The assumed distribution of probability of detection in each year of a 15 year scrapie epidemic [30].

<p>The assumed distribution of probability of detection in each year of a 15 year scrapie epidemic <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032884#pone.0032884-McIntyre1" target="_blank">[30]</a>.</p

Cost-effectiveness plane examining all flocks (high, moderate and low risk) with different proportions of susceptible genotypes.

<p>In this analysis, we have found the unit cost of pre-clinical testing that makes the total CSFS and MT (including compensation, labour and testing) equivalent costs. The cost effectiveness planes vary by test sensitivity (rows 50–90%) and proportions of susceptible genotype (columns 10–40%) The outlined points on the plot represent dominated strategies. The origin in each panel represents no intervention. In high-risk flocks, the CSFS and MT are more efficient than the single test strategy (ST) at high proportions of susceptible genotypes within the flock (i.e. >30%). At lower proportions of susceptible genotypes (i.e. ≤30%) in high risk flocks, MT is the dominated strategy. MT has to be cheaper, and this is exacerbated if prevalence or test sensitivity drops.</p

Costs and effects (infected-sales-averted) for each scrapie control strategy assuming Defra pay all costs.

<p>This illustrates the costs and effects for high risk farms using CSFS and pre-clinical tests with a sensitivity of 90%, when the proportion of genotypes in the flock is 40%. The incremental cost effectiveness ratio (ICER) is also presented where appropriate.</p

Description of costs incurred for Compulsory Scrapie Flock Scheme, single and multiple pre-clinical testing strategies.

<p>Description of costs incurred for Compulsory Scrapie Flock Scheme, single and multiple pre-clinical testing strategies.</p

Cost-effectiveness plane examining all flocks (high, moderate and low risk) assuming 40% proportion of susceptible genotypes under three preclinical test unit costs (0.5, 1.0 and 1.5 times threshold price that would give CSFS and MT equal costs).

<p>The MT strategy is clearly dominated in the 1.5 times scenario having a much greater cost than CSFS with lower effectiveness (fewer infected sheep sales avoided.).</p

Additional file 4: of Relative abundance of Mycobacterium bovis molecular types in cattle: a simulation study of potential epidemiological drivers

Graph showing number of breakdowns attributed to novel MVLA-types per month in NI over the study period (PDF 14 kb

Additional file 1: of Using whole genome sequencing to investigate transmission in a multi-host system: bovine tuberculosis in New Zealand

Supplementary text 1.1: Filter Sensitivity Analysis. Supplementary text 1.2: Investigating Highly Distinct Isolates. Supplementary text 1.3: Temporal Signal. Supplementary text 1.4: Hierarchical Model Selection. Supplementary text 1.5: Influence of the Priors. Table S1. Results from investigating highly distinct isolates. Table S2. Results from hierarchical model selection. (DOCX 36 kb

Rarefaction curves indicating the mean subtype richness of each region at different sampling efforts.

<p>Rarefaction curves were generated using the function rarefy in the R package Vegan using A) a strict subtype definition (9 total subtypes) and B) a relaxed subtype definition (32 total subtypes). 95% confidence intervals are indicated by a dotted line. The 7 regions are labeled with shapes indicated in the key at the bottom of the figure. Regions are abbreviated as follows: Québec = QC, Alberta = AB, Ontario = ON, the Atlantic region = AT, Manitoba = MB, British Columbia = BC, and Saskatchewan = SK.</p

Phylogenetic clustering of MAP isolates among Canadian regions.

<p>A) Circularized maximum likelihood phylogenetic tree of 182 Canadian MAP isolates, rooted to the Type III isolate. Tips are colored according to province of origin (Alberta = blue, Ontario = light blue, British Colombia = red, Québec = orange, Saskatchewan = yellow, the Atlantic provinces = pink, Manitoba = purple). The branches leading to the nine subtypes are labeled with a square. Dotted lines indicate the threshold for the different subtype definitions used in the rarefaction analysis. B) Map of the 7 Canadian regions in which MAP isolates were obtained. C) The statistics (AI = association index, PS = parsimony score, MC = monophyletic clade size statistic), number of samples from each of the 7 regions, observed mean, null mean, and significance (p-value) are presented. Low AI and PS scores indicate a strong association, whereas high MC scores indicate a strong association.</p

Maximum likelihood phylogenetic tree of sequenced MAP isolates.

<p>Phylogenetic tree of global (n = 26, labeled with a black dot (•)) and Canadian (n = 182) isolates based on 9,670 variant sites using the TPM1uf nucleotide substitution model. The tree is rooted to the Type I sequence. A magnification of the phylogeny excluding the Type I, III, and B isolates is outlined in dotted lines. The dominant subtype is shaded in grey. Bootstrap values with branch support ≥ 70% are displayed.</p