Rapid phenotypic diagnosis of pathogens and drug resistance using transcriptional expression signatures

1. A method comprising:

contacting an uncultured clinical urine or blood sample from a mammalian subject, wherein the sample is known or suspected to comprise pathogenic bacteria comprising Escherichia coli , with one or more test compounds selected from the group consisting of a fluoroquinolone antibiotic, aminoglycoside antibiotic, and ampicillin, to provide a test sample;

treating the test sample under conditions that release messenger ribonucleic acid (mRNA) from any pathogenic bacteria present in the clinical urine sample 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 an antibiotic test compound as compared to organisms that are resistant, wherein the target mRNA is one or more of recA, carA, deoC, figF, htrL, uvrA, ybhK, uup, fabD, cysD, glnA, opgG, ftsQ, b1649, dinD, pyrB, wbbK, or hdeA mRNA, wherein the exposure occurs for a time and under conditions in which binding between the probes and the target mRNA can occur, and wherein the mRNA is crude and unpurified when contacted with the probes and the method does not include amplifying the mRNA; and

determining a level of binding between the probes and target mRNA, thereby determining a level of the target mRNA.

2. The method of claim 1 , wherein the method comprises contacting the uncultured clinical urine or blood sample with two or more antibiotic test compounds.

3. The method of claim 1 , wherein the uncultured clinical urine or blood sample is contacted with the one or more antibiotic test compounds for less than four hours.

4. The method of claim 1 , wherein the uncultured clinical urine or blood sample comprises a plurality of different pathogenic bacteria.

5. The method of claim 1 , wherein the plurality of nucleic acid probes comprises probes that bind specifically to recA mRNA and probes that bind specifically to uvrA mRNA.

6. The method of claim 1 , comprising partitioning the uncultured clinical urine sample, and contacting the individual partitions with different antibiotic test compounds.

7. The method of claim 1 , wherein the test compound is a fluoroquinolone or aminoglycoside antibiotic.

8. A method comprising:

contacting an uncultured clinical blood or urine sample, wherein the sample is known or suspected to comprise pathogenic bacteria comprising Staphylococcus aureus , from a mammalian subject with methicillin to provide a test sample;

treating the test sample under conditions that release messenger ribonucleic acid (mRNA) from any pathogenic bacteria present in the clinical blood sample 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 methicillin as compared to organisms that are resistant, wherein the target mRNA is mecA, wherein the exposure occurs for a time and under conditions in which binding between the probes and the target mRNA can occur, and wherein the mRNA is crude and unpurified when contacted with the probes and the method does not include amplifying the mRNA; and

determining a level of binding between the probes and target mRNA, thereby determining a level of the target mRNA.

9. The method of claim 8 , wherein the uncultured clinical blood sample is contacted with the methicillin for less than four hours.

10. The method of claim 8 , wherein the uncultured clinical blood or urine sample comprises a plurality of different pathogenic bacteria.

11. A method comprising:

contacting an uncultured clinical sputum, urine, or blood sample from a mammalian subject, wherein the sample is known or suspected to comprise pathogenic bacteria comprising Mycobacterium tuberculosis , with one or more antibiotic test compounds selected from the group consisting of isoniaid, rifampin, streptomycin, and a fluoroquinolone antibiotic, to provide a test sample;

treating the test sample under conditions that release messenger ribonucleic acid (mRNA) from any pathogenic bacteria present in the clinical urine sample 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 an antibiotic test compound as compared to organisms that are resistant, wherein the target mRNA is one or more kasA, fadD32, accD6, efpA, Rv3675.1, bioD, hisl, era, Rv2296, Rv0813, rpsR, alkA, recA, ltp1, lhr, CHP, bcpB, gcvB, or groEL mRNA, wherein the exposure occurs for a time and under conditions in which binding between the probes and the target mRNA can occur, and wherein the mRNA is crude and unpurified when contacted with the probes and the method does not include amplifying the mRNA; and

determining a level of binding between the probes and target mRNA, thereby determining a level of the target mRNA.

12. The method of claim 11 , wherein:

the one or more antibiotic test compounds comprise isoniazid, and the target mRNA comprises kasA, fadD32, accD6, efpA, or Rv3675.1;

the one or more antibiotic test compounds comprise Rifampin, and the target mRNA comprises bioD, hisI, era, or Rv2296;

the one or more antibiotic test compounds comprise a fluoroquinolone antibiotic, and the target mRNA comprises rpsR, alkA, recA, ltp1, lhr, kasA, or accD6; or

the one or more antibiotic test compounds comprise streptomycin, and the target mRNA comprises Rv0813, accD6, KasA, CHP, bcpB, gcvB, or groEL.

13. The method of claim 11 , wherein the method comprises contacting the uncultured clinical blood or urine sample with two or more antibiotic test compounds.

14. The method of claim 11 , wherein the uncultured clinical blood or urine sample is contacted with the one or more antibiotic test compounds for less than four hours.

15. The method of claim 11 , wherein the uncultured clinical blood sample further comprises a plurality of different pathogenic bacteria.

16. The method of claim 11 , comprising partitioning the uncultured clinical blood or urine sample, and contacting the individual partitions with different antibiotic test compounds.

17. A method comprising:

contacting an uncultured clinical urine or blood sample from a mammalian subject with ciprofloxacin, wherein the sample is known or suspected to comprise pathogenic bacteria comprising Pseudomonas aeruginosa , to provide a test sample;

treating the test sample under conditions that release messenger ribonucleic acid (mRNA) from any pathogenic bacteria present in the clinical urine sample 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 an antibiotic test compound as compared to organisms that are resistant, wherein the target mRNA is one or more of PA 4175, mpl, or proA mRNA, wherein the exposure occurs for a time and under conditions in which binding between the probes and the target mRNA can occur, and wherein the mRNA is crude and unpurified when contacted with the probes and the method does not include amplifying the mRNA; and

determining a level of binding between the probes and target mRNA, thereby determining a level of the target mRNA.

18. The method of claim 17 , wherein the uncultured clinical blood or urine sample is contacted with the ciprofloxacin for less than four hours.

19. The method of claim 17 , wherein the uncultured clinical blood sample further comprises a plurality of different pathogenic bacteria.