Systems and methods for detection of cells using engineered transduction particles

• US 9,133,497 B2
• Filed: 02/02/2015
• Issued: 09/15/2015
• Est. Priority Date: 03/13/2013
• Status: Active Grant

• Current Assignee: Roche Molecular Systems Inc (Roche Holding AG)
• Original Assignee: GeneWEAVE BioSciences, Inc. (Roche Holding AG)
• Inventors: Rey, Diego Ariel, Roy, Shaunak, Griswold, Ryan C., Olson, Kenneth G., Richardson, Bruce J., Stellmacher, Rick V., Frei, Werner
• Primary Examiner(s): BOWERS, NATHAN ANDREW
• Application Number:
  US14/611,902
• Publication Number:
  US 20150148261A1
• Time in Patent Office: 225 Days
• US Class Current: 1/1
• CPC Class Codes: B01L 2200/028 Modular arrangements
• CPC Class Codes: B01L 2200/16 Reagents, handling or storing thereof
• CPC Class Codes: B01L 2300/021 Identification, e.g. bar codes
• CPC Class Codes: B01L 2300/042 Caps; Plugs
• CPC Class Codes: B01L 2300/047 Additional chamber, reservoir
• CPC Class Codes: B01L 2300/049 Valves integrated in closure
• CPC Class Codes: B01L 2300/0672 Integrated piercing tool
• CPC Class Codes: B01L 2400/0478 pistons
• CPC Class Codes: B01L 2400/06 Valves, specific forms thereof
• CPC Class Codes: B01L 2400/0683 mechanically breaking a wall or membrane within a channel or chamber
• CPC Class Codes: B01L 3/502 with fluid transport, e.g. in multi-compartment structures centrifugal-type cuvettes G01N21/07; analysis by separation into components G01N30/00; automatic analysers G01N35/00
• CPC Class Codes: B01L 3/50825 Closing or opening means, corks, bungs closures for containers B65D; means for removing stoppers B67B7/02
• CPC Class Codes: B01L 3/52 Containers specially adapted for storing or dispensing a reagent B01L3/02 takes precedence; containers for medical or pharmaceutical purposes A61J1/00; containers in general B65D; storing or dispensing test elements G01N33/4875; automated reagent dispensing G01N35/1002
• CPC Class Codes: B01L 3/523 with means for closing or opening
• CPC Class Codes: B01L 3/54 Labware with identification means identification of carriers, materials or components in automatic analysers G01N35/00732
• CPC Class Codes: B01L 3/545 for laboratory containers
• CPC Class Codes: B01L 7/00 Heating or cooling apparatus autoclaves B01J3/04; Heat insulating devices
• CPC Class Codes: C12Q 1/02 involving viable microorganisms
• CPC Class Codes: C12Q 1/04 Determining presence or kind of microorganism; Use of selective media for testing antibiotics or bacteriocides; Compositions containing a chemical indicator therefor C12Q1/6897 takes precedence
• CPC Class Codes: C12Q 1/06 Quantitative determination
• CPC Class Codes: C12Q 1/10 : Enterobacteria
• CPC Class Codes: C12Q 1/14 : Streptococcus; Staphylococcus
• CPC Class Codes: C12Q 1/66 : involving luciferase
• CPC Class Codes: C12Q 1/6897 : involving reporter genes operably linked to promoters
• CPC Class Codes: G01J 1/00 : Photometry, e.g. photographic exposure meter spectrophotometry G01J3/00; specially adapted for radiation pyrometry G01J5/00 ; exposure meters built in cameras G03B17/06
• CPC Class Codes: G01N 2035/00346 : Heating or cooling arrangements
• CPC Class Codes: G01N 2035/0405 : manipulating closing or opening means, e.g. stoppers, screw caps, lids or covers
• CPC Class Codes: G01N 21/01 : Arrangements or apparatus for facilitating the optical investigation
• CPC Class Codes: G01N 21/03 : Cuvette constructions
• CPC Class Codes: G01N 21/13 : Moving of cuvettes or solid samples to or from the investigating station handling materials for automatic analysis G01N35/00
• CPC Class Codes: G01N 21/76 : Chemiluminescence; Bioluminescence
• CPC Class Codes: G01N 21/763 : Bioluminescence
• CPC Class Codes: G01N 2333/005 : from viruses
• CPC Class Codes: G01N 2333/195 : from bacteria

Abstract

Systems and methods for detecting and/or identifying target cells (e.g., bacteria) using engineered transduction particles are described herein. In some embodiments, a method includes mixing a quantity of transduction particles within a sample. The transduction particles are associated with a target cell. The transduction particles are non-replicative, and are engineered to include a nucleic acid molecule formulated to cause the target cell to produce a series of reporter molecules. The sample and the transduction particles are maintained to express the series of the reporter molecules when target cell is present in the sample. A signal associated with a quantity of the reporter molecules is received. In some embodiments, a magnitude of the signal is independent from a quantity of the transduction particle above a predetermined quantity.

