Patent Publication Number: US-2019194765-A1

Title: Systems and methods for detection of cells using engineered transduction particles

Description:
CROSS-REFERENCE TO RELATED APPLICATIONS 
     This application is a continuation of U.S. patent application Ser. No. 15/388,750, entitled “Systems and Methods for Detection of Cells Using Engineered Transduction Particles,” filed Dec. 22, 2016, which is a divisional of U.S. patent application Ser. No. 14/480,269, now U.S. Pat. No. 9,456,391, entitled “Systems and Methods for Detection of Cells Using Engineered Transduction Particles,” filed Sep. 8, 2014, which is a continuation of U.S. patent application Ser. No. 14/048,974, now U.S. Pat. No. 8,829,473, entitled “Systems and Methods for Detection of Cells Using Engineered Transduction Particles,” filed Oct. 8, 2013, which is a divisional of U.S. application Ser. No. 13/802,461, now U.S. Pat. No. 9,481,903, entitled “Systems and Methods for Detection of Cells Using Engineered Transduction Particles,” filed Mar. 13, 2013, which claims priority to and the benefit of U.S. Provisional Application Ser. No. 61/779,177, entitled “Non-Replicative Transduction Particles and Transduction Particle-Based Reporter Systems,” filed Mar. 13, 2013, all of which are incorporated herein by reference in their entirety. 
    
