Table 1.

Molecular typing methods for Mycobacterium bovis.

Method	Advantages	Disadvantages
IS6110-RFLP	The number of copies and their positions in the genome may vary from isolate to isolate (van Embden et al., 1993), providing identical profiles of isolates from animals involved in recent transmission chains, and different genetic patterns in isolates from animals not associated with infection (Aranaz et al., 1999).	Requires large amounts of DNA (1–2 μg) and technical skills; it is slow and has little discriminating power in isolates with less than 6 IS6110 copies (Gutacker et al., 2002); there is difficulty in reproducing results and comparing them among different laboratories (Supply et al., 2001b); and the majority of M. bovis isolates have a low number of IS6110 copies-in general, only 1 or 2 (Haddad et al., 2004).
PGRS	Higher discriminating power in isolates with 6 or less IS6110 copies (Rozo and Ribón, 2010); useful tool for confirming the identity of strains matched by IS6110 or to type low-copy number stains (Kanduma et al., 2003); for the majority of M. bovis strains, except those originating from certain animal species like goats, PGRS sequences, in terms of copy number, much more polymorphic than the DR region, which is more polymorphic than the IS6110; it is considered more stable than the IS6110-RFLP patterns and shows 100% reproducibility.	Requires large amounts of high quality DNA (Asgharzadeh and Kafil, 2007; Doroudchi et al., 2000) and technical skills; it has lower discriminating power in isolates with multiple copies (Bauer et al., 1999); the large number of bands produced by this technique makes interpretation of the gels difficult, limiting its application as a primary typing technique (Kanduma et al., 2003).
Spoligotyping	This technique is fast, robust, low cost and can differentiate strains of M. bovis and M. tuberculosis; the results can be fully expressed in a simple, digital format, which facilitates inter- and intra-laboratory results comparisons, as has been demonstrated for VNTR; this method may differentiate better when the location of more spacers is investigated; it can potentially be applied directly to pathological samples (Kamerbeek et al., 1997).	The discriminatory power of this method is lower than IS6110-RFLP typing when high copy number strains are being analyzed.
VNTR	Powerful approach to high-resolution genotyping of isolates (Supply et al., 2001b); it is reproducible, fast and specific for M. tuberculosis complex isolates (Supply et al., 2001b); potential approach to detect and genotype bacteria of the M. tuberculosis complex directly in a range of clinical samples (Roring et al., 2002); the results can be fully expressed in a simple, digital format, which facilitates inter- and intra-laboratory results comparisons; it has shown 100% reproducibility.	The discriminatory power of this method is lower than IS6110-RFLP (for high copy number strains) and spoligotyping (Kremer et al., 1999); detection via electrophoresis is inexpensive, but automated detection involving fluorescence is not.