Number of strong interactions per drug
Strong synergies and antagonisms
For the drugs of the selected combinations, strong interactions are shown (FDR < 0.05 and effect size > |0.1|). The effect size is quantified as absolute value of first or third quartile for synergy and antagonism, respectively, of the distribution of Bliss scores for the selected combination (Methods).
Growth curves
Optical density at 595 nm (OD595nm) was monitored over time until cells reached stationary phase (Methods). OD595nm values are shown after background subtraction, before normalizing by no-drug controls (Methods). The arrangement of the plots is the same as in the corresponding checkerboard plot (see “Checkerboards”), with the curves arrayed to form 4x4 concentration matrices for each drug combination, including single-drug controls (left column for donor and bottom row for recipient drugs) and no-drug controls. The three concentrations at which each drug was tested – expressed in µg/ml - are annotated together with drug names in each single-drug column or row. Experiments can be selected according to each drug testing mode (as donor or recipient – see Methods), plate batch (corresponding to recipient biological replicate), donor drug biological replicate. Note that for single-donor controls (left column), growth curves from three single-donor control wells in the selected plate are shown; for single-recipient controls, growth curves from the recipient control plates included in the selected batch are shown (Methods). Each subplot shows two growth curves from technical replicate wells.
Checkerboard viewer
4x4 checkerboards assembled as explained in “Growth curves”. Shown values correspond to optical density at 595 nm (OD595nm) measured at the transition between exponential and stationary phase (8h for S. aureus, 5.5 h for B. subtilis and 3.7 h for S. pneumoniae). This value was then normalized by the robust mean of corresponding values from six no-drug controls included in each plate (Methods). Each subplot indicates which drug of the pair was tested as donor, the single-donor biological replicate, the recipient plate batch used and which technical replicate of the plate is shown. Concentrations – expressed in µg/ml - are shown next to drug names for each subplot. Significance and effect size values are shown for each combination. Adjusted p-value 'padj' is based on a non-parametric (resampling) test and 'efsize' is the upper or lower quartile of all the Bliss scores observed for this combination (Methods).
Interaction score matrix
For each combination, all Bliss interaction scores observed in the screen are shown. Negative Bliss scores indicate synergy, positive scores indicate antagonism. In rows we enumerate concentration ratios of the combination. Concentrations are expressed in µg/ml. Columns follow the notation: (plate batch, donor biological replicate, technical replicate well, drug tested as donor). Grey cells indicate that the concentration ratio was not tested in that particular [batch - biological replicate - donor mode]. The cumulative effect size of the combination is shown on top of the heatmap, as first quartile value of the interaction score distribution for synergies, and third quartile for antagonisms (Methods).
Drug annotation
The table shows manually curated drug annotation (Supplementary Tables 1 and 6). The column “Main or non-antibiotic screen” specifies whether drugs are part of the main antibiotic screen in S. aureus, S. pneumoniae and B. subtilis or of the non-antibiotic screen performed in S. aureus DSM 20231. Drugs of the selected combination are highlighted in orange.