Mycobacterium tuberculosis ESX phase variant barcoded minipool mouse infection

We sought to investigate the impacts on bacterial fitness of common ESX-1 associated phase variants in a mouse infection model. To do so, we infected WT B6 and TCR-alpha KO mice by the aerosol route with a pooled collection of barcoded Mycobacterium tuberculosis strains. This pooled infection consisted of 2 independently generated barcoded strains of WT, espR-ins, and espA-del strains, as well as one barcoded eccB1 knockout strain to model a complete ESX-1 deficiency. Mice were sacrificed on day 0 and day 30, at which point mouse lungs were homogenized and bacteria was plated and scraped to extract DNA for sequencing.