    
     BACKGROUND 
     The embodiments described herein relate to systems and methods for detection of cells using engineered transduction particles. More particularly, the embodiments described herein relate to methods for detecting bacteria using replication-deficient transduction particles as a reporter system. The embodiments described herein also relate to a container and instrument within which the detection of bacteria can be performed in an integrated, closed system with walkaway functionality. 
     Detection of bacteria, especially drug resistant strains, is a critical step in diagnosing and limiting spread of bacterial infections. For example, MRSA is a drug-resistant version of the common  Staphylococcus aureus  bacteria that is carried by a significant portion of the population in the U.S. Most infections of MRSA occur in hospitals, and can have a high mortality rate (MRSA infections kill approximately 19,000 people in the U.S. every year). Accordingly, there is a need for efficient, accurate and rapid identification of the bacterial strains (including their phenotype and/or genotype and other molecular targets) that cause infection, such as MRSA. Particularly important is the ability to identify the bacterial phenotype and/or genotype and other molecular targets from a variety of different samples (e.g., human samples, environmental samples, plant samples, veterinary samples, food samples or the like), so that the appropriate treatment and control regimen can be started in a timely fashion. 
     One known method for identifying bacteria includes bacterial culture. Culturing is highly sensitive, but often takes two to three days (or even longer) to yield a result, and is therefore not suitable for rapid diagnosis or for efficient screening purposes. Known culturing methods are often performed using systems that require highly trained personnel to perform the assay, and are therefore not suitable for use in a variety of different settings. Known culturing methods are also prone to contamination, which can result in false positives and/or misidentification of the bacteria. Moreover, known culturing methods employ specifically tailored culture protocols for identification of various bacterial species, thus testing a broad bacteria panel can rapidly elevate the cost. 
     Direct bacterial immunodetection, that is, detection using an antibody antigen reaction, is another method for bacterial detection. Known methods of immunodetection can produce results more quickly and at a lower cost than a culture, but are often limited by the availability of selective antibodies for the bacterial strain of interest and available antibodies are prone to cross-reactivity. Such known methods are also less sensitive than culturing, so there is often nevertheless a requirement of bacterial amplification that can lengthen the assay time. 
     Other known methods for detection of bacterial cells include isolation and analysis of nucleic acid such as DNA or RNA. Known methods for isolating nucleic acids from a sample often include several stringent sample preparation steps that require expensive and specialized equipment. In particular, such steps include 1) removing the proteins within a sample containing bacteria or cells by adding a protease; 2) breaking down the remaining bulk sample to expose the nucleic acids contained therein (also referred to as cell lysing); 3) precipitating the nucleic acid from the sample; 4) washing and/or otherwise preparing the nucleic acid for further analysis; 5) analyzing the nucleic acid to identify the species. After preparing the sample, known analysis methods can include polymerase chain reaction (PCR), gene sequencing, gene fingerprinting, fluorescence, immunoassay, electrochemical immunoassay, microarrays, any other suitable technique or a combination thereof. PCR has found widespread commercial usage but often requires multiple steps involving expensive reagents and instrumentation. Many known methods involving PCR are not suitable for bench top testing (e.g., they require relatively skilled personnel). Moreover, known PCR methods employ thermal cycling and/or elevated temperatures, which can increase the cost, time and/or complexity of the analysis. Finally, because PCR methods for detecting DNA sequences lyse the sample cells, such methods cannot distinguish between live and dead cells. 
     Some known systems and methods for cell identification include the use of bacteriophages to identify and/or detect certain bacteria. In some known methods, phages that are tagged with a reporter molecule can be used to target and infect a specific bacterial strain. After infection, the phages can undergo a lytic cycle (i.e., break the cell wall killing the target bacteria) and/or a lysogenic cycle (i.e., replication of the phage along with the bacteria without killing the bacteria), followed by detection of the amplified progeny phage. Such known methods relying on phage detection often include limiting or complex steps. For example, some known phage detection-based methods for identification rely on phage replication (during which the bacteria can be lysed), and typically require cell culturing for facilitating this process. Some known phage detection-based methods require removal or “unbinding” of specifically bound phages from the samples using carefully metered and/or pH controlled reagents. Moreover, some known phage detection-based methods rely on careful metering of the amount of phage added and/or include opening or closing of the reaction chamber to add/remove reagents, which can lead to contamination and/or premature mixing of reagents leading to erroneous results and making the assay complex in nature. 
     Other phage-based methods employ bacteriophages that are engineered to deliver into the target bacteria a nucleotide that can include a reporter gene, which cause the target bacteria to express a reporter molecule. Some known methods include phages that replicate during the assay, however, which can result in an undesirable lysing of the cells within which the reporter molecules are to be produced. Other known phage-based methods employ bacteriophages in which the replicative functions are suppressed during the assay conditions. Such known methods, however, are difficult to implement due to the tight range of conditions (e.g., temperature conditions) under which the replicative functions will remain suppressed. Such methods are not easily controlled, and thus can result in lytic activity. Still other methods suggest the use of temperate phages that undergo a lysogenic cycle instead of a lytic cycle. Such known methods, however, are also susceptible to sporadic lytic activity. Incorporation of native phage life cycles may also lead to limiting of the reporter phage host range due to superinfection immunity by target cells that may be lysogenized with a prophage. Thus, although known methods of this type have been performed in an academic setting, they are not applicable in a clinical setting. 
     In addition to the above-described drawbacks regarding the use of phage-based methods, known methods do not employ automation or instrumentation for enabling a “walk away” bacteriophage identification system. For example, many known systems do not accommodate closed system handling and/or measurement of a signal that is produced by certain reporter molecules, such as for example, a flash luminescence reaction. Thus, known systems and methods require skilled personnel and intimate handling of the samples, which can increase the possibility of false positives or negatives. 
     Thus, a need exists for improved apparatus and methods for rapid, cost effective and facile detection and identification of bacterial species in clinical samples. 
     SUMMARY 
     Systems and methods for detecting and/or identifying target cells (e.g., bacteria) using engineered viral vectors and/or 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. 
     In some embodiments, a container includes a housing, a delivery member, and an actuator. The housing, which can be removably coupled to a reaction chamber, defines a reagent volume. The delivery member is coupled to the housing and defines a pathway between the reagent volume and the reaction chamber when the housing is coupled to the reaction chamber. A first end portion of the delivery member is disposed within the reagent volume and a second end portion of the delivery member is disposed outside of the reagent volume. The actuator has a plunger portion disposed within the reagent volume that can be moved within the reagent volume along a longitudinal axis of the housing to produce a flow or reagent from the reagent volume via the pathway. The delivery member is configured to direct the flow of the reagent exiting the second end portion of the delivery member in an exit direction non-parallel to the longitudinal axis of the housing. 
     In some embodiments, an instrument includes a retention assembly, an activation assembly and an actuator. The retention assembly includes a first gripper, a second gripper and a biasing member. The first gripper and the second gripper are configured to contact a first portion of a sample container to limit movement of the sample container. The sample container defines a reaction volume and a reagent volume. The activation member is movably coupled to the retention assembly, and is configured to engage a second portion of the sample container to convey a reagent from the reagent volume into the reaction volume. The actuator is configured to move the activation member relative to the retention assembly between a first position and a second position. In the first position, a surface of the activation member is in contact with a surface of the retention assembly to maintain the first gripper and the second gripper in an opened configuration. In the second position, the surface of the activation member is spaced apart from the surface of the retention assembly such that the biasing member urges the first gripper and the second gripper into a closed configuration. A plunger portion of the activation member is configured to move within the reagent volume when the activation member moves toward the second position. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
