RESULTS: Post-experiment sample processing: Frozen cell samples were transferred to the benchtop and partially thawed. The partially frozen cell slurry was transferred using a sterile disposable rubber spatulas into sterile 50-mL conical centrifuge tubes and placed immediately on ice. The culture volume recovered was recorded for later calculations. Samples were further processed for (i) viable counts; (ii) isolation of rifampicin-resistant (RFM^R) mutants; (iii) total RNA isolation; or (iv) Omnilog phenotype microarray profiling. (i) For viable counts, cultures were diluted serially tenfold in TSY medium, dilutions plated on TSY, and colonies counted after incubation at 37°C for 24 hours. (ii) To select for RFM^R mutants, cultures were concentrated by centrifugation, plated without dilution onto TSY+RFM (5 µg/mL) plates, and colonies counted after incubation at 37°C for 24 hours. The frequency of mutation to RFM^R was calculated by dividing the total number of RFM^R mutants by the total number of viable cells from each culture. Individual RFM^R mutants were streak-purified and saved as frozen -70°C glycerol stocks for further characterization by DNA sequencing. (iii) For total RNA isolation, cells were recovered by centrifugation (10,000 rpm, 20 min, 4°C) in a benchtop centrifuge. Supernatants were discarded and cell pellets immediately processed on ice for total RNA extraction. (iv) For Omnilog phenotype microarray experiments, frozen samples were thawed, washed once in Phosphate-Buffered Saline, diluted to the appropriate cell concentration in Inoculating Fluid, and inoculated into PM-11, PM-12, and PM-13 plates containing various concentrations of 72 different antibiotics. Plates were incubated at 37°C in the Omnilog instrument (Biolog, Inc.) and plate images recorded at 15-min intervals for 24 hours. Antibiotic resistance profiles were compared between FL and GC samples for significant differences.