Instrument and system for rapid microogranism identification and antimicrobial agent susceptibility testing

1. A system for automated microorganism identification and antibiotic susceptibility testing comprising:

a reagent cartridge comprising a plurality of wells;

a reagent stage wherein the reagent stage comprises an annular shape defining an interior opening, wherein the reagent stage is configured to rotate in a first plane and wherein the reagent stage is configured to receive the reagent cartridge;

a cassette comprising a plurality of microfluidic sample channels structured to receive samples, each of the plurality of microfluidic sample channels comprising an inlet port configured to receive a pipette tip;

a cassette stage located within the interior opening of the reagent stage, wherein the cassette stage is configured to rotate in a second plane parallel to the first plane and to move laterally in the second plane, and wherein the cassette stage is configured to receive the cassette;

a pipettor assembly configured to move a plurality of reagents between the plurality of wells of the reagent cartridge and the inlet ports of each of the plurality of microfluidic sample channels;

an optical detection system configured to obtain darkfield and fluorescence photomicrographs of one or more microorganisms contained in the plurality of microfluidic sample channels; and

a controller configured to direct operation of the system and process microorganism information derived from photomicrographs obtained by the optical detection system.

2. The system according to claim 1 , wherein the plurality of microfluidic sample channels are arranged in a radial configuration about a center of the cassette, and wherein each microfluidic sample channel comprises one or more of an outlet port and an inlet port.

3. The system of claim 1 , wherein the reagent cartridge further comprises an opening, and wherein the plurality of wells of the reagent cartridge comprise at least one well comprising a nucleic acid probe and at least one well comprising an antimicrobial agent, wherein the at least one well comprising the nucleic acid probe and the at least one well comprising the antimicrobial agent are separate wells.

4. The system of claim 3 , wherein the at least one well comprising the nucleic acid probe further comprises a universal microbial probe.

5. The system of claim 3 , wherein the at least one well comprising an antimicrobial agent comprises a well comprising amikacin, a well comprising ampicillin, a well comprising ampicillin/sulbactam, a well comprising aztreonam, a well comprising cefazolin, a well comprising cefepime, a well comprising cefaroline, a well comprising cefazidime, a well comprising ciprofloxacin, a well comprising colistin, a well comprising daptomycin, a well comprising doxycycline, a well comprising ertapenem, a well comprising erythromycin, a well comprising gentamicin, a well comprising imipenem, a well comprising linezolid, a well comprising meropenem, a well comprising minocycline, a well comprising macrolide-lincosamide-streptogramin B, a well comprising cefoxitin, a well comprising piperacillin/tazobactam, a well comprising streptomycin, a well comprising tobramycin, a well comprising trimethoprim/sulfamethoxazole, and a well comprising vancomycin wherein the at least one well comprising the antimicrobial agent are separate wells.

6. The system of claim 1 , wherein the reagent cartridge further comprises a sample vial.

7. The system of claim 1 , wherein the reagent cartridge further comprises a pipette tip rack.

8. The system of claim 1 , wherein the reagent cartridge further comprises at least one teaching well formed in an outer surface thereof and sized to receive a pipette tip.

9. The system of claim 1 , wherein the plurality of the wells of the reagent cartridge comprise reagents and have respective ports providing access to the reagents with a pipette tip.

10. The system of claim 1 , wherein the plurality of the wells of the reagent cartridge comprise gel electrofiltration (GEF) wells shaped to house GEF apparatus.

11. The system of claim 1 , wherein the reagent cartridge further comprises at least one electrical contact accessible from an exterior of the reagent cartridge.

12. The system of claim 11 , wherein the at least one electrical contact comprises a pair of spaced apart electrical contacts positioned at one end of the reagent cartridge and configured for engagement by causing the reagent cartridge to translate and engage other electrical contacts of the system.

13. The system of claim 1 , wherein at least some of the wells of the plurality of the wells of the reagent cartridge are sealed by a film.

14. The system of claim 1 , wherein the reagent cartridge further comprises one or more of at least one well comprising a wash solution, at least one well comprising a permeabilization solution, at least one well comprising a buffer, at least one well comprising a universal cell stain, and at least one well comprising water.

15. The system of claim 14 , wherein the universal stain comprises acridine orange or propidium iodide.

16. The system of claim 1 , wherein the reagent cartridge further comprises one or more of at least one well comprising cation adjusted Mueller-Hinton broth and at least one well comprising Mueller-Hinton agar.

17. The system of claim 16 , wherein the cation adjusted Mueller-Hinton broth comprises 1% phytone tryptose cation adjusted Mueller-Hinton broth and/or the Mueller-Hinton agar comprises 1% phytone tryptose cation adjusted Mueller-Hinton agar.

18. The system of claim 1 , wherein the cassette further comprises:

a cassette component;

a glass support; and

a laminate layer positioned between the glass support and the cassette component.

19. The system of claim 18 , wherein the glass support is coated with at least one member selected from the group consisting of poly-L-lysine and indium tin oxide.

20. The system of claim 18 , wherein the microfluidic sample channels are formed in the laminate layer.

21. The system of claim 18 , wherein the microfluidic sample channels are formed in the laminate layer and in the cassette component.

22. The system of claim 1 , wherein at least a portion of the cassette is an optically clear polymer.

23. The system of claim 1 , wherein at least a portion of a surface of the cassette comprises an optically clear conductive layer.

24. The system of claim 1 , wherein the cassette comprises:

an optically clear polymer, and

a lower surface that is at least partially coated with an optically clear conductive layer.

25. The system of claim 24 , wherein the optically clear conductive layer comprises indium tin oxide at a resistance of about 70 to about 100 ohms/square.

26. The system of claim 1 , wherein the plurality of microfluidic sample channels are arranged in a radial configuration across the cassette.

27. The system of claim 1 , wherein each microfluidic sample channel further comprises an outlet port.

28. The system of claim 1 , wherein the inlet ports are toward the outer perimeter of the cassette.

29. The system of claim 1 , wherein the inlet ports are located near the center of the cassette and the outlet ports are near the perimeter of the cassette.