         FIG. 1  is a block diagram of a system for bacteria identification, according to an embodiment. 
         FIGS. 2 and 3  are schematic illustrations of a cartridge according to an embodiment, in a first configuration and a second configuration. 
         FIG. 4  illustrates a flow diagram of a method for detecting a target cell in a sample, according to an embodiment. 
         FIG. 5  is a schematic illustration of a transduction particle and an engineered nucleic acid molecule contained therein, according to an embodiment. 
         FIGS. 6A, 6B, and 6C  show schematic illustrations of a method for identification of a target cell, according to an embodiment. 
         FIG. 7A and 7B  show a schematic illustration of transduction particles interacting with target cells at a first time ( FIG. 7A ) and a second time ( FIG. 7B ), according to an embodiment. 
         FIG. 8  illustrates a flow diagram of a method for the identification of a viable target cell, according to an embodiment. 
         FIG. 9  is a schematic illustration of a formulation of an engineered nucleic acid, according to an embodiment. 
         FIG. 10  illustrates a flow diagram of a method for genotypic identification of a target cell, according to an embodiment. 
         FIGS. 11A, 11B, 11C, and 11D  show schematic illustrations of genotypic method for identification of a target cell, according to an embodiment. 
         FIGS. 12-14  are schematic cross sectional views of a sample container according to an embodiment, in a first configuration, a second configuration and a third configuration, respectively. 
         FIGS. 15-17  are side views of a container assembly according to an embodiment, in a first configuration, a second configuration and a third configuration, respectively. 
         FIG. 18  is a perspective view of a container assembly according to an embodiment. 
         FIG. 19  shows an exploded view of the container assembly of  FIG. 18 . 
         FIG. 20  shows a top view of a housing included in the container assembly of  FIG. 19 . 
         FIG. 21  shows a perspective bottom view of the housing included in the container assembly of  FIG. 19 . 
         FIG. 22  shows a perspective view of a reagent container included in the container assembly of  FIG. 19 , according to an embodiment. 
         FIGS. 23-25  are side cross-sectional views of a portion of the container of  FIG. 19  in a first configuration, a second configuration and a third configuration, respectively. 
         FIG. 26  shows a perspective view of a container assembly, according to an embodiment. 
         FIG. 27  shows a perspective bottom view of a housing included in the container assembly of  FIG. 26 . 
         FIG. 28  shows a side cross-sectional view of the container assembly of  FIG. 26 . 
         FIG. 29  is a side cross-sectional view of a container assembly, according to an embodiment. 
         FIGS. 30-32  are side cross-sectional views of a container assembly according to an embodiment, in a first configuration, a second configuration and a third configuration, respectively. 
         FIG. 33  shows an exploded side cross-section of a container assembly, according to an embodiment. 
         FIGS. 34-36  are side cross-sectional views of the container assembly of  FIG. 33  in a first configuration, a second configuration and a third configuration, respectively. 
         FIGS. 37 and 38  are side cross-sectional schematic illustrations of a container assembly according to an embodiment in a first configuration and a second configuration, respectively. 
         FIGS. 39 and 40  are side cross-sectional schematic illustrations of a container assembly according to an embodiment in a first configuration and a second configuration, respectively. 
         FIG. 41  is side cross-sectional schematic illustration of a container assembly, according to an embodiment. 
         FIG. 42  illustrates a flow diagram of a method of signal detection, according to an embodiment. 
         FIGS. 43-45  are schematic side views of a portion of an instrument according to an embodiment, in a first configuration, a second configuration and a third configuration, respectively. 
         FIGS. 46-48  are schematic side views of a portion of an instrument according to an embodiment, in a first configuration, a second configuration and a third configuration, respectively. 
         FIGS. 49 and 50  are schematic side views of a detection portion of an instrument according to an embodiment, in a first configuration and a second configuration, respectively. 
         FIG. 51  shows a perspective view of an instrument, according to an embodiment. 
         FIG. 52  shows an inclined front view of the instrument of  FIG. 51  with a lid opened. 
         FIG. 53  shows an inclines front view of a housing included in the instrument of  FIG. 51 . 
         FIG. 54  shows a back view of the housing shown in  FIG. 53 . 
         FIGS. 55-57  show perspective views of a portion of the internal components and subassemblies of the instrument of  FIG. 51  with the housing removed for clarity. 
         FIG. 58  shows a perspective view of a power supply included in the instrument of  FIG. 51 . 
         FIG. 59  shows a perspective view of a processor included in the instrument of  FIG. 51 . 
         FIG. 60  shows a perspective view of a communications module included in the instrument of  FIG. 51 . 
         FIG. 61  shows a perspective view of the instrument of  FIG. 51  in a first configuration. 
         FIG. 62  shows a perspective view of a cartridge included in the instrument of  FIG. 51 . 
         FIG. 63  shows a perspective view of a cartridge receiver included in the instrument of  FIG. 51 . 
         FIG. 64  is a side view of the cartridge of  FIG. 62  and the cartridge receiver of  FIG. 63  in a coupled configuration. 
         FIG. 65  shows a perspective view of a heater assembly included in the instrument of  FIG. 51 . 
         FIG. 66  is a partially exploded view of the heater assembly of  FIG. 65 . 
         FIG. 67  shows a back view of the heater assembly of  FIG. 65 . 
         FIG. 68  is a perspective view of a drive assembly included in the instrument of  FIG. 51 , according to an embodiment. 
         FIG. 69  shows a front view of the drive assembly of  FIG. 68 . 
         FIGS. 70 and 71  show the drive assembly of  FIG. 68  in a first configuration and a second configuration, respectively. 
         FIG. 72  shows a perspective view of an electronic circuit system for controlling the drive assembly included in the instrument of  FIG. 51 . 
         FIG. 73  shows a perspective view of a manipulator assembly according to an embodiment included in the instrument of  FIG. 51 . 
         FIG. 74  shows an exploded view of the manipulator assembly of  FIG. 73 . 
         FIG. 75  shows a side view of the manipulator assembly of  FIG. 73  in a first (or “open grip”) configuration. 
         FIG. 76  shows a side view of the manipulator assembly of  FIG. 73  in a second (or “closed grip”) configuration. 
         FIG. 77  shows a perspective view of the manipulator assembly of  FIG. 73  in second (“closed grip”) configuration and transporting a container. 
         FIGS. 78 and 79  show side views of the manipulator assembly of  FIG. 73  in the first (“open grip”) configuration and engaging a container. 
         FIG. 80  shows a side cross-section of the manipulator assembly of  FIG. 78  in the open configuration and engaging the container in a “first plunge” operation. 
         FIG. 81  shows a side cross-section of the manipulator assembly of  FIG. 73  in the second (“closed grip”) configuration. 
         FIGS. 82 and 83  are a side view and a perspective view, respectively, of the manipulator assembly of  FIG. 73  in a third configuration (“closed grip”) configuration engaging the container in a “second plunge” operation. 
         FIG. 84  shows a side cross section of the manipulator assembly of  FIG. 82 . 
         FIG. 85  shows a perspective view of a detector assembly, according to an embodiment, included in the instrument of  FIG. 51 . 
         FIG. 86  shows a top view of a portion of the detector assembly of  FIG. 85 . 
         FIG. 87  shows a perspective view of the detector assembly of  FIG. 85  with a housing removed. 
         FIG. 88  shows an exploded view of the detector assembly of  FIG. 85  with the housing removed. 
         FIG. 89  shows a perspective view of a shutter included in the detector assembly of  FIG. 85 , according to an embodiment. 
         FIG. 90  shows a side cross-section of the shutter of  FIG. 89 . 
         FIGS. 91-94  are side cross-sectional views of the detector assembly of  FIG. 85  in a first configuration, a second configuration, a third configuration and a fourth configuration, respectively. 
         FIG. 95  shows a perspective view of a circuitry included in the instrument of  FIG. 51  for controlling the detector assembly of  FIG. 85 , according to an embodiment. 
         FIG. 96  illustrates a flow diagram of a method for receiving a signal, according to an embodiment. 
         FIG. 97  illustrates a flow diagram of a method for manipulating a container, according to an embodiment. 
     
