Individuals with chronic lung diseases such as cystic fibrosis and COPD are particularly vulnerable to bacterial infections. Clinically, these infections are challenging to manage and often persist for years, leading to chronic, difficult-to-treat infections. Over time, the bacteria diversify and adapt to the lung environment and the antibiotics used in treatment. In this talk, I will present our work using metagenomics and spatial transcriptomics to unravel bacterial adaptation and host-pathogen interactions. Our findings are transforming our fundamental understanding of chronic lung infections.​