Odds ratios for explanatory variables with 95% credible intervals.

<p>Odds ratios for explanatory variables with 95% credible intervals.</p

Slaughterhouse effects.

<p>Posterior variances against posterior means for the slaughterhouse hierarchical intercepts terms, shown against each other (left-hand panel) and mapped to the spatial locations of the slaughterhouses (right-hand panel). The larger the point, the more precisely the term has been estimated, with blue points corresponding to slaughterhouses that find more cases than expected, and red points corresponding to slaughterhouses that find less cases than expected, according to the fitted model.</p

Animal-level variables used in regression model.

<p>Animal-level variables used in regression model.</p

Descriptive plots of numbers of breakdowns of different types over time.

<p>Number of Officially TB Free Suspended (OTFS) and Officially TB Free Withdrawn (OTFW) breakdowns, and the number of OTFW breakdowns initiated either through slaughterhouse surveillance (SLH) or skin (SICCT) testing per year, stratified by Parish Testing Interval (PTI). (Note the different <i>y</i>-axis scales in each plot). The trend lines and 95% confidence intervals are obtained from simple loess smoothing.</p

Descriptive plots of proportions of breakdowns of different types over time.

<p>Proportions of total breakdowns (BD) that are Officially TB Free Withdrawn (OTFW), and proportion of OTFW breakdowns that are initiated in the slaughterhouse (SLH) per year, stratified by Parish Testing Interval (PTI). (Note the different <i>y</i>-axis scales in each plot). The trend lines and 95% confidence intervals are obtained from simple loess smoothing.</p

Break-even points for vaccine efficacy under alternative testing scenarios using γ-DIVA test.

<p>We estimate the break-even point for a protective benefit of BCG vaccination at the herd level under three alternative testing scenarios. We model DIVA testing using parameter estimates that optimize DIVA specificity of 99.4% under the constraint of maintaining a DIVA sensitivity comparable to tuberculin testing of 64.4%. We consider four key measures of the epidemiological, and economic, costs associated with bTB testing: <b>A</b> the number of animals condemned as reactors; <b>B</b> the number of tests (tuberculin and DIVA) needed to clear restrictions; <b>C</b> The number of infected animals left in herds after restrictions are lifted (burden of infection missed by testing) <b>D</b> The number of herds that experience a breakdown before the herd clears the singleton challenge. For all panels, solid black lines indicate the median break-even point for the baseline scenario with no vaccination. Dashed lines indicate the 95% quantiles of the baseline scenario. The distribution for each measure is calculated from 100 simulations with parameters drawn from the (approximate) posterior distributions of our estimated model, with each parameter set simulated once for each herd within our representative study population (of 6,601 herds).</p

Age-stratified patterns of reactors in Great Britain.

<p><b>A</b> The relative risk of infection by age RR(a) measured relative to the risk for 0–1 year old cattle, Error bars denote 95% credible intervals. RR(a) is calculated as the ratio of the force of infection for each age group divided by the estimate for the 0–1 year old group. The force of infection is a combined estimate for all national herds (beef and dairy) calculated from reactor cattle reported between 2004–2009 as described in [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004038#pcbi.1004038.ref021" target="_blank">21</a>]. <b>B</b> The probability of “confirmation” of reactor animals by the presence of visible lesions or culture as a function of age at slaughter, estimated as the proportion of reactor animals within each (200 day) age-class that demonstrated visible lesions or a positive culture result. Estimates are calculated using all reactor animals from within our study population of herds. The qualitative pattern is robust between different test-types and parish testing intervals [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004038#pcbi.1004038.ref021" target="_blank">21</a>].</p

Markov events for SORI(V) stochastic transmission model.

<p>Markov events for SORI(V) stochastic transmission model.</p

SORI model fit to age-distributions of reactors.

<p>SORI model predictive distributions for the age of reactors (<b>A</b>). Age of “confirmed” reactors with evidence of visible lesions (<b>B</b>). Slaughterhouse cases (<b>C</b>) and the proportion of animals with visible lesions stratified by age (<b>D</b>). Solid points and lines indicate empirical target distributions, model predictive distributions are once again overplotted as shaded density strips where the intensity of color is proportional to the probability density at that point [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004038#pcbi.1004038.ref034" target="_blank">34</a>].</p

Epidemiological target measures for ABC.

<p>Epidemiological target measures for ABC.</p