    
    
     DETAILED DESCRIPTION 
     Systems and methods for detecting and/or identifying target cells (e.g., bacteria) using engineered viral vectors and/or 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. Similarly stated, the transduction particles are formulated to bind to and deliver a nucleic acid molecule into the 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. 
     In some embodiments, a method for detecting a target cell includes mixing with a sample a series of transduction particles associated with the target cell. The transduction particles are engineered to include a nucleic acid molecule formulated to cause the target cell to produce a series of reporter molecules. The transduction particles are devoid of a wild-type DNA that is capable of exhibiting wild-type viral functions associated with a virus from which the series of transduction particles are derived. The sample and the series of transduction particles are maintained such that the series of reporter molecules is only expressed when the target cell is present in the sample. A signal associated with the quantity of reporter molecules is then received. In some embodiments, the magnitude of the signal is independent from the quantity of the series of transduction particles above a predetermined quantity. Similarly stated, in some embodiments, the strength of the signal is substantially independent from the quantity of the series of transduction particles. 
     In some embodiments, a method for detecting a target cell includes mixing within a sample a series of transduction particles associated with the target cell. The series of transduction particles are engineered to be incapable of lysogenic replication and to include a nucleic acid molecule formulated to cause the target cell to produce a series of reporter molecules. The sample and the series of transduction particles are maintained to express the series of reporter molecules when the sample includes the target cell. The method also includes receiving a signal associated with a quantity of the series of the reporter molecules. 
     In some embodiments, a container includes a housing, a first actuator and a second actuator. The housing is configured to be removably coupled to a reaction chamber (e.g., which can contain a sample including a target cell). The housing defines a first reagent volume and a second reagent volume, and includes a delivery portion that defines a first pathway between the first reagent volume and the reaction chamber and a second pathway between the second reagent volume and the reaction chamber. The first actuator has a plunger portion disposed within the first reagent volume, and an engagement portion configured to be manipulated to move the plunger portion within the first reagent volume. The second actuator has a plunger portion disposed within the second reagent volume, and an engagement portion of the second actuator is configured to be manipulated to move the plunger portion within the second reagent volume. The engagement portion of the second actuator at least partially surrounds the engagement portion of the first actuator. 
     In some embodiments, a container includes a housing, a delivery member, and an actuator. The housing, which can be removably coupled to a reaction chamber (e.g., that contains a target cell), defines a reagent volume. The delivery member is coupled to the housing and defines a pathway between the reagent volume and the reaction chamber when the housing is coupled to the reaction chamber. A first end portion of the delivery member is disposed within the reagent volume and a second end portion of the delivery member is disposed outside of the reagent volume. The actuator has a plunger portion disposed within the reagent volume that can be moved within the reagent volume along a longitudinal axis of the housing to produce a flow or reagent from the reagent volume via the pathway. The delivery member is configured to direct the flow of the reagent exiting the second end portion of the delivery member in an exit direction non-parallel to the longitudinal axis of the housing. 
     In some embodiments, a container includes a housing, a delivery member, and an actuator. The housing defines a reagent volume and is removably coupleable to a reaction chamber. The delivery member is coupled to the housing and defines a pathway between the reagent volume and the reaction chamber when the housing is coupled to the reaction chamber. A first end portion of the delivery member is disposed within the reagent volume and defines a first portion of the pathway. A second end portion of the delivery member is disposed outside the housing and defines a second portion of the pathway. A center line of the second portion of the pathway is angularly offset from a center line of the first portion of the pathway. The actuator has a plunger portion disposed within the reagent volume and is configured to be moved within the reagent chamber along a longitudinal axis of the housing to produce a flow of a reagent from the reagent volume via the pathway. 
     In some embodiments, a method for detecting a target cell includes placing a reaction chamber containing a sample and a series of reporter molecules in operable communication with a detector. A reagent is conveyed into the reaction chamber via a delivery member such that the reagent flows along a surface of the reaction chamber and into the sample. In this manner, aeration of the sample and the reagent and/or the production of bubbles within the sample is minimized The reagent is formulated to react with the series of reporter molecules to enable and/or enhance the production of a signal associated with a quantity of the series of reporter molecules. The signal is received by a detector. 
     In some embodiments, an instrument includes a retention member, an activation member and an actuator. The retention member is configured to contact a first portion of a sample container, which defines a reaction volume and a reagent volume, to limit movement of the sample container. The activation member is coupled to the retention member, and is configured to engage a second portion of the sample container to convey a reagent from the reagent volume into the reaction volume. The actuator is configured to move the activation member relative to the retention member between a first position, a second position and a third position. In the first position, the retention member is configured to be spaced apart from the first portion of the sample container. In the second position, the activation member is configured to be spaced apart from the second portion of the sample container and the retention member is configured to contact the first portion of the sample container. In the third position, the activation member is configured to be engaged with the second portion of the sample container to convey the reagent such that the retention member is in contact with the first portion of the sample container. 
     In some embodiments, an instrument includes a retention assembly, an activation assembly and an actuator. The retention assembly includes a first gripper, a second gripper and a biasing member. The first gripper and the second gripper are configured to contact a first portion of a sample container to limit movement of the sample container. The sample container defines a reaction volume and a reagent volume. The activation member is movably coupled to the retention assembly, and is configured to engage a second portion of the sample container to convey a reagent from the reagent volume into the reaction volume. The actuator is configured to move the activation member relative to the retention assembly between a first position and a second position. In the first position, a surface of the activation member is in contact with a surface of the retention assembly to maintain the first gripper and the second gripper in an opened configuration. In the second position, the surface of the activation member is spaced apart from the surface of the retention assembly such that the biasing member urges the first gripper and the second gripper into a closed configuration. A plunger portion of the activation member is configured to move within the reagent volume when the activation member moves toward the second position. 
     In some embodiments, an instrument includes a housing and a shutter having a portion movably disposed within the housing between a first shutter position and a second shutter position. The housing defines a channel configured to receive a sample container, and further defines a detection volume configured to place the channel in communication with a detector. The housing including a first seal surface and a second seal surface. A first portion of the sample container and the first seal surface are configured to isolate the detection volume from a volume outside of the housing when a second portion (e.g., a distal end portion) of the sample container is disposed within the detection volume. A seal surface of the shutter and the second seal surface of the housing are configured to isolate the detection volume from the channel of the housing when shutter is in the first shutter position. The channel of the housing is in communication with the detection volume when the shutter is in the second shutter position. 
     In some embodiments, an instrument includes a housing and a shutter having a portion movably disposed within the housing between a first shutter position and a second shutter position. The housing defines a channel configured to receive a sample container, and also defines a detection volume configured to place the channel in communication with a detector. An actuation portion of the shutter is configured to engage a distal end portion of the sample container to move the shutter from the first shutter position to the second shutter position when the distal end portion of the container is moved towards the detection volume. A seal surface of the shutter and a seal surface of the housing are configured to isolate the detection volume from the channel of the housing when shutter is in the first shutter position. The channel of the housing is in communication with the detection volume when the shutter is in the second shutter position. 
     In some embodiments, an instrument includes a housing and a shutter disposed within the housing between a first shutter position and a second shutter position. The housing defines a channel configured to receive a sample container, and also defines a detection volume configured to place the channel in communication with a detector. The shutter defines a calibration port configured to receive a calibration light source, such as, for example, an LED. A seal surface of the shutter and a corresponding seal surface of the housing are configured to isolate the detection volume from the channel of the housing when shutter is in the first shutter position. The calibration port is in communication with the detection volume when shutter is in the first shutter position. The channel of the housing is in communication with the detection volume and the calibration port is isolated from the detection volume when the shutter is in the second shutter position. 
     In some embodiments, a method for receiving a signal includes receiving a first signal associated with a magnitude of light emission in a detection volume, at a first time. The detection volume is optically isolated from a channel by a movable shutter, which is in a first position. The method also includes applying a force to a sample container at least partially disposed within a channel such that a distal end portion of the sample container moves the shutter from the first position to a second position, and such that the distal end portion of the sample container is disposed within the detection volume. In this configuration, the channel is in optical communication with the detection volume. The method further includes receiving, a second signal associated with a magnitude of light emission in the detection volume at a second time, when the distal end portion of the sample container is in the detection volume. 
     As described herein, the terms “gene,” “DNA” and “nucleotide” mean the whole or a portion of the genetic sequence of the target bacteria or the vector. 
     As described herein, the term “plasmid” means the engineered gene, sequence and/or molecule contained within the vector that includes regulatory elements, nucleic acid sequences homologous to target genes, and various reporter constructs for causing the expression of reporter molecules within a viable cell and/or when an intracellular molecule is present within a target cell. 
     Systems, devices and methods for detecting and identifying target cells (e.g., bacteria) can include a transduction particle that can identify and bind to the target cell and deliver into the target cell an engineered nucleotide. As shown in the block diagram of  FIG. 1 , in some embodiments, a system  100  includes a genetically engineered transduction particle  110 , a container  120 , a reporter  130 , and a detection instrument  140 . As described in detail herein, the system  100  is configured to manipulate, handle and/or actuate the container  120  and/or the detection instrument  140  such that the transduction particle  110  can, when mixed with a sample S that contains a particular target, produce the reporter  130 . In this manner, the system  100  and methods associated therewith can be thought of as a “switchable” assay, meaning that no amount of the reporter  130  is present in the sample until the conditions (e.g., the presence of the target cell) are such that the reporter  130  is produced. 
     The transduction particle  110  can be any suitable particle capable of delivering via transduction non-viral DNA and/or RNA into a target cell. For example, in some embodiments, the transduction particle can be derived from a bacteriophage, or can be a non-biologically derived vector that is capable of introducing nucleic acid molecules into the target bacteria in the sample S. The transduction particle  110  is further engineered and/or configured to carry an engineered molecule, for example, recombinant DNA, RNA, nucleotide, plasmid, ribozyme, aptamer, and/or protein. In some embodiments, the transduction particle  110  does not contain any DNA from the viral vector (e.g., bacteriophage) from which it was derived. Similarly stated, in some embodiments, the transduction particle is a viral vector devoid of a wild-type DNA capable of exhibiting wild-type viral functions associated with the virus from which the viral vector is derived. In some embodiments, a transduction particle includes any of the transduction particles described herein. 
     In some embodiments, the transduction particle  110  is incapable of replicating via either the lytic or lysogenic cycle. By eliminating all forms of replication from the transduction particle, the target cells will be maintained (i.e., not destroyed, killed or lysed) during the production of the reporter molecules, thereby improving the accuracy and reliability of the methods used therewith. In this manner, the assays described herein reduce and/or eliminate the likelihood of a false negative, making the methods applicable in a clinical setting. In particular, because wild-type viral functions of viral particles can exhibit lysogenic replication and require the capability for lytic replication, attempts to suppress the replicative functions (e.g., the lytic cycle) may not provide sufficient certainty that the lytic cycle will not result in some population of assays. To demonstrate the advantages of the use a transduction particle in which the replication capability is eliminated, the lytic activity of two temperate  S. aureus  phages on ten MRSA clinical isolates was examined via plaque assay. As shown in Table 1, the phage phi11 exhibited lytic activity on each of the ten clinical MRSA isolates, and the phage phi80alpha exhibited lytic activity on six of the ten clinical MRSA isolates. As shown, assays relying on the natural lysogenic cycle of phages (e.g., the temperate phages as tested) can be expected to exhibit lytic activity sporadically. Accordingly, in some embodiments, the transduction particle  110 , and other transduction particles described herein, is engineered to be non-replicative or replication deficient (i.e., incapable of replication). 
     
       
         
           
               
               
               
               
             
               
                 TABLE 1 
               
               
                   
               
               
                   
                 PFFGE 
                   
                   
               
               
                 MRSA Isolate 
                 Type 
                 phi11 
                 phi80alpha 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
            
               
                 1. 
                 USA200 
                 x 
                   
               
               
                 2. 
                 USA1000 
                 x 
               
               
                 3. 
                 USA800 
                 x 
                 x 
               
               
                 4. 
                 USA300 
                 x 
                 x 
               
               
                 5. 
                 USA300 
                 x 
                 x 
               
               
                 6. 
                 USA100 
                 x 
               
               
                 7. 
                 USA300 
                 x 
                 x 
               
               
                 8. 
                 USA100 
                 x 
               
               
                 9. 
                 USA300 
                 x 
                 x 
               
               
                 10. 
                 USA100 
                 x 
                 x 
               
               
                   
               
            
           
         
       
     
