Microarray-Based Comparative Genomics: Genome Plasticity in Mycobacterium bovis

Mycobacterium bovis is the causative agent of bovine tuberculosis, a disease responsible for annual losses to global agriculture of $3 billion and with serious repercussions for public health and animal welfare. The UK program for the control of bovine tuberculosis involves regular testing of cattle with a crude preparation of mycobacterial antigens (tuberculin), followed by compulsory slaughter of positive reactors. However, in the last decade the number of herd breakdowns has been increasing across the UK, especially in the south-west, where prevalence has now risen to 3.5% of cattle herds. This has worrying implications for the control strategy, which currently costs ∼£25 million/year. A range of techniques exist for the genetic typing of M. bovis isolates. These include restriction fragment length polymorphism (RFLP) with probes such as the polymorphic glycine-rich sequences (PGRS), a minisatellite method (VNTR), and spacer-oligonucleotide typing (spoligotyping). The application of these techniques has allowed the integration of molecular and epidemiological data to aid in disease control. The current method of choice for isolates at the Veterinary Laboratories Agency (VLA) is spoligotyping, a rapid simple method based on a polymorphic region called the direct repeat (DR) locus [1]. This locus is composed of multiple 36bp DR copies that are interspersed by non-repetitive, unique short sequences called spacers. Isolates of M. bovis differ in the presence or absence of spacers and adjacent DRs, allowing a barcode to be generated for each molecular type (Figure 1). At the VLA approximately 16 000 strains have been spoligotyped. Analysis of this data shows that