Systems and methods for detection of cells using engineered transduction particles

• US 10,240,212 B2
• Filed: 12/22/2016
• Issued: 03/26/2019
• Est. Priority Date: 03/13/2013
• Status: Active Grant

• Current Assignee: Roche Molecular Systems (Roche Holding AG)
• Original Assignee: GeneWEAVE BioSciences, Inc. (Roche Holding AG)
• Inventors: Rey, Diego Ariel, Roy, Shaunak, Teixeira, Leonardo Maestri, Griswold, Ryan C., Olson, Kenneth G., Richardson, Bruce J., Yee, Victor H., Frei, Werner
• Primary Examiner(s): Babic, Christopher M
• Assistant Examiner(s): Aron, Kimberly A.
• Application Number:
  US15/388,750
• Publication Number:
  US 20170152576A1
• Time in Patent Office: 824 Days
• Field of Search: None
• 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 of detecting the presence a target cell within a biological sample using an instrument, comprising:

conveying a plurality of transduction particles associated with the target cell from a reagent module into a sample container containing the biological sample, the reagent module coupled to the sample container during the conveying such that the sample container is fluidically isolated from an exterior volume, the plurality of transduction particles engineered to be non-replicative and to include a nucleic acid molecule formulated to cause the target cell to produce a plurality of reporter molecules, the plurality of transduction particles formulated to bind to and deliver the nucleic acid molecule into the target cell;

maintaining, after the conveying, the biological sample and the plurality of transduction particles within the sample container for a time period to allow the plurality of reporter molecules to be produced within the sample container when the target cell is present in the biological sample;

exerting a force on the reagent module to place a seal surface of the reagent module in contact with a corresponding surface of the instrument to optically isolate the sample container from the exterior volume, the seal surface in a fixed location relative to the sample container;

conveying, after the exerting, a reagent from the reagent module into the sample container, the reagent formulated to react with the plurality of reporter molecules to catalyze production of a signal, the seal surface being maintained in contact with the corresponding surface during the conveying the reagent; and

receiving via a detector of the instrument, the signal associated with a quantity of the plurality of reporter molecules.

2. The method of claim 1, wherein the plurality of transduction particles is derived from a bacteriophage and is engineered to be incapable of lysogenic replication and lytic replication.

3. The method of claim 1, wherein the plurality of transduction particles includes a viral vector devoid of a wild-type DNA capable of exhibiting wild-type viral functions associated with a virus from which the viral vector is derived.

4. The method of claim 1, wherein the target cell is a bacteria selected from the group consisting of Escherichia, Mycobacterium, Staphylococcus, Li steria, Clostridium, Enterococcus, Streptococcus, Helicobacter, Rickettsia, Haemophilus, Xenorhabdus, Acinetobacter, Bordetella, Pseudomonas, Aeromonas, Actinobacillus, Pasteurella, Vibrio, Legionella, Bacillus, Calothrix, Methanococcus, Stenotrophomonas, Chlamydia, Neisseria, Salmonella, Shigella, Campylobacter and Yersinia.

5. The method of claim 1, wherein a reporter molecule from the plurality of reporter molecules is any one of a bacterial luciferase, a eukaryotic luciferase, a fluorescent protein, an enzyme suitable for colorimetric detection, a protein suitable for immunodetection, a peptide suitable for immunodetection, or a nucleic acid that function as an apatamer or that exhibits enzymatic activity.

6. The method of claim 1, wherein:

the plurality of transduction particles is stored within the reagent module such that the plurality of transduction particles is fluidically isolated from the biological sample after the reagent module is coupled to the sample container and before the conveying the plurality of transduction particles; and

the conveying the plurality of transduction particles includes manipulating an actuator of the reagent module to convey the plurality of transduction particles into the biological sample.

7. The method of claim 6, wherein the maintaining includes maintaining the biological sample at a temperature of less than or equal to approximately 45degrees Celsius, the time period being less than approximately eight hours.

8. The method of claim 7, wherein:

the actuator of the reagent module is a first actuator; and

the conveying the reagent includes manipulating, a second actuator of the reagent module to convey the reagent into the biological sample.

9. The method of claim 8, wherein the reagent includes a fatty aldehyde, the signal being a light emission signal associated with a flash luminescence reaction.