     The transduction particle  110  is characterized by being associated with and/or specific to one or more target cells. Similarly stated, the transduction particle  110  is formulated to bind to and deliver a nucleic acid molecule into the target cell. For example, the transduction particle can be selected, engineered and/or produced to bind to any bacteria, e.g.,  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.    
     In some embodiments, the non-replicative transduction particle  110 , as well as any of the non-replicative transduction particles described herein, can be developed by packaging nucleic acid into the structural components of a virus and/or bacteriophage where the packaged nucleic acid is devoid from exhibiting native viral and/or bacteriophage functions that allow for the virus and/or bacteriophage to replicate whether the replication is via a lytic or lysogenic pathway. 
     In one embodiment, a plasmid packaging system can be developed in which the small terminase gene containing the pac-site of a pac-type prophage is deleted and then complemented via a plasmid. When the lytic cycle of the lysogenized prophage is induced, the bacteriophage packaging system packages plasmid DNA into progeny bacteriophage structural components rather than packaging native bacteriophage DNA. The packaging system thus produces non-replicative transduction particles carrying plasmid DNA. 
     In another embodiment, genomic island (GI)-packaging systems can be exploited such that exogenous nucleic acid sequences are packaged by the bacteriophage. This can be accomplished by incorporating such exogenous nucleic acids sequences into the GI. Natural GI-packaging systems result in both non-replicative GI-containing transduction particles as well as native replicative phage, thus in order to eliminate the native phage from this process, the small terminase gene of the prophage is deleted. The small terminase gene sequence contains the pac-site sequence of the native phage and thus this deletion has the effect of preventing the packaging of native phage DNA. If at the same time a GI to be packaged includes its own pac-site and a small terminase gene that expresses a suitable small terminase protein, then only GI DNA will be amenable for packaging in this system. By incorporating exogenous DNA into this system, non-replicative transduction particles that incorporate GI DNA and exogenous DNA can be produced. 
     The transduction particle  110  can be further produced and/or engineered to contain genes and/or a nucleic acid molecule for expressing a reporter  130  that can be detected (e.g., via the instrument  140 ). The reporter  130  can be any one of a bacterial luciferase, a eukaryotic luciferase, a fluorescent protein (e.g., GFP, etc.), an enzyme suitable for colorimetric detection (e.g., horseradish peroxidase) a protein suitable for immunodetection (e.g., protein A, etc.), a peptide or peptide tag suitable for immunodetection (e.g., 3X FLAG, etc.) and/or a nucleic acid that functions as an aptamer or that exhibits enzymatic activity. More particularly, the transduction particle  110  does not produce the reporter  130  autonomously and/or does not include the reporter  130 . Instead, transduction particle  110  is configured to communicate an engineered nucleic acid molecule contained therein into the target cell, e.g., bacteria, such that the engineered nucleic acid molecule uses the natural transcription and translation functions of the bacteria DNA to produce the reporter  130 . Thus, the reporter  130  can be thought of as a “switchable” reporter, meaning that no amount of the reporter  130  is present in the sample until the conditions (e.g., the presence of the target cell) are such that the reporter  130  is produced. In this manner, the methods described herein include no washing of non-bound reporter  130 , no signal subtraction to account for initial quantities of reporter or the like. Thus, the system  100  and the methods associated therewith allows for the development of a homogeneous assay. Further, no temperature cycling is required, and heating at a low temperature, for example 37 degrees Celsius, for a short time can be sufficient. 
     The reporter system formulated to cause the expression of the reporter  130  and any of the reporter systems disclosed herein can be developed for reporting on the presence of viable bacteria and/or target cells by incorporating into the non-replicative transduction particle  110  (or any of the other transduction particles disclosed herein) a reporter molecule under the control of a promoter. When this transduction particle  110  introduces the reporter system into a cell within the host range of the transduction particle  110 , the promoter is able to drive the expression of the reporter molecule. 
     In one embodiment, a MSSA/MRSA reporter assay can be developed and/or performed using any suitable system and method as described herein (such as, for example the system  1000 ). In such embodiments, a non-replicative transduction particle (e.g., the transduction particle  110 , the transduction particle  160  or the like) is developed from a  S. aureus -specific bacteriophage and the bacterial luciferase genes luxAB under the control of a constitutive promoter are incorporated. When this transduction particle introduces the reporter system into  S. aureus , the constitutive promoter can express luxAB suitable for reporting on the presence of a viable  S. aureus . If in addition, the antibiotic cefoxitin, or a similar anti-biotic, is also added prior to or simultaneously with mixing the transduction particles with  S. aureus  cells, if the cells do not contain and express the mecA gene, no luxAB will be expressed in the assay, thus indicating that the cells are MSSA (i.e., sensitive to inhibition by cefoxitin). If, however, the cells do contain and express the mecA gene, luxAB will be expressed in the assay, thus indicating that the cells are MRSA (i.e., resistant to inhibition by cefoxitin). 
     Although described as being developed for reporting on the presence of viable bacteria, in other embodiments the reporter  130  and any of the applicable reporter systems (e.g., the reporter  630 ) can be developed for reporting on the presence of target genes within target bacteria. In this system a promoter-less reporter gene is placed downstream of a nucleic acid sequence that is homologous to a target gene sequence and this reporter construct is incorporated into a non-replicative transduction particle. When the transduction particle introduces the reporter construct into a target cell, the reporter gene will not be expressed unless the target cell contains the target gene and a homologous recombination event integrates the reporter gene within the target gene loci in the target cell such that the reporter gene becomes operatively linked to the target gene promoter within target cell. 
     In one such embodiment, a MRSA reporter system can be developed by incorporating into a  S. aureus -specific non-replicative transduction particle (e.g., the transduction particle  110 , the transduction particle  160  or the like) a reporter construct consisting of a nucleic acid sequence that is homologous to the mecA gene upstream of promoter-less bacterial luciferase genes, luxAB. When the transduction particle introduces the reporter construct into a target  S. aureus  cell, the reporter gene will not be expressed unless the target cell contains the target mecA gene and a homologous recombination event integrates the luxAB genes within the mecA gene loci in the target cell such that the reporter gene becomes operatively linked to the mecA gene promoter within target cell. 
     In some embodiments, transduction particle  110 , the nucleic acid molecule contained within the transduction particle  110  and/or the reporter systems associated therewith can include any of the portions of the recombinant bacteriophages shown and described in U.S. Patent Publication No. 2010/0112549, entitled “Microorganism Detection Method and Apparatus,” filed as an International Patent Application on Apr. 18, 2008, which is incorporated herein by reference in its entirety. 
     The sample S can be any sample that possibly contains the target bacteria, for example, human nasal swab, blood, urine, veterinary samples, food samples, and/or environmental samples. In some embodiments, the sample S can be a raw sample as obtained from the source that does not need any preparation, e.g., any separation or washing steps are not needed. Thus, the system  100  and the methods associated therewith are homogeneous. In some embodiments, the sample S can include a low load of target cell (e.g., nasal swab for MRSA detection). When used with such samples, the system  100  and the methods associated therewith can include a heating and/or incubation period to promote cell replication, which results in higher production of the reporter molecules  130 , for example, to generate a signal that is greater than a minimum signal threshold. 
     In other embodiments, the sample S can have a higher load of target cell (e.g., positive bacterial blood culture). In such cases, cell replication is not needed to produce a positive signal sufficient to identify the target cell. In some such embodiments, the sample can be maintained at a specific condition e.g., maintained at a temperature of greater than or equal to approximately room temperature, 25 degrees Celsius, or 37 degrees Celsius for a predefined time period e.g., less than approximately 4 hours. In such embodiments, the temperature and time period at which the sample S is maintained are such that the quantity of reporter molecules  130  produced is sufficient to generate a measurable signal, independent of cell replication. In such embodiments, the sample can be maintained at the predefined temperature for a longer time period, e.g., 6 hours, 8 hours, up to 18 hours, or even longer. 
