Raw Data Files for Collateral Sensitivity Profiling in Drug-Resistant Escherichia coli Identifies Natural Products Suppressing Cephalosporin Resistance

• DOI: 10.5281/zenodo.7746641
• Publication Date: 2023-01-19
• Authors: Dennis Y. Liu; Laura Phillips; Darryl M. Wilson; Kelly M. Fulton; Susan M. Twine; Alex Wong; Roger G. Linington
• Keywords: Collateral Sensitivity, Antimicrobial Resistance, Natural Products Discovery, High-Throughput Screening; 3. Good health

Raw Data Files for the Following Publication: Collateral Sensitivity Profiling in Drug-Resistant Escherichia coli Identifies Natural Products Suppressing Cephalosporin Resistance E_coli_CSP_Antibioitic_MIC_R1.csv; E_coli_CSP_Antibioitic_MIC_R2.csv; E_coli_CSP_Antibioitic_MIC_R3.csv: Raw MIC values for all 80 antibiotic compounds against wild type and 29 drug-resistant strains of E. coli, as specified in the main manuscript. Antibiotics are arranged along the horizontal axis with their structural class indicated one row above. Drug-resistant strains, along with their mutant gene and strain designation, are arranged along the vertical axis. All values are in micromolar. >128 denotes MIC values greater than 128 micromolar. E_coli_CSP_NP_Library_OD600.csv: Raw OD600 absorbance values from CSP screening of 6,195 natural product extract prefractions against wild type and 29 drug-resistant strains of E. coli, as described in the main manuscript. Drug-resistant strains are arranged along the horizontal axis. Extracts are arranged along the vertical axis. Extracts that begin with RLCA denote Burkoholderia-derived extracts. Extracts that begin with RLUS denote marine Actinobacterial extracts. Extracts with the same letter and number code but different alphabetical character at the end (A to F) denote different prefractions of the same extract. All values represent the difference of the T20 and T0 measurements. E_coli_CSP_NP_Secondary_Screen_MIC.csv: Raw MIC values for 117 natural product extract prefractions selected for secondary screening, screened against wild type and 29 drug-resistant strains of E. coli as 16x two-fold dilution series, as described in the main manuscript. Drug-resistant strains are arranged along the horizontal axis. Extracts are arranged along the vertical axis. Extracts that begin with RLCA denote Burkoholderia-derived extracts. Extracts that begin with RLUS denote marine Actinobacterial extracts. Extracts with the same letter and number code but different alphabetical character at the end (A to F) denote different prefractions of the same extract. Since extract concentrations cannot be determined, the MIC values have been annotated using relative concentration values (1 = stock concentration, 0.5 = 1x two-fold dilution, 0.25 = 2x two-fold dilution, etc.). E_coli_CSP_Borrelidins_OD600: Normalized percent growth values (100% maximum growth; 0% no growth) for borrelidins A, F, H, and P between 256/128 uM to 0.0078/0.0039 uM against select strains: wild type E. coli MG1655, Cip2KB, Cef8, Cef1, Cef6, Cef7, Kn15, RK2, MG1655 (thrS) -IPTG, MG1655 (thrS) +IPTG, Cef6 (thrS) -IPTG, Cef6 (thrS) +IPTG, Cef7 (thrS) -IPTG, Cef7 (thrS) +IPTG. All strains were tested in triplicate. E_coli_CSP_Resistance_Passaging_MIC: Ceftazidime MIC values obtained during the serial passaging experiment under four separate conditions (Cef, ceftazidime in increasing concentrations; Cef+BorA_32uM, ceftazidime in increasing concentrations and borrelidin A at 32 uM; Cef+BorA_128uM, ceftazidime in increasing concentrations and borrelidin A at 128 uM; Cef+Nor, ceftazidime in increasing concentrations and norfloxacin in increasing concentrations) over 12 days. Each condition was tested using three replicates sourced from a wild type strain of E. coli MG1655. E_coli_CSP_Resistance_Passaging_MIC_12th_Day: Raw MIC values for ceftazidime, cefadroxil, cefaclor, norfloaxcin, ciprofloxacin, and borreidin A against the drug-resistant strains obtained from the serial passaging experiment under four separate conditions (Cef, ceftazidime in increasing concentrations; Cef+BorA_32uM, ceftazidime in increasing concentrations and borrelidin A at 32 uM; Cef+BorA_128uM, ceftazidime in increasing concentrations and borrelidin A at 128 uM; Cef+Nor, ceftazidime in increasing concentrations and norfloxacin in increasing concentrations). Each condition was tested in triplicate, with three replicate samples selected for each condition. Test antibiotics are arranged along the horizontal axis while the drug-resistant strains are arranged along the vertical axis. E_coli_CSP_Checkerboard_Assay_OD600: Normalized percent growth values for checkerboard co-dosing assays between borrelidin A x ceftazidime and borrelidin A x ampicillin against E. coli MG1655, Ce7, and RK2. Borrelidin A is co-dosed with either ceftazidime or ampicillin using a combination concentrations from 128 uM to 15.6 nM.