Evolution of Mycobacterium tuberculosis transcription regulation is associated with increased transmission and drug resistance [RNA-seq]
Mycobacterium tuberculosis (Mtb) has co-evolved with humans for thousands of years leading to variation in clinical virulence, transmissibility, and disease phenotypes. To identify bacterial contributors to this phenotypic diversity, we developed new RNA-seq and phylogenomic analysis tools to capture hundreds of Mtb isolate transcriptomes, link transcriptional variation to genetic variation, and find associations between variants and epidemiologic traits. Across 274 Mtb clinical isolates, we uncovered unexpected diversity in expression of virulence genes which could be linked to known and previously unrecognized regulators. Surprisingly, we found that many isolates harbor variants associated with decreased expression of EsxA (Esat6) and EsxB (Cfp10), which are virulence effectors, dominant T cell antigens, and immunodiagnostic targets. Across >55,000 isolates, these variants associate with increased transmissibility, especially in drug resistant Mtb strains. Our data suggest expression of key Mtb virulence genes is evolving across isolates in part to optimize fitness under drug pressure, with sobering implications for immunodiagnostics and next-generation vaccines. Overall design: Clinical isolates from Vietnam and Peru were grown to the same OD in rich media. RNA-Seq libraries were captured to compare in vitro transcriptomes across clinical isolates to determine if transcriptional regulation plays a role in disparate phenotypes between Mtb clinical isolates.