     In some embodiments, the container  120  that can contain a first reagent, for example, a bacterial nutrient or growth media (e.g., minimal essential media) and/or suitable buffer (e.g. Amies, PBS, TRIS, HEPES, etc) for maintaining the target cell in a viable state, promoting bacterial cell growth or the like. In some embodiments, an antibiotic, for example, cefoxitin can also be included in the first reagent, for example, when a viable cell assay is intended. A sample S containing the target cell can be added to the sample container  120  followed by addition of the transduction particle  110  to the sample container  120  according to any of the methods and using any of the instruments described herein. If the target cells are present, the transduction particle  110  transfers the nucleic acid sequence contained therein into the target cell such that the nucleotide contained in the transduction particle  110  is integrated with the genes of the target cell, e.g., host bacteria. In some embodiments, the container  120  is configured to fluidically isolate the sample S from a region outside the container  120 . In such embodiments, the transduction particle  110  is maintained in fluidic isolation from the sample S before the transduction particle  110  is mixed therein. In some embodiments, the maintaining can include maintaining the sample S for a time period such that the quantity of the plurality of the reporter molecules  130  sufficient to produce the signal is produced independent from target cell replication. As described herein, mixing includes disposing the transduction particle  110  into the sample S while maintaining isolation between the region and the container  120 . 
     In some embodiments, the container  120  can be configured to include any additional reagent that is formulated to react with the reporter molecules  130  to produce, catalyze and/or enhance the production of the signal. For example, the reporter molecule  130  can be luciferase and the container  120  can be configured to contain an aldehyde reagent formulated to trigger, initiate and/or catalyze a luminescence reaction that can be detected by the production of the signal. In some embodiments, the reagent can include a 6-carbon aldehyde (hexanal), a 13-carbon aldehyde (tridecanal) and/or a 14-carbon aldehyde (tetradecanal), inclusive of all the varying carbon chain length aldehydes therebetween. In some embodiments, the container  120  can be configured to maintain the additional reagent in fluidic isolation from sample S before being disposed into the sample S. In this manner the timing of the delivery of the additional reagent into the sample S can be controlled. In some embodiments, the system  100  can include a mechanism for adding the additional reagent at any suitable time and/or in any suitable manner to induce the detectable signal. For example, as described in more detail herein, in some embodiments, the system  100  and/or the container  120  can include a mechanism for conveying an additional reagent into the sample S at a predetermined velocity (or flow rate) to promote the desired level of mixing. 
     The instrument  140  can be any appropriate instrument to detect the reporter molecule  130  and/or a reaction catalyzed by the reporter molecule  130 . For example, the instrument  140  can include optical (e.g. photomultiplier tubes, fluorometers, spectrometers, colorimetric detection on a lateral flow assay, imaging based detection, CCDs, luminescence detectors for detecting bioluminescence, colorimetric or fluorometric microarrays) and/or electrical detection means (e.g. electrochemical amperometric, potentiometric, conductometric, impedrometric, and/or any other electrochemical sensors). 
     In some embodiments, the system  100  and/or the methods associated therewith can be configured to be a rapid test that does not require any amplification of the target cells. Using the system  100  and the methods described herein, a relatively small time, for example, 1 hour, 2 hour, 3 hour or 4 hour, up to 18 hours can be needed for the target cell containing the nucleic acid sequence from the transduction particle  110  to produce a sufficient quantity of reporter molecules  130  that can be detected. In some embodiments, the system  100  can be configured to be a closed system after collection of sample S and/or addition of transduction particle  110 . Said another way, in some embodiments, the container is maintained in fluidic isolation from the external environment after the addition of the sample S. This can, for example, reduce chances of contamination. As described above, because the system  100  can accommodate raw sample, the system  100  and the methods associated therewith do not require any washing or fluid transfer steps away from the sample S. The system  100  can therefore be easy to operate, be rapid, inexpensive, and be easily automated. In some embodiments, the system  100  can be a platform system that can be configured to operate in various regimes, for example, viable cell reporting, gene reporting, measuring bacterial resistance and/or susceptibility to antibiotics, and/or bacterial toxin detection, etc. Additional examples of components and methods associated with and/or complementary to the system  100  are described further. 
       FIGS. 2 and 3  are schematic illustrations of a system  1000  according to an embodiment. The system  1000  is configured to be communicatively coupled to any suitable laboratory information system (LIS)  1900 , and includes an instrument  1100  that is configured to manipulate and/or receive a container  1700 . The system  1000  can be used to identify target cells in a clinical environment according to any suitable method, such as any of the methods described herein. 
     The container  1700  can be any suitable container that can be manipulated and/or actuated by the instrument  1100  or any other instruments described herein. The container  1700  defines an internal volume within which a sample S can be disposed as shown by arrow AA. In some embodiments, the container  1700  can include a solution  1702  disposed in the internal volume of the container  1700  for interacting with the sample S. The solution  1702  can be predisposed in the internal volume defined by the container  1700  or added after the sample S is conveyed into the container  1700 . The solution  1702  can include, for example, a bacterial nutrient and/or growth media (e.g., undefined medium, defined medium, differential medium, minimal media, selective media, etc.) to enable bacteria to grow and multiply, a buffer to maintain pH (e.g., Amies, PBS, HEPES, TRIS, TAPSO, Bicine, MES, MOPS, Tricine, PIPES, SSC, succinic acid, etc.) and/or a surfactant (e.g., Tween 20, Tween 80, TritonX, X-114, CHAPS, DOC, NP-40 CTAB, SDS, etc.). In some embodiments, the solution  1702  can also include antibiotics (e.g. cefoxitin, oxacillin, cefotetan, amoxycillin, penicillin, erythromycin, azythromycin, cephalosporins, carbapenems, aminoglycosides, sulfonamides, quinolones, oxazolidinones, etc.). The inclusion of antibiotics can kill or otherwise prevent the expression and/or generation of a signal from reporter molecule from all drug-susceptible bacteria, e.g., in a bacteria cell viability and/or susceptibility assay of the types shown and described herein. 
     In some embodiments, the solution  1702  can be tailored to enhance growth, shorten lag phase, sustain, and/or attack a particular target cell, e.g., bacterium. In some embodiments, specific versions of the solution  1702  can be employed for specific target cells and/or samples. For example, a first preparation of the solution  1702  can be tailored for nasal swab samples containing MRSA, a second preparation of the solution  1702  can be tailored for urine samples containing  E. coli , a third preparation of the solution  1702  can be tailored for stool samples containing  C. difficile , and the like 
     The container  1700  can be configured to receive a first reagent  1710  containing a transduction particle and/or an engineered viral vector as shown by the arrow BB ( FIG. 2 ). In some embodiments, the container  1700  can further receive any other reagents in connection with the implementation of any of the methods described herein. In some embodiments, the transduction particle  1710 , and/or any other reagents can be predisposed in the container  1700 , such that, for the example the vector  1710  or any other reagents do not need to be separately added to the container  1700  after the sample S is placed therein. For example, in some embodiments, the transduction particle  1710  can be disposed in a cap or separate portion (not shown) of the container  1700  such that the respective solutions (e.g., the solution  1702 , the sample S and the transduction particle  1710 ) can remain isolated from each other during shipping, initial handling or the like. The container  1700  can be further configured to convey the respective solutions into the interior volume of the container  1700  at a suitable time. For example, in some embodiments, the cap can have frangible portions that can be broken by the instrument  1100  and/or the user at a desired time. For example, the frangible portions can be broken using plungers, crushing manually, or any other suitable mechanism. In some embodiments, the container  1700  can be multi-portion container such that, for example, the container  1700  can have frangible portions, each portion containing a separated fluid. The container  1700  can be configured such that while fluids can be predisposed in the container  1700  and urged to mix at specific times, the container  1700  does not contain any fluid transfer paths, fluid transfer mechanisms (e.g., electrophoretic transfer, electrokinetic transfer, pumps, etc.), valves and/or any complex fluid transport schemes. 
