A method of performing rapid antibiotic susceptibility testing, comprising: performing a multiplexed identification test panel for the presence of a panel of microbial cell types on a first lysate, the first lysate having been obtained from a first sample that is suspected of containing microbial cells; obtaining, from a second sample that is suspected of containing the microbial cells, at least a primary aliquot and a reference aliquot, wherein the primary aliquot and the reference aliquot comprise growth media, and wherein the first sample and the second sample are derived from a common subject; adding, to the primary aliquot, at least one selected antibiotic, the selected antibiotic having been selected, at least in part, based on the results of the multiplexed identification test panel; incubating the primary aliquot and the reference aliquot under conditions suitable for promoting microbial growth for testing the effectiveness of the selected antibiotic; separating microbial cells from the primary aliquot and resuspending the separated microbial cells to obtain a primary suspension; separating microbial cells from the reference aliquot and resuspending the separated microbial cells to obtain a reference suspension; lysing the microbial cells in the primary suspension and the reference suspension, thereby obtaining a primary lysate and a reference lysate; performing reverse transcription and amplification on the primary lysate to detect nucleic acids associated with members of the multiplexed identification test panel, thereby obtaining a primary assay signal; performing reverse transcription and amplification on the reference lysate to detect nucleic acids associated with members of the multiplexed identification test panel, thereby obtaining a reference assay signal; comparing the primary assay signal and the reference assay signal to obtain a measure of the effectiveness of the selected antibiotic against the microbial cells. performing a multiplexed identification test panel for the presence of a panel of microbial cell types on a first lysate, the first lysate having been obtained from a first sample that is suspected of containing microbial cells; obtaining, from a second sample that is suspected of containing the microbial cells, at least a primary aliquot and a reference aliquot, wherein the primary aliquot and the reference aliquot comprise growth media, and wherein the first sample and the second sample are derived from a common subject; adding, to the primary aliquot, at least one selected antibiotic, the selected antibiotic having been selected, at least in part, based on the results of the multiplexed identification test panel; incubating the primary aliquot and the reference aliquot under conditions suitable for promoting microbial growth for testing the effectiveness of the selected antibiotic; separating microbial cells from the primary aliquot and resuspending the separated microbial cells to obtain a primary suspension; separating microbial cells from the reference aliquot and resuspending the separated microbial cells to obtain a reference suspension; lysing the microbial cells in the primary suspension and the reference suspension, thereby obtaining a primary lysate and a reference lysate; performing reverse transcription and amplification on the primary lysate to detect nucleic acids associated with members of the multiplexed identification test panel, thereby obtaining a primary assay signal; performing reverse transcription and amplification on the reference lysate to detect nucleic acids associated with members of the multiplexed identification test panel, thereby obtaining a reference assay signal; comparing the primary assay signal and the reference assay signal to obtain a measure of the effectiveness of the selected antibiotic against the microbial cells.