Innovations in the molecular epidemiology of tuberculosis.

The application of genotyping tools to the analysis of tuberculosis (TB) has allowed us to identify clinical isolates of Mycobacterium tuberculosis to strain level. M. tuberculosis fingerprinting has been applied at different levels: a) in the laboratory, to optimize identification of cross-contamination events which can lead to a false diagnosis; b) in the patient, to determine whether recurrences are due to reactivations or exogenous reinfections or to identify cases coinfected by more than one strain; c) at the micropopulation level, to identify clusters of cases infected by the same strains (recent transmission) and to differentiate them from orphan cases that are most probably due to reactivations; and d) at the macropopulation level, to define the global distribution of M. tuberculosis lineages, to monitor the international spread of high-risk strains, and to explore the evolutionary features of M. tuberculosis. In recent years, important methodological and strategic advances have been applied at these different levels of analysis. Rather than provide an exhaustive review, the present study focuses on specific advances in micropopulation and macropopulation analysis.