Protocol for ex vivo competition and sequencing of mycobacterium isolated from infected guinea pigs.

We describe steps for gDNA isolation from mycobacterium strains isolated from guinea pig lungs. We detail steps for infection of guinea pigs with , followed by growth, gDNA isolation, and whole genome sequencing. We also describe an competition experiment to determine the selective advantage of one strain over another. We include details for WGS and mutation spectrum analysis. The protocol can be used to identify mutations that arise in other pathogenic bacteria. For complete details on the use and execution of this protocol, please refer to Naz et al. (2021).