     The container  1700  can be any suitable container for containing the sample S in a manner that permits the monitoring, identification and/or detection of a target cell, e.g., bacteria, within the sample S. In some embodiments, at least a portion of the container  1700  can be substantially transparent, for example, to allow viewing, and/or optical monitoring of the contents contained therein. The container  1700  can be any suitable size or shape, for example, cylindrical square, rectangular, elliptical, conical, etc. The container  1700  can be constructed from any suitable material, for example, glass, plastic, acrylic, etc. In some embodiments, the container  1700  can be a commercially available container, for example a centrifuge tube, an eppendorf® tube, a glass vial, flat bottomed vial/tube, round bottomed vial/tube or any other suitable container. In some embodiments, the container  1700  can also include additional components, for example, swabs for collecting patients&#39; samples, cap to protect container  1700  from atmosphere and/or containing assay reagents, labels for identification, bar codes, RFID tags, etc. 
     Sample S and any other samples described herein can be any suitable sample S that can potentially contain the target cell, e.g., bacteria. For example, the sample S can be a human sample (e.g., a nasal swab, mucosal swab, saliva sample, blood sample, urine sample, fecal sample, tissue biopsy, bone marrow and/or cerebrospinal fluid), veterinary sample, food sample, plant sample, and/or environmental sample. In some embodiments, the sample S can be a raw and substantially unprocessed sample. In such embodiments, the system  1000  (including the container  1700  and/or the instrument  1100 ) is configured such that no modifications to the sample are required to run the methods associated described in connection with the system  1000 . In other embodiments, however, the sample S can undergo minor processing, for example, filtration, sedimentation or any other process required to produce a suitable sample. Such processing can be performed by any suitable mechanism of the instrument  1100 . 
     The transduction particle and/or engineered viral vector  1710  and any of the transduction particles and/or vectors disclosed herein, can be any suitable transduction particle that can specifically identify and bind to a target cell, and perform the functions described herein. In some embodiments, the transduction particle  1710  can be derived from a bacteriophage. Examples of suitable transduction particles  1710  can include vectors biologically derived from, for example, T2, T4, T7, T12, R17, M13, MS2, G4, p1, enterobacteria phage P4, Phi X 174, N4, pseudomonas phage, lambda phage, and/or any other vector. In some embodiments, the transduction particle  1710  includes modified DNA from the phage from which the vector  1710  is derived. In some embodiments, the biologically derived transduction particle  1710  does not include any DNA associated with the phage from which it was derived. Said another way, the transduction particle  1710 , e.g., a vector, is devoid of a wild-type DNA capable of exhibiting wild-type viral functions associated with a virus from which the transduction particle  1710  is derived. In some embodiments, the lack of any phage DNA removes the capability of the transduction particle  1710  to reproduce, replicate or propagate. Said another away, after infecting the bacteria, neither the lytic cycle nor the lysogenic cycle of the transduction particle  1710  and/or the target bacteria can cause the transduction particle  1710  to multiply or amplify. Similarly stated, in some embodiments, the transduction particle and/or engineered viral vector  1710  is non-replicative, i.e., cannot undergo lytic or lysogenic replication. 
     In some embodiments, the transduction particle and/or engineered viral vector  1710  can be formulated, selected and/or engineered to include and/or carry an engineered molecule, for example, recombinant DNA, RNA, nucleic acid sequence, nucleotide, plasmid, ribozyme, aptamer and/or protein. In some embodiments, the transduction particle  1710  can be configured to specifically identify and detect the presence of a viable target bacteria e.g.,  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 . In some embodiments, the transduction particle  1710  can be configured to specifically identify a bacteria genotype including specific gene targets and other molecular targets indicative of the genotype and/or phenotype of the bacteria, e.g., methicillin resistant  Staphylococcus aureus  (MRSA),  E. coli, Salmonella, C. difficile , vancomycin-resistant Enterococci (VRE), or any other bacteria. In one such embodiment, the plasmid can include a nucleic acid molecule that is homologous for a specific gene sequence associated with the DNA of the target bacteria. For example, the transduction particle  1710  can be engineered and/or configured to include a plasmid that incorporates nucleic acid sequences homologous to the mecA gene found in MRSA, e.g., in an assay for the detection of MRSA (as described above). 
     The transduction particle  1710  can be further configured to contain genes and/or a nucleic acid molecule for expressing a detectable reporter molecule  1730 . The reporter molecule  1730  can be any one of a bacterial luciferase, eukaryotic luciferase, fluorescent protein, enzyme suitable for colorimetric detection, protein suitable for immunodetection, peptide suitable for immunodetection or a nucleic acid that functions as an aptamer or that exhibits enzymatic activity. In some embodiments, a reagent (or substrate, not shown in  FIGS. 2 and 3 ) can be added to the solution  1702  to urge the reporter molecule  1730  to produce a detectable signal. For example, in some embodiments, tridecanal can be added to allow the luciferase to catalyze a luminescence reaction that can be detected. In some embodiments, two or more transduction particles  1710  specific towards two separate target cells can be used together in the same reagent, for example, to detect multiple bacteria simultaneously. 
     The instrument  1100  includes the detector  1200 , and is configured to receive, manipulate and/or handle the container  1700  to convey, mix and/or add the sample S, the solution  1702  and/or the transduction particles  1710 , and detect and/or identify a constituent within the sample S. In particular, the instrument  1100  can include any suitable systems/mechanisms (not shown in  FIGS. 2 and 3 ) for handling/manipulating the container  1700 . For example, the instrument  1100  can include receptacles, racks, vices, jaws, grippers or any other suitable mechanism for removably receiving the container  1700 . In some embodiments, the instrument  1100  can include mechanisms for manipulating and/or changing the configuration of the container  1700 . For example, the instrument  1100  can include plungers, conveyor belts, stepper motors (e.g. to move and position the container  1700  in X/Y/Z plane), rollers, shakers, clamps, X/Y movable tables, encoders, any other instrumentation for positioning or manipulating the container  1700  or a combination thereof. For example, the container  1700  can be disposed in a receptacle included in the instrument  1100  that can transport the container  1700  via a conveyor belt to a location in the instrument  1100  (see e.g.,  FIG. 3 ) where the detector  1200  can interface with the container  1700  and detect the signal produced by the reporter molecule  1730  that indicates the presence of target cell (e.g., bacteria). In some embodiments, the instrument  1100  can include a gripper and an actuator mechanism, configured such that the gripper prevents and/or limits movement of the container  1700  when signal is being detected by the detector  1200 . In this manner, the instrument  1100  can minimize signal noise by holding and maintaining the container  1700  at a predetermined distance from the detector  1200 . Moreover, such a mechanism can ensure that the position of the container  1700  is maintained when the actuator actuates the container  1700 , for example, to convey fluid from one portion of the container  1700  to another. 
     In some embodiments, the container  1700  and/or the instrument  1100  can also include light seal mechanisms, for example, shutters, to light seal the container  1700 . In this manner, the instrument can limit and/or prevent ambient light from interfering with the signal produced by the reporter  1730 . Such systems can also limit and/or prevent any undesired motion of the container  1700  during signal detection. In some embodiments, the container  1700  and instrument  1100  are configured such that the entire process including loading of the container  1700 , handling/manipulation of the container  1700  by the instrument  1100 , and signal detection by the detector  1200  occurs in a closed process. Said another way, detection of bacteria in the container  1700  by the instrument  1100  can be performed without opening the container  1700 , does not require fluid handlers or any reagents in the instrument, and does not require any sample manipulation. 
