Supplementary Figure 4: Characterization of strains that display sensitivity to killing by ciprofloxacin. | Nature Methods

Supplementary Figure 4: Characterization of strains that display sensitivity to killing by ciprofloxacin.

From: A multiplexable assay for screening antibiotic lethality against drug-tolerant bacteria

Supplementary Figure 4

a, MIC values of 38 strains that displayed as hits in the SPOCK screen of the Keio collection. 12-point concentration curves were generated, and MIC values were plotted (mean ± range; n = 2 biologically independent experiments). Note that no strains that displayed high fluorescence showed significant shifts in ciprofloxacin MIC relative to wild-type E. coli. b, Ciprofloxacin-induced killing in liquid LB of the 38 strains that displayed as hits in the SPOCK screen of the Keio collection. Strains were grown to saturation for 24 h in final volumes of 100 µl in 96-well microtiter plates, at which time ciprofloxacin was added at a concentration of 1 µg/ml. Cultures were incubated for an additional 24 h prior to plating. Survival is calculated as the viability of each strain after ciprofloxacin treatment relative to untreated control cultures of each strain, which is depicted as the red dotted line (mean ± range; n = 2 biologically independent experiments). c, Culture density of each Keio strain after 24 h of incubation, prior to the addition of ciprofloxacin. The red dotted line shows the absolute density of wild-type E. coli (mean ± range; n = 2 biologically independent experiments). d, Stationary phase sensitivity of the 38 SPOCK assay hits to ciprofloxacin in liquid media, relative to colony fluorescence values. Strains were grown for 24 h in liquid LB, at which time ciprofloxacin (1 µg/ml) was added and cells were grown for an additional 24 h prior to plating (mean; n = 2 biologically independent experiments). Light blue circles show strains that were used in follow-up experiments. The red dotted line depicts wild-type E. coli survival. e, Growth kinetics of 38 SPOCK assay hit strains. Overnight cultures were inoculated 1/10,000 into fresh LB media in final volumes of 100 µl in 96-well microtiter plates. Optical density at 600 nm was read every 10 min over 24 h, and the mean of every growth curve was plotted (mean; n = 2 biologically independent experiments). Wild-type E. coli is shown in blue. The five strains that were selected for follow-up investigations are shown in light blue.

Source Data

Back to article page