FIG 3.

Whole-genome screen for modifiers of cefoxitin susceptibility. (A) Volcano plot illustrating candidate genes important for cefoxitin susceptibility. On the x axis is the log₂ fold change (log₂FC) in insertion mutant abundance in cefoxitin (FOX) compared to that in no drug. The y axis is the inverse Mann-Whitney U P value (1/MWU p-val), which roughly measures the concordance between mutants with insertions at individual TA sites across a gene. Genes were depleted (red) if the log₂FC was ≤2 and the 1/MWU p-val was ≥100. Genes were enriched (blue) if the log₂FC was ≥2 and the 1/MWU p-val was ≥100. (B) Selected genes enriched or depleted in cefoxitin were tabulated. Genes important for envelope integrity and peptidoglycan recycling were depleted. ydgH, an enriched, poorly characterized gene, is also highlighted. (C) Growth of various S. marcescens gene deletion mutants in cefoxitin 4 μg/ml. Growth is depicted as CFU_mutant/CFU_Wt (in cefoxitin) divided by CFU_mutant/CFU_Wt (in LB alone). Although no mutant had large defects in LB alone, due to stochastic errors in dilution to starting CFU, this improved the repeatability of the experiment. *, P ≤ 0.05; **, P ≤ 0.01; unpaired two-tailed t test, unadjusted.