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Abstract: Control of bovine tuberculosis (bTB) relies on regular testing of cattle with a crude preparation of mycobacterial antigens termed purified protein derivative (PPD). Worldwide production of bovine PPD uses the Mycobacterium bovis AN5, a strain that was originally isolated circa 1948 in Great Britain (GB). Despite its worldwide use, the AN5 strain is poorly characterised. AN5 was adapted to grow on glycerol in a process similar to that used for the derivation of the BCG vaccine strains; during this process, it is known that BCG deleted the genes for some potent antigens. Our previous analysis of the genome of M. bovis AN5 showed that it had not suffered extensive gene deletion events during in vitro adaptation. However, glycerol adaptation of AN5 strain may have caused differences in its global gene expression profile that could affect antigen expression. To assess this, we determined the transcriptome profile of AN5 and compared it to expression data for two endemic GB strains of M. bovis that account for ∼61% of all GB bTB cases. Genes expressed at lower levels in AN5 compared to M. bovis field isolates were then screened for antigenicity in naturally infected animals. Using this approach a number of genes were found to be expressed at lower levels in AN5, including those for known antigens. Our results show that field strains of M. bovis show some significant differences in gene expression to AN5, and that this differential gene expression may impact on the antigen profiles expressed by AN5 during in vitro culture. [Copyright &y& Elsevier]