* vGI status for vGI-1b, vGI-19 – vGI-22 either duplicated (dp) or deleted (dl), else no entry designates present as a single copy region. IS900 insertion site analysis To determine which IS900 sites were absent relative to the K10 reference genome, PCR primers were designed to specifically amplify each of the known 17 IS900 loci (Table  6). These were used

to confirm the insertion of IS900 into each locus in SGC-CBP30 cell line the reference strain K10 and were also all positive in all 316 F strains and a caprine isolate CAM87. Both vaccine strains IIUK2000 and 2eUK2000 were missing IS900(MAP1722) whereas IS900(MAP1033) was also missing from vaccine strain 2eUK2000 but present in all other strains including vaccine strain IIUK2000. Comparative qPCR of IS900 copy number relative to MAP2114c, demonstrated a range of IS900 copies in vaccine strains that corresponded to the trend in hybridisation signals observed in MAPAC scatterplots GSK2126458 (Figure  1a & 1b). The ratio of copy number however was surprisingly

higher than predicted, with vaccine strains IIUK2000 and 2eUK2000 having only 13 copies whilst MAPK10 and 316 F strains gave signals correspondent with 16–19 relative IS900 copy numbers (Table  7). Functional analysis of tellurite resistance One MAP specific gene predicted to be deleted in vGI-19 was MAP3730 (Table  1), a S-adenosylmethionine-dependent methyltransferase with homologues to tellurite resistance mafosfamide genes (tehB) involved in bacterial virulence and persistence [27, 28]. The functionality of this gene in mycobacteria has not previously been investigated. Using a solid culture plate assay we compared tellurite resistance (MIC) of MAP strains with and without the vGI-19 deletion (Table  7). This demonstrated a wide MIC range (8 – >512 μg/ml) between strains, with significant reductions associated with vGI-19 (316FNOR1960) deletion over full genome complement strains. Of note however was the very low level of tellurite

resistance (8 μg/ml) found in strains containing the vGI-20 (IIUK2000 & 2eUK2000) deletion. Assessment of virulence using a mouse model The virulence of vaccine strains 316FUK2001, IIUK2001 and 7-Cl-O-Nec1 clinical trial 2eUK2001 was compared with wild type strain JD87/107 in a mouse model. Ten mice from each of five groups (four inoculated with the different MAP strains and a negative control group inoculated with PBS) were killed at 4, 8 and 12 weeks post inoculation. Body, spleen and liver weights were recorded. Samples of the liver were taken for bacteriological culture and histopathology. Mean bodyweights increased with age, but no statistically significant difference was observed in mean body weight between any of the vaccine strains and the control wild type strain at any of the time points (p=0.11).