Tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) is the second major cause of death from infectious diseases worldwide [1]. Over the last two decades, molecular typing methods such as IS6110-RFLP [2], spoligotyping [3] and MIRU-VNTR [4] have been applied and have revolutionised our understanding of the epidemiology of TB, by providing novel insights into the genetic diversity and population structure of M. tuberculosis complex (MTBC) [5]. Epidemiological data generated through genotyping has been used extensively to further the understanding of TB disease dynamics [6]. For example, at the individual level, cases of recurrence or treatment failure can be explained in terms of reactivation of the same strain, exogenous re-infection or due to polyclonal infection [7]. At a population level, the origins and transmission dynamics of outbreaks can be determined [8–10]; while at global level, TB genotypic lineages have been defined and used to monitor their geographical distribution and spread

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