Antibiotic susceptibility of microorganisms and related compositions, methods and systems

1. A method to detect a nucleic acid of a microorganism in a sample of an isolate or specimen including the microorganism, the method comprising

contacting the sample with an antibiotic to provide an antibiotic-treated sample,

quantitatively detecting in the antibiotic-treated sample an accessible nucleic acid of the microorganism, the detecting performed

in the absence of a lysis treatment of the antibiotic-treated sample targeting the microorganism; or

in the presence of a lysis treatment of the antibiotic-treated sample targeting the microorganism, the lysis treatment following pre-lysis mechanical separation of cells from the nucleic acid in the antibiotic-treated sample to remove the inaccessible nucleic acids from the sample,

the contacting and the quantitatively detecting performed to obtain a detected accessible antibiotic-treated nucleic acid concentration value of the microorganism in the antibiotic-treated sample.

2. The method of claim 1 , wherein the method further comprises concurrently or after the contacting and before the detecting:

performing an enhancing treatment of the antibiotic-treated sample.

3. The method of claim 1 , the method further comprising detecting an accessible nucleic acid concentration ratio in the sample by

comparing the detected accessible antibiotic-treated nucleic acid concentration value with a detected reference nucleic acid concentration value of a nucleic acid concentration parameter of the microorganism in the sample.

4. The method of claim 3 , wherein the reference nucleic acid concentration value of the nucleic acid concentration parameter is an accessible control nucleic acid concentration value obtained by

detecting an accessible nucleic acid concentration for the nucleic acid of the microorganism in a control sample of the isolate or specimen comprising the microorganism, the detecting in the control sample performed

in the absence of a lysis treatment of the control sample

when the detecting in the antibiotic-treated sample is performed in the absence of a lysis treatment of the antibiotic-treated sample; or

in the presence of a lysis treatment of the control sample following pre-lysis mechanical separation of microorganism from the nucleic acid in the antibiotic-treated sample,

when the detecting in the antibiotic-treated sample is performed in the presence of a lysis treatment of the antibiotic-treated sample following pre-lysis mechanical separation of the microorganism from the nucleic acid in the antibiotic-treated sample,

the detecting an accessible nucleic acid concentration in the control sample is performed to provide the accessible control nucleic acid concentration value for the nucleic acid of the microorganism.

5. The method of claim 3 , wherein the accessible reference nucleic acid concentration value is a total nucleic acid concentration value obtained by

detecting the total nucleic acid concentration of the microorganism in a control sample of an isolate or specimen comprising the microorganism and either treated or not treated with the antibiotic, to provide the total nucleic acid concentration value for the nucleic acid of the microorganism.

6. The method of claim 3 , wherein the detecting is performed in the presence of a lysis treatment of the antibiotic-treated sample targeting the microorganism, the lysis treatment following pre-lysis mechanical separation of the microorganism from the nucleic acid in the antibiotic-treated sample, and the method further comprises

establishing susceptibility of the microorganism to the antibiotic when the accessible nucleic acid concentration ratio is above an accessible threshold of susceptibility.

7. The method of claim 6 , wherein the reference nucleic acid concentration value of the nucleic acid concentration parameter is an accessible control nucleic acid concentration and wherein the accessible nucleic acid concentration ratio is more than 2 or less than 0.5.

8. The method of claim 7 , wherein the duration of the contacting of the sample with an antibiotic is 20 minutes or less, and wherein the nucleic acid concentration ratio is alternatively selected from more than 2 or less than 0.5, more than 3 or less than 0.33, more than 5 or less than 0.2, more than 10 or less than 0.1, more than 15 or less than 0.067, or more than 20 or less than 0.05.

9. The method of claim 8 , wherein the nucleic acid is DNA.

10. The method of claim 8 , wherein the nucleic acid is RNA.

11. The method of claim 7 , wherein the contacting of the sample with an antibiotic is performed for 30 minutes or less, and wherein the nucleic acid concentration ratio is more than 3 or less than 0.33, more than 5 or less than 0.2, more than 10 or less than 0.1, more than 15 or less than 0.067, or more than 20 or less than 0.05.

12. The method of claim 11 , wherein the nucleic acid is DNA.

13. The method of claim 11 , wherein the nucleic acid is RNA.

14. The method of claim 6 , wherein the pre-lysis mechanical separation is performed by filtering the microorganism from the nucleic acid in the antibiotic-treated sample.

15. The method of claim 6 , wherein the method further comprises purifying or extracting the nucleic acid from the antibiotic-treated sample before the detecting.

16. The method of claim 3 , wherein the detecting is performed in the presence of a lysis treatment of the antibiotic-treated sample targeting the microorganism, the lysis treatment following pre-lysis separation of the microorganism from the nucleic acid in the antibiotic-treated sample, and the method further comprises

establishing resistance of the microorganism to the antibiotic when the accessible nucleic acid concentration ratio is below a second accessible threshold of resistance.

17. The method of claim 1 , wherein the quantitatively detecting is performed by performing RNA-seq and obtaining the accessible antibiotic-treated nucleic acid concentration value based on the sequence data.

18. The method of claim 1 , wherein the quantitatively detecting is performed by performing DNA-seq and obtaining nucleic acid concentration ratio based on the sequence data.

19. The method of claim 1 , wherein contacting the sample with an antibiotic is performed for up to 90 minutes.

20. The method of claim 1 , wherein contacting the sample with an antibiotic is performed for up to 45 minutes.

21. The method of claim 1 , wherein contacting the sample with an antibiotic is performed for up to 30 minutes.

22. The method of claim 1 , wherein contacting the sample with an antibiotic is performed for up to 15 minutes.

23. The method of claim 1 , wherein contacting the sample with an antibiotic is performed for up to 5 minutes.

24. The method of claim 1 , wherein the detecting is performed by contacting the sample with a probe specific for a nucleic acid of the microorganism and/or for any nucleic acid complementary to the nucleic acid of the microorganism.

25. The method of claim 1 , wherein the antibiotic is a beta-lactam.

26. The method of claim 1 , wherein the antibiotic is a carbapenem.

27. The method of claim 1 , wherein the contacting results in the antibiotic disrupting a cell envelope of the microorganism.

28. The method of claim 1 , wherein the microorganism is Neisseria gonorrhoeae.

29. The method of claim 1 , wherein the microorganism belongs to the family Enterobacteriaceae.