Systems and methods for detection of cells using engineered transduction particles

• US 9,546,391 B2
• Filed: 09/08/2014
• Issued: 01/17/2017
• 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: Matthews, Damian S., Rey, Diego Ariel, Roy, Shaunak, Frei, Werner, Richardson, Bruce J., Griswold, Ryan C., Olson, Kenneth G., Yee, Victor H.
• Primary Examiner(s): BOWERS, NATHAN ANDREW
• Application Number:
  US14/480,269
• Publication Number:
  US 20150132795A1
• Time in Patent Office: 862 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. An apparatus, comprising:

a sample container defining a reaction chamber;

a housing configured to be coupled to the sample container such that the reaction chamber is fluidically isolated from an exterior volume when the housing is coupled to the sample container, the housing defining a reagent volume and a delivery pathway, the reagent volume containing a reagent, the reagent being fluidically isolated from the reaction chamber when the housing is coupled to the sample container and is in a first configuration, the reagent being in fluid communication with the reaction chamber when the housing is in a second configuration, the housing including a seal surface in a fixed location relative to the sample container when the housing is coupled to the sample container, the seal surface configured to contact a corresponding surface of an instrument to optically isolate the reaction chamber from the exterior volume when a first distal force is exerted on the housing and the sample container is disposed within the instrument; and

an actuator including an engagement portion and a plunger portion, the plunger portion configured to move within the reagent volume in a distal direction along a longitudinal axis of the housing in response to a second distal force exerted on the engagement portion to transition the housing from the first configuration to a second configuration and to produce a flow of the reagent from the reagent volume to the reaction chamber via the delivery pathway, the seal surface configured to maintain contact with the corresponding surface when the housing is transitioned from the first configuration to the second configuration.

2. The apparatus of claim 1, wherein:

a delivery portion of the housing defines the delivery pathway, a first portion of the delivery pathway defined along a bottom surface of the delivery portion, a second portion of the delivery pathway extending through the delivery portion.

3. The apparatus of claim 1, wherein:

an exit portion of the delivery pathway defines an exit axis that intersects a sidewall of the sample container when the housing is coupled to the sample container.

4. The apparatus of claim 1, wherein:

the plunger portion of the actuator and a portion of the housing are configured to collectively optically isolate the reagent volume from the exterior volume.

5. The apparatus of claim 1, wherein:

the reagent volume includes a reagent container containing the reagent; and

the actuator being configured to produce the flow of the reagent from the reagent container to the reaction chamber via the delivery pathway.

6. The apparatus of claim 5, wherein:

the housing includes a puncture member, the actuator configured to apply the second distal force to the reagent container such that the puncture member punctures the reagent container to place the reagent container in fluid communication with the reaction chamber when the housing is transitioned from the first configuration to the second configuration.

7. The apparatus of claim 6, wherein:

the reagent container includes a frangible portion configured to rupture in response to (1) the second distal force applied by the actuator moving the frangible portion into contact with the puncture member.

8. The apparatus of claim 5, wherein:

the reagent container includes a side wall and a distal end surface, the side wall being curved, the distal end surface being flat and including a frangible portion.

9. The apparatus of claim 1, wherein:

the reagent is a first reagent; and

the sample container contains a second reagent disposed therein.

10. The apparatus of claim 1, wherein the housing is a first housing, the apparatus further comprising:

a second housing configured to be removably coupled to the sample container such that the reaction chamber is fluidically isolated from the exterior volume when the second housing is coupled to the sample container; and

a sample collection swab, the sample collection swab coupled to the second housing and disposed within the reaction chamber when the second housing is coupled to the sample container.

11. The apparatus of claim 9, wherein the second reagent 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 to produce a plurality of reporter molecules.

12. The apparatus of claim 1, wherein:

the reagent includes at least one of a non-replicative bacteriophage-based transduction particle formulated to cause a target cell to produce a reporter molecule, a tridecanal, an antimicrobial agent, a nucleic acid delivery compound engineered to include a nucleic acid molecule formulated to cause a target cell to produce a reporter molecule, a eukaryotic or a bacterial luciferase substrate.

13. The apparatus of claim 1, further comprising:

a machine-readable label disposed on an exterior surface of the housing, the label including information associated with at least one of a target cell, a serial number, a lot number, an expiration date, or a warning information.

14. The apparatus of claim 6, wherein:

the puncture member is fixedly coupled to the housing; and

the reagent container is disposed between the puncture member and the actuator.

15. An apparatus, comprising:

a sample container defining a reaction chamber;

a housing configured to be coupled to the sample container such that the reaction chamber is fluidically isolated from an exterior volume when the housing is coupled to the sample container and the housing is in a first configuration, the housing including a seal surface in a fixed location relative to the sample container when the housing is coupled to the sample container, the seal surface configured to contact a surface of an instrument to optically isolate the reaction chamber from the exterior volume when a first distal force is exerted on the housing and the sample container is disposed within the instrument, the housing defining a reagent volume containing a reagent container including a reagent, the housing including a puncture member fixedly coupled to the housing, the puncture member configured to puncture a frangible portion of the reagent container to produce a flow of the reagent from the reagent container to the reaction chamber when the housing is transitioned from the first configuration to a second configuration; and

an actuator including an engagement portion and a plunger portion, the plunger portion configured to be moved within the reagent volume in response to a second distal force exerted on the engagement portion to transition the housing from the first configuration to the second configuration, the seal surface configured to maintain contact with the surface of the instrument when the housing is transitioned from the first configuration to the second configuration.

16. The apparatus of claim 15, wherein:

the puncture member defines a flow pathway configured to direct the flow of the reagent from the reagent volume to the reaction chamber.

17. The apparatus of claim 15, wherein:

the housing defines a delivery pathway configured to direct the flow of the reagent from the reagent volume in a direction non-parallel to a sidewall of the reaction chamber when the housing is coupled to the sample container and the housing is transitioned from the first configuration to the second configuration.

18. The apparatus of claim 15, wherein:

a delivery portion of the housing defines a delivery pathway configured to direct the flow of the reagent from the reagent volume to the reaction chamber, a first portion of the delivery pathway defined along a bottom surface of the delivery portion, an exit portion of the delivery pathway extending through the delivery portion.

19. The apparatus of claim 15, wherein:

the plunger portion of the actuator and a portion of the housing are collectively configured to isolate the reagent volume from a volume outside the housing.

20. The apparatus of claim 15, wherein:

the reagent is a first reagent; and

the sample container includes a second reagent disposed therein.

21. The apparatus of claim 20, wherein the second reagent 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 to produce a plurality of reporter molecules.

22. The apparatus of claim 15, wherein:

the reagent includes at least one of a non-replicative bacteriophage-based transduction particle formulated to cause a target cell to produce a reporter molecule, a tridecanal, an antimicrobial agent, a nucleic acid delivery compound engineered to include a nucleic acid molecule formulated to cause a target cell to produce a reporter molecule, a eukaryotic or a bacterial luciferase substrate.

23. The apparatus of claim 15, wherein:

the reagent within the reagent container includes at least one of a non-replicative bacteriophage-based transduction particle formulated to cause a target cell to produce a reporter molecule, a tridecanal, an antimicrobial agent, a nucleic acid delivery compound engineered to include a nucleic acid molecule formulated to cause a target cell to produce a reporter molecule, a eukaryotic or a bacterial luciferase substrate; and

the reagent container includes a curved portion against which the plunger portion of the actuator exerts the second distal force, the curved portion opposite the frangible portion.