Co-incubating confined microbial communities
Provided herein are devices and methods that enable co-incubation of microorganisms. Also provided are methods of making such devices for co-incubation of microorganisms, and various applications of such devices.
1. A method to detect viability of cells of a microorganism, the method comprising:
providing a sample solution containing cells of the microorganism;
generating sets of plugs from the sample solution in a microfluidic device, the sets of plugs comprising
at least one antibiotic set of plugs comprising cells of the microorganism and an antibiotic, each plug comprising a carrier fluid that is immiscible with the sample solution, a cell or no cell of the microorganism, and the antibiotic, and
at least one control set of plugs comprising cells of the microorganism, each plug comprising a carrier fluid that is immiscible with the sample solution, a cell or no cell of the microorganism;
incubating the sets plugs for a period of time; and
detecting viability of the cells of the microorganism in the sets of plugs by detecting presence or absence of a signal produced by viable cells of the microorganism.
2. The method of claim 1 , wherein the at least one antibiotic sets of plugs and at least one control set of plugs comprise plugs with no cell of the microorganism.
3. The method of claim 1 , wherein the at least one antibiotic sets of plugs and at least one control set of plugs comprise plugs with a single cell of the microorganism.
4. The method of claim 1 , wherein the period of time is less than 3 hours.
5. The method of claim 1 , wherein each plug of the sets of plugs further comprises a viability indicator.
6. The method of claim 1 , wherein the at least one antibiotic set of plugs comprises a plurality of antibiotic sets of plugs each comprising a different antibiotic.
7. The method of claim 1 , wherein the antibiotic is selected from the group consisting of a beta-lactam, a cephalosporin, a fluoroquinolone, and a macrolide.
8. The method of claim 7 , wherein the antibiotic is selected from the group consisting of ampicillin, oxacillin, cefoxitin, levofloxacin, vancomycin, and erythromycin.
9. The method of claim 1 , wherein the at least one antibiotic set of plugs comprise the antibiotic at a breakpoint concentration in the plugs.
10. The method of claim 1 , wherein the sample solution comprises culture media capable of supporting bacterial growth.
11. The method of claim 1 , wherein the sample solution comprises blood plasma.
12. The method of claim 1 , wherein the generating comprises flowing the sample solution in said carrier fluid through a microfluidic channel of the microfluidic device.
13. The method of claim 1 , wherein the generating comprises
providing the sets of plugs in an array of preformed plugs;
introducing the sample solution into the array of preformed plugs.
14. The method of claim 13 , wherein the array of preformed plugs comprises a plurality of antibiotic sets of plugs, each antibiotic set of plugs comprising a different antibiotic.
15. The method of claim 13 , wherein the antibiotic is selected from the group consisting of a beta-lactam, a cephalosporin, a fluoroquinolone, and a macrolide.
16. The method of claim 15 , wherein the antibiotic is selected from the group consisting of ampicillin, oxacillin, cefoxitin, levofloxacin, vancomycin, and erythromycin.
17. The method of claim 13 , wherein the at least one antibiotic set of plugs comprise the antibiotic at a breakpoint concentration in the plugs.
18. The method of claim 13 , wherein the providing and the introducing comprise flowing the array of preformed plugs in said carrier fluid through a microfluidic channel of the microfluidic device.
19. The method of claim 1 , wherein the detecting is performed after or during the incubating.
20. The method of claim 1 , wherein the detecting is performed to detect susceptibility of the microorganism to the antibiotic.
21. The method of claim 20 , wherein the sample solution is from a sample of a patient and the method further comprises
administering to the patient the antibiotic, when susceptibility of the microorganism to the antibiotic is detected.
22. The method of claim 1 , wherein the generating, the incubating, and the detecting are performed with high-throughput microfluidic methods.