SYSTEM AND METHODS FOR DETECTION OF CELLS USING ENGINEERED TRANSDUCTION PARTICLES

• US 20170152576A1
• Filed: 12/22/2016
• Published: 06/01/2017
• 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, TEIXEIRA, Leonardo Maestri, GRISWOLD, Ryan C., OLSON, Kenneth G., RICHARDSON, Bruce J., YEE, Victor H., ROY, Shaunak
• Granted Patent: US 10,240,212 B2
• Time in Patent Office: Days
• 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:

mixing with a sample a plurality of transduction particles associated with a target cell, the plurality of transduction particles engineered 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, the plurality of transduction particles being non-replicative;

maintaining the sample and the plurality of transduction particles to express the plurality of reporter molecules when the target cell is present in the sample; and

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

2. The method of claim 1, wherein the plurality of transduction particles is 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, Listeria, 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 sample is within a sample container that is fluidically isolated from a region outside of the sample container by a reagent module coupled to the sample container;

the plurality of transduction particles is stored within the reagent module such that the plurality of transduction particles is fluidically isolated from the sample before the mixing; and

the mixing includes manipulating an actuator of the reagent module to convey the plurality of transduction particles into the sample while maintaining fluidic isolation between the region and the sample container.

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

8. The method of claim 7, wherein the actuator of the reagent module is a first actuator, the method further comprising:

manipulating, after the maintaining, a second actuator of the reagent module to convey a reagent into the sample, the reagent formulated to react with the plurality of reporter molecules to catalyze production of the signal.

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, 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;

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

actuating the instrument to;

manipulate the reagent module to convey a 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 sample and the plurality of transduction particles within a predetermined temperature range to express the plurality of reporter molecules when the target cell is present in the sample; and

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

11. The method of claim 10, wherein the 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 instrument is configured to maintain the sample and the plurality of transduction particles at a substantially constant temperature to express the plurality of reporter molecules.

13. The method of claim 12, wherein:

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

the target cell within the sample is non-isolated.

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

15. The method of claim 10, wherein:

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

the actuating the instrument further causes the instrument to;

manipulate, during the receiving of the light signal, the reagent module to convey a reagent into the reaction chamber of the sample container, the reagent including a fatty aldehyde formulated to catalyze the luminescence reaction.

16. 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, the reaction chamber devoid of a reporter molecule associated with a target cell;

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

actuating the instrument to;

manipulate the reagent module to convey a plurality of transduction particles 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 the reporter molecules associated with the target cell;

maintain the sample and the plurality of transduction particles within the reaction chamber in fluidic isolated from the exterior volume such that none of the plurality of the reporter molecules are added from the exterior region, the sample and the plurality of transduction particles being maintained for a time period to express the plurality of reporter molecules when the target cell is present in the sample; and

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

17. The method of claim 16, wherein the instrument is configured to maintain the sample and the plurality of transduction particles at a substantially constant temperature to express the plurality of reporter molecules.

18. The method of claim 16,

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

and

the target cell within the sample is non-isolated.

19. The method of claim 16, wherein:

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

the actuating the instrument further causes the instrument to;

manipulate, during the receiving of the light signal, the reagent module to convey a reagent into the reaction chamber of the sample container, the reagent including a fatty aldehyde formulated to catalyze the luminescence reaction.