The potential use of spoligotyping—a polymerase chain reaction based typing system for differentiation of strains of Mycobacterium tuberculosis—for studying the epidemiology of tuberculosis in developing countries which do not routinely perform mycobacterial culture is described in this issue ofThorax by Heyderman et al in a study from Zimbabwe.1 How does this newer method compare with the now more established molecular typing methods for tuberculosis?

The most commonly used typing system for tuberculosis is IS6110 based restriction fragment length polymorphism (RFLP).2Extensive experience with IS6110 based RFLP typing has shown that there is a high degree of heterogeneity in typing patterns. This means that the technique is highly discriminatory so that it is unlikely that two organisms will share indistinguishable typing patterns by chance.3-6 This property has allowed RFLP typing to be used in a variety of ways. For example, typing can be used to confirm outbreaks of tuberculosis7 ,8 or incidents of suspected laboratory cross contamination,9 ,10 and the technique has been used to investigate the relative importance of reactivation versus reinfection in patients with a second episode of tuberculosis.11 ,12 Studies which type all available isolates from a defined geographical area over a specified time period can help to estimate the importance of recent transmission and to identify risk factors for the spread of tuberculosis.4-6

There are a number of difficulties with standard IS6110 typing—for example, the technique is less discriminatory in isolates with low copy numbers of IS6110 (secondary typing using techniques based on different genetic markers such as direct repeat (DR) typing or polymorphic GC …