The pathobiology ofMycobacterium abscessusrevealed through phenogenomic analysis

The medical and scientific response to emerging pathogens is often severely hampered by ignorance of the genetic determinants of virulence, drug resistance, and clinical outcomes that could be used to identify therapeutic drug targets and forecast patient trajectories1–5. Taking the newly emergent multidrug-resistant bacteriaMycobacterium abscessusas an example6, we show that combining high dimensional phenotyping with whole genome sequencing in a phenogenomic analysis can rapidly reveal actionable systems-level insights into bacterial pathobiology. Usingin vitroandin vivophenotyping, we discovered three distinct clusters of isolates, each associated with a different clinical outcome. We combined genome-wide association studies (GWAS) with proteome-wide computational structural modelling7to define likely causal variants, and employed direct coupling analysis (DCA)8to identify co-evolving, and therefore potentially epistatic, gene networks. We then usedin vivoCRISPR-based silencing to validate our findings, defining a novel secretion system controlling virulence inM. abscessus, and illustrating how phenogenomics can reveal critical pathways within emerging pathogenic bacteria.