Intra-host diversity and transmission dynamics of Mycobacterium tuberculosis tracked in serially sampled isolates from patients from Florida, USA using deep sequencing

In this study we investigate within-host evolution in an attempt to describe its impact on recent transmission estimates. What sets our study apart is that we profile a well-documented M. tuberculosis transmission cluster involving three cases linked by reverse contact tracing and traditional genotyping. The availability of pre-treatment and serial isolates under standard chemotherapy allowed us to investigate within-host evolution during transmission and under drug pressure within the same cluster. In addition, we used very deep sequencing to track the population turnover of minority alleles to less than 0.5% abundance