Extended Data Fig. 8: Tn-seq analysis identifies genetic determinants of antibiotic adaptation at the mucosal surface.

A. Full experimental design of the Tn-seq during antibiotic tolerance at the mucosal surface. The library was grown on CF HBE cells, treated with CIP or TOB (or no treatment for the control), and then an outgrowth step (7 to 12 hours) on LB was performed for all samples. The three outgrowth samples were sequenced. Blue lines represent the comparisons made using the TRANSIT software to assess the conditional essentiality of genes (comparisons #4-5), and the “no antibiotic” condition was used as the control (see Methods for full experimental details) B. Fitness effects of transposon insertions in representative genes and their categories discovered in our antibiotic tolerance Tn-seq. Genes are separated by CIP and TOB-specific hits. These do not represent all the genes that made the significance cutoff. See Supplementary Table 6 for the complete dataset. All experiments were performed with CF HBE cells. Abbreviations: CIP, ciprofloxacin; CF, cystic fibrosis; HBE cells, human bronchial epithelial cells; TOB, tobramycin. The data underlying this figure can be found in the source data available with this manuscript (see Data Availability session).