     Although only one container  1700  is shown in  FIG. 2  and  FIG. 3 , in other embodiments the instrument  1100  can be configured to receive a series of containers  1700 . For example, the instrument  1100  can include a container rack or magazine, within which a user can removably dispose multiple containers  1700  that can contain multiple samples S for analysis. In some embodiments, the containers  1700  can be loaded on the instrument  1100  in a batch process. In other embodiments, the containers  1700  can be delivered to the instrument  1100  in a “flow through” process. For example, the containers  1700  can be disposed on a conveyor belt that can deliver a plurality of containers  1700  sequentially to the reader of the instrument  1100 . In some embodiments, the instrument  1100  can be automated and be configured for “walk away” analysis. For example, the user can load a plurality of containers  1700  for analysis, on the instrument  1100  and walk away. The instrument  1100  can automatically perform container  1700  manipulation and detection on all the containers  1700 . 
     The detector  1200  can be any suitable detector than can detect the signal produced by the reporter molecule  1730 . For example, the detector  1200  can be an optical detector such as, for example, a fluorescence detector (e.g. to detect a fluorescent reporter molecule such as GFP, etc.), a luminescence detector (e.g. to detect bioluminescence produced by a reporter molecule such as luciferase), color detector (e.g. to detect a colored precipitant produced by a reporter enzyme such as HRP), a spectrometer, and/or an image capture device. In some embodiments, the detector  1200  can further include a light source associated with the mechanism for detection. Although described as being primarily based on optical detection, in some embodiments, the detector  1200  can be an electrochemical detector. For example, the detector  1200  can include an amperometric detector, potentiometric detector, conductometric, and/or impedometric detector, configured to detect a current, voltage, or conductance, resistance/impedance change produced by the reporter molecules  1730 . In some embodiments employing electrochemical detection, the detector  1200  can be configured to come in physical contact with the sample solution  1706  ( FIG. 3 ) that contains the sample S, solution  1702 , transduction particle  1710 , reporter molecule  1730 , and/or any other substrate that can be necessary for inducing a signal from the reporter molecule. 
     In some embodiments, the detector  1200  can use other detection methods, e.g., surface acoustic wave, surface plasmon resonance, Raman spectroscopy, magnetic sensors, and/or any other suitable detection method known in the art. In some embodiments, the detector  1200  can only provide a qualitative answer, for example, a YES/NO answer on the presence of target cell. In other embodiments, however, the detector  1200  can quantify the target cell, for example, determine the cfu/ml of target bacteria in the sample S according to any of the methods described herein. In some embodiments, the detector  1200  can include an end read system, .e.g., to allow flexible placement of a label on the container  1700 . In some embodiments, the end read system includes direct contact of a transparent end of the container  1700  with the detector, e.g., to minimize optical instruments and/or background signal interference. In some embodiments, the detector  1200  is devoid of an incident light source. Said another way, no external light is needed for signal detection from the reporter molecules  1730  produced by the target cell disposed in the container  1700 . 
     In some embodiments, the systems  100 , 1000 , or any other systems described herein can be used to identify and/or detect a target cell, such as a bacteria. In particular, in some embodiments, the system  1000  can be used in conjunction with a replication-deficient transduction particle to identify and/or detect a target cell. By employing a replication-deficient transduction particle, the likelihood of a false negative (e.g., caused by cell destruction from the lytic cycle) is minimized and/or eliminated, thereby producing a result that is suitable in a clinical setting. Such methods can be used, for example, as a screening tool in hospitals. In particular,  FIG. 4  is a flow chart of a method  150  according to an embodiment. 
     As shown in  FIG. 4 , the method  150  includes mixing with a sample a substance including transduction particles associated with a target cell,  152 . Similarly stated, the transduction particles are formulated to bind to and deliver a nucleic acid molecule into the target cell. The transduction particles are engineered to include a nucleic acid molecule formulated to cause the target cell to produce a series of reporter molecules. The series of transduction particles are non-replicative. Similarly stated, the transduction particles can be formulated and/or engineered to be incapable of lysogenic or lytic replication. In this manner, the target cells will be maintained (i.e., not destroyed, killed or lysed) during the production of the reporter molecules. Thus, the method  150  reduces and/or eliminates the likelihood of a false negative, which can result when the target cells are lysed thereby preventing and/or reducing the production of the reporter molecules. 
     The transduction particles can be any suitable transduction particles of the types shown and described herein. For example, in some embodiments, the transduction particles can be an engineered 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. In some embodiments, the transduction particles can be engineered to be derived from a bacteriophage. For example, in some embodiments, the transduction particles can be developed by packaging nucleic acid into the structural components of a virus and/or bacteriophage where the packaged nucleic acid is devoid from exhibiting native viral and/or bacteriophage functions that allow for the virus and/or bacteriophage to replicate whether the replication is via a lytic or lysogenic pathway. 
     In one embodiment, a plasmid packaging system can be developed in which the small terminase gene containing the pac-site of a pac-type prophage is deleted and then complemented via a plasmid. When the lytic cycle of the lysogenized prophage is induced, the bacteriophage packaging system packages plasmid DNA into progeny bacteriophage structural components rather than packaging native bacteriophage DNA. The packaging system thus produces non-replicative transduction particles carrying plasmid DNA. 
     In another embodiment, genomic island (GI)-packaging systems can be exploited such that exogenous nucleic acid sequences are packaged by the bacteriophage. This can be accomplished by incorporating such exogenous nucleic acids sequences into the GI. Natural GI-packaging systems result in both non-replicative GI-containing transduction particles as well as native replicative phage, thus in order to eliminate the native phage from this process, the small terminase gene of the prophage is deleted. The small terminase gene sequence contains the pac-site sequence of the native phage and thus this deletion has the effect of preventing the packaging of native phage DNA. If at the same time a GI to be packaged includes its own pac-site and a small terminase gene that expresses a suitable small terminase protein, then only GI DNA will be amenable for packaging in this system. By incorporating exogenous DNA into this system, non-replicative transduction particles that incorporate GI DNA and exogenous DNA can be produced. 
     In some embodiments, the transduction particles can be selected, engineered and/or formulated to specifically bind to, and transfer the nucleic acid molecule contained therein into the viable cells. For example, the transduction particles can be selected, engineered and/or produced to bind to and deliver a nucleic acid molecule into any bacteria, e.g.,  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.    
     The sample and the series of transduction particles are maintained such that the series of the reporter molecules is produced when the sample includes the target cell,  154 . Similarly stated, the sample and the series of transduction particles are maintained to express the plurality of reporter molecules when the target cell is present in the sample. In this manner, production of the reporter molecules, and the detection thereof, indicates that the target cell is present in the sample. More particularly, the transduction particles do not produce the reporter molecules autonomously and/or do not include the reporter molecule. Instead, transduction particles are engineered, configured and/or formulated to communicate the nucleic acid molecule contained therein (i.e., an engineered plasmid) into the target cell. Upon being delivered into the target cell, reporter molecules are produced using the natural transcription and translation functions of the target cell and via