10. A method of detecting the presence of a target cell within a biological sample, 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 the biological sample, the reagent module containing a plurality of transduction particles associated with the target cell and a reagent;

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

actuating the instrument to cause the instrument to;

manipulate the reagent module to convey the plurality of transduction particles into the reaction chamber of the sample container, the plurality of transduction particles associated with a target cell, the plurality of transduction particles engineered to be non-replicative and to include a nucleic acid molecule formulated to cause the target cell to produce a plurality of reporter molecules;

maintain the biological sample and the plurality of transduction particles within the reaction chamber within a predetermined temperature range to allow the plurality of reporter molecules to be produced within the reaction chamber when the target cell is present in the biological sample;

move the reagent module within the instrument to place a seal surface of the reagent module contact with a corresponding surface of the instrument to optically isolate the reaction chamber from the exterior volume, the seal surface in a fixed location relative to the sample container;

manipulate the reagent module to convey the reagent into the reaction chamber of the sample container, the reagent formulated to react with the plurality of reporter molecules to catalyze production of a signal, the seal surface being maintained in contact with the corresponding surface when the reagent module is manipulated; and

receive the signal associated with a quantity of the plurality of reporter molecules.

11. The method of claim 10, wherein the biological sample is a raw sample that has not undergone a separation operation or a washing operation, the raw sample being maintained within the sample container fluidically isolated from the exterior volume after the distal end portion of the sample container is disposed into the instrument.

12. The method of claim 10, wherein:

the biological sample is a raw sample that has not undergone a separation operation or a washing operation; and

the target cell within the biological sample is non-isolated.

13. The method of claim 10, wherein the instrument is configured to maintain the biological sample and the plurality of transduction particles in fluidic isolation from the exterior volume such that no reporter molecules are added from the exterior volume.

14. The method of claim 10, wherein:

the signal is a light emission associated with a flash luminescence reaction; and

the reagent comprises a fatty aldehyde formulated to catalyze the luminescence reaction.

15. A method of detecting the presence of a target cell within a biological sample, 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 the biological sample, the reaction chamber devoid of a reporter molecule before the coupling, the reagent module defining a first volume and a second volume, the first volume containing a plurality of transduction particles associated with the target cell, the second volume containing a reagent;

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

actuating the instrument to cause the instrument to;

manipulate the reagent module to convey the plurality of transduction particles from the first volume into the reaction chamber of the sample container, the plurality of transduction particles associated with the target cell, the plurality of transduction particles engineered to be non-replicative and to include a nucleic acid molecule formulated to cause the target cell to produce a plurality of reporter molecules;

maintain the biological sample and the plurality of transduction particles within the reaction chamber in fluidic isolation from the exterior volume for a time period to allow the plurality of reporter molecules to be produced within the reaction chamber when the target cell is present in the biological sample;

exert a force on the reagent module to place a seal surface of the reagent module in contact with a corresponding surface of the instrument to optically isolate the reaction chamber from the exterior volume, the seal surface in a fixed location relative to the sample container;

manipulate the reagent module to convey the reagent from the second volume into the reaction chamber of the sample container, the reagent formulated to react with the plurality of reporter molecules to catalyze production of a signal, the seal surface being maintained in contact with the corresponding surface when the reagent module is manipulated; and

receive the signal associated with a quantity of the plurality of reporter molecules.

16. The method of claim 15, wherein the instrument is configured to maintain the biological sample and the plurality of transduction particles at a substantially constant temperature to allow the plurality of reporter molecules to be produced.

17. The method of claim 15, wherein:

the biological sample is a raw sample that has not undergone a separation operation or a washing operation; and

the target cell within the biological sample is non-isolated.

18. The method of claim 15, wherein:

the signal is a light emission associated with a flash luminescence reaction; and

the reagent comprises a fatty aldehyde formulated to catalyze the luminescence reaction.

19. The method of claim 15, wherein the target cell is a bacteria selected from the group consisting of Escherichia, Mycobacterium, Staphylococcus, Listeria, Clostridium, Enterococcus, Streptococcus, Helicobacter, Rickettsia, Haemophilus, Xenorhabdus, Acinetobacter, Bordetella, Pseudomonas, Aeromonas, Aetinobacillus, Pasteurella, Vibrio, Legionella, Bacillus, Calothrix, Methanococcus, Stenotrophomonas, Chlamydia, Neisseria, Salmonella, Shigella, Campylobacter and Yersinia.