Pathways and strategies followed in the genomic epidemiology of Mycobacterium tuberculosis

The progressive reduction of costs in next-generation sequencing is responsible for the speed with which new genomic epidemiological approaches are being used. However, this speed has meant a lack of consensus on the way the genomic pathway is being addressed. Alternative pathways, strategies, and shortcuts have been proposed during this initial period of the genomic epidemiology era in tuberculosis. The aim of this review is not to make a systematic analysis of these different approaches but to show how various lines of progression are being followed, each looking for different ways of integrating the language of genomics. This review covers several aspects, from paths that provide high-quality data from cultured isolates to strategies that attempt to shorten response times through challenging analyses directly on specimens or primary cultures. The review presents strategies proposed by several groups, ranging from those that focus on universal population-based systematic application to others proposing shortcuts by targeting selected relevant strains. Finally, the decision to analyze complete genomic content vs abbreviated analysis of preselected sets of genes is discussed. The reader is shown the exciting variety of efforts being made to find the best fit between genomics and the demands and challenges of the epidemiology of tuberculosis.