A method of determining the drug sensitivity of a pathogen, the method comprising: contacting a sample comprising a pathogen with one or more, or two or more, test compounds, to provide a test sample; treating the test sample under conditions that release messenger ribonucleic acid (mRNA) from the pathogen into the test sample; exposing the test sample to a plurality of nucleic acid probes, comprising a plurality of subsets of probes, wherein each subset comprises one or more probes that bind specifically to a target mRNA that is differentially expressed in organisms that are sensitive to a test compound as compared to organisms that are resistant, wherein the exposure occurs for a time and under conditions in which binding between the probe and target mRNA can occur; determining a level of binding between the probe and target mRNA, thereby determining a level of the target mRNA; and comparing the level of the target mRNA in the presence of the test compound to a reference level, wherein a difference in the level of target mRNA relative to the reference level of target mRNA indicates whether the pathogen is sensitive or resistant to the test compound; wherein the one or more nucleic acid probes are selected from Table 2 for one or more of the genes selected from the E.coli ampicillin resistance genes, E. coli aminoglycoside resistance genes, E. coli fluoroquinolone resistance genes, Pseudomonas aeruginosa fluoroquinolone resistance, Pseudomonas aeruginosa tobramycin resistance genes, Staphylococcus aureus methicillin resistance genes, Enterococcus faecalis vancomycin resistance genes, Mycobacterium tuberculosis streptomycin resistance, Mycobacterium tuberculosis rifampicin resistance, Mycobacterium tuberculosis isoniazid resistance, Mycobacterium tuberculosis fluorquinlone resistance and M. tuberculosis ethambutol resistance recited in Table 2, wherein the one or more nucleic acid probes consists of a nucleic acid sequence of SEQ ID NOs:98-120, 125-139, 143-170 and 227, or any combination thereof. contacting a sample comprising a pathogen with one or more, or two or more, test compounds, to provide a test sample; treating the test sample under conditions that release messenger ribonucleic acid (mRNA) from the pathogen into the test sample; exposing the test sample to a plurality of nucleic acid probes, comprising a plurality of subsets of probes, wherein each subset comprises one or more probes that bind specifically to a target mRNA that is differentially expressed in organisms that are sensitive to a test compound as compared to organisms that are resistant, wherein the exposure occurs for a time and under conditions in which binding between the probe and target mRNA can occur; determining a level of binding between the probe and target mRNA, thereby determining a level of the target mRNA; and comparing the level of the target mRNA in the presence of the test compound to a reference level, wherein a difference in the level of target mRNA relative to the reference level of target mRNA indicates whether the pathogen is sensitive or resistant to the test compound; wherein the one or more nucleic acid probes are selected from Table 2 for one or more of the genes selected from the E.coli ampicillin resistance genes, E. coli aminoglycoside resistance genes, E. coli fluoroquinolone resistance genes, Pseudomonas aeruginosa fluoroquinolone resistance, Pseudomonas aeruginosa tobramycin resistance genes, Staphylococcus aureus methicillin resistance genes, Enterococcus faecalis vancomycin resistance genes, Mycobacterium tuberculosis streptomycin resistance, Mycobacterium tuberculosis rifampicin resistance, Mycobacterium tuberculosis isoniazid resistance, Mycobacterium tuberculosis fluorquinlone resistance and M. tuberculosis ethambutol resistance recited in Table 2, wherein the one or more nucleic acid probes consists of a nucleic acid sequence of SEQ ID NOs:98-120, 125-139, 143-170 and 227, or any combination thereof.