Claims

1. A method, comprising:

coupling a reagent module to a sample container such that a reaction chamber defined by the sample container is fluidically isolated from an exterior volume, the reaction chamber containing a sample, a seal surface of the reagent module being in a fixed location relative to the sample container after the coupling;

disposing, after the coupling, at least a distal end portion of the sample container into an instrument; and

actuating the instrument to;

produce a force on the reagent module to (1) move at least the distal end portion of the sample container into a detection volume of the instrument, and (2) place the seal surface into contact with a corresponding surface of the instrument to optically isolate the detection volume;

cause an optical assembly to receive, when the distal end portion of the sample container is in the detection volume, a signal associated with a magnitude of light emission in the detection volume; and

manipulate, during the receiving of the signal, the reagent module to convey a reagent into the reaction chamber of the sample container.

2. The method of claim 1, wherein:

the instrument is configured to maintain the force during the receiving of the signal.

3. The method of claim 2, wherein:

the force is a first force, the first force is applied by an actuator,

the manipulating the reagent module by the instrument includes applying, by the actuator, a second force.

4. The method of claim 1, wherein:

when the distal end portion of the sample container is moved into the detection module a shutter of the instrument is moved from a first position to a second position, the detection volume being optically isolated from a volume outside of the detection volume by the shutter when the shutter is in the first position.

5. The method of claim 1, wherein the reagent includes at least one of a eukaryotic or a bacterial luciferase substrate.

6. The method of claim 1, wherein the reagent includes tridecanal, the light emission being associated with a flash luminescence reaction.

7. The method of claim 1, wherein the reagent is a second reagent, the second reagent including tridecanal, the reagent module containing a first reagent including at least one of an antimicrobial agent or a nucleic acid delivery compound engineered to include a nucleic acid molecule formulated to cause a target cell within the sample to produce a plurality of reporter molecules, wherein the actuating the instrument further causes the instrument to:

manipulate, before the receiving of the signal, the reagent module to convey the first reagent into the reaction chamber of the sample container.

8. The method of claim 1, wherein the reagent module includes a non-replicative, bacteriophage-based transduction particle formulated to cause a target cell within the sample to produce a reporter molecule, wherein the actuating the instrument further causes the instrument to:

manipulate, before the receiving of the signal, the reagent module to convey the transduction particle into the reaction chamber of the sample container.

9. The method of claim 1, wherein:

the reagent module defines a delivery path having a centerline that intersects a side wall of the sample container such that when the reagent is conveyed into the reaction chamber, at least a portion of the reagent flows along the side wall and into the reaction chamber.

10. The method of claim 1, wherein:

the reagent module includes a reagent container containing the reagent,

the manipulating the reagent module includes puncturing the reagent container to place the reagent in fluid communication with reaction chamber.

11. The method of claim 1, wherein the light emission is conveyed from the reaction chamber through a planar, distal end surface of the sample container.

12. The method of claim 1, wherein the sample includes at least one of an antimicrobial agent or a nucleic acid delivery compound engineered to include a nucleic acid molecule formulated to cause a target cell within the sample to produce a plurality of reporter molecules.

13. The method of claim 1, further comprising:

removing from the instrument, after the signal is received, the sample container coupled to the reagent module.

14. The method of claim 1, wherein:

the instrument includes a manipulator assembly configured to produce the force to move the distal end portion of the sample container and to manipulate the reagent module.

15. The method of claim 1, wherein the light emission is associated with a luminescence reaction and is conveyed from the reaction chamber through a distal end surface of the sample container.

16. The method of claim 1, wherein:

the reagent module includes a non-replicative, bacteriophage-based transduction particle formulated to cause a target cell within the sample to produce a reporter molecule associated with a luminescence reaction;

the actuating the instrument further causes the instrument to manipulate, before the receiving of the signal, the reagent module to convey the transduction particle into the reaction chamber of the sample container; and

the reagent includes tridecanal formulated to catalyze the luminescence reaction.

17. The method of claim 1, wherein:

the reagent module includes a non-replicative, bacteriophage-based transduction particle formulated to cause a target cell within the sample to produce a reporter molecule associated with a luminescence reaction; and

the actuating the instrument further causes the instrument to;

manipulate, before the receiving of the signal, the reagent module to convey the transduction particle into the reaction chamber of the sample container; and

heat, after the transduction particle within the reaction chamber, the distal end portion of the sample container.