent in Northern Ireland. The VNTR assay discriminated 40 different profiles, the most prevalent of which constituted 21 per cent of the total, compared with 14 profiles discriminated by spoligotyping, the most prevalent of which constituted 65 per cent. No significant differences were observed between the prevalences of the VNTR profiles in the years from 1999 to 2003. A preliminary evaluation indicated that most genotypes predominated in particular areas of the country. This VTNR typing assay was found to be highly discriminating, with the performance characteristics to support its systematic application to the molecular epidemiology of bovine TB.

Risk factors for toxic mastitis in cows.

A case-control study of the management and disease risk factors associated with toxic mastitis in cows was carried out. Seventy-one cases satisfied all the selection criteria, and a subset of 41 cases in which pure growths of Escherichia coil were cultured from milk samples was also investigated. Conditional multiple logistic regression analysis of the 71 cases and matched controls revealed no statistically significant associations. However, among the subset of 41 cases and matched controls, the administration of calcium parenterally at calving (P < 0.01) and assistance at calving (P < 0.01) were both associated with toxic mastitis. Controlling for assistance at calving, the odds of a cow developing E coli toxic mastitis if it had received calcium parenterally at calving were 23 times higher than for a cow that had not received calcium. Similarly, controlling for the administration of calcium at calving, the odds of a cow developing E coli toxic mastitis if it had received assistance at calving were 11 times higher than for a cow that did not receive assistance.

Clinical and laboratory findings in cases of toxic mastitis in cows in Northern Ireland.

This paper describes the clinical and laboratory findings from 264 cases of toxic mastitis in cows in Northern Ireland between October 1995 and May 1997. Nearly all the cases occurred during the winter housing period, with 84 per cent occurring between November and March inclusive, and 30 per cent in March. Sixty per cent of the cases occurred within one month of calving, and 29 per cent within four days of calving. The most common clinical signs were lethargy (92 per cent), discoloured milk (90 per cent), anorexia (72 per cent), tachypnoea (23 per cent), diarrhoea (23 per cent), recumbency (18 per cent) and staggering (15 per cent). Severe pyrexia (18 per cent) and clinical dehydration (44 per cent) were relatively common findings. Pure growths of Escherichia coli were isolated from 50 per cent of the milk samples, but 11 per cent yielded no bacterial growth. In vitro sensitivity tests indicated that enrofloxacin was effective against 98 per cent of the bacteria isolated, and framycetin and amoxycillin/clavulanic acid against 91 per cent. Abnormally high blood urea levels were observed in 31 per cent of cases, high blood creatinine levels in 42 per cent, and severe leucopenia in 56 per cent. Of the cases which were followed up, 14 per cent died, 21 per cent were culled early and a further 22 per cent lost milk production from the affected quarter.

Attitudes toward computers. A test of construct validity.

A study was undertaken to examine the factors that influence student and registered nurse attitudes toward computers. This article provides a report of the psychometric findings related to the use of Stronge and Brodt's Nurses' Attitudes Toward Computerization questionnaire. The convenience sample consisted of 394 registered nurses employed in a large metropolitan hospital and 299 baccalaureate student nurses. Principal component analysis was performed identifying three factors for the nurse sample, including nurses' work, organizational issues, and barriers to use. Four factors emerged in the student sample: nurses' work, barriers, organizational issues, and efficiency issues. These findings were inconsistent with previous studies and the underlying categories identified by Stronge and Brodt. Further development of the understanding of the substantive components of attitudes toward computers is recommended.

Comparative analysis of three instruments designed to measure self-care agency.

A number of instruments are used to measure Orem's (1985) concept of self-care agency. Their use reflects basic assumptions that both the instrument and the underlying tenets of the theory are valid. The purpose of this study was to examine the latent traits associated with three instruments designed to measure self-care agency. These included Denyes' (1980) Self-Care Agency, Kearney and Fleischer's (1979) Exercise of Self-Care Agency, and Hanson and Bickel's (1985) Perception of Self-Care Agency. The convenience sample consisted of 513 adult, nonhospitalized subjects who completed the three instruments. Common factor analysis and canonical correlation were used to identify latent traits and their relationships. The findings support the multidimensionality of Orem's (1985) concept of self-care agency. However, the use of one instrument does not adequately reflect this multidimensionality.