P73

Bacterial populations are known to be heterogeneous yet are typically represented as a single consensus genome. While small variant heterogeneity is frequently investigated, heterogeneous structural variants (SVs) have received less scrutiny. Here, we develop a framework to discern heterogeneous structural variation from long-read sequencing data. Applying this framework to 137 Mycobacterium tuberculosis complex (MTBC) clinical isolates identified high-confidence heterogeneous SVs present in multiple strains. Several of these SVs interrupt cis-regulatory and coding regions of clinically noteworthy genes. These include a proposed vaccine component and diagnostic marker for active TB, a cell envelope constituent, and important virulence mediators.  Most heterogeneous SVs recapitulated known MTBC macroevolutionary events on a microevolutionary timescale, suggesting the evolution of M. tuberculosis genome structure exhibits recurrent properties. These findings spotlight homologous recombination and IS-transposition as influential determinants of MTBC evolution that constitutively generate structural heterogeneity to confer a more plastic genome structure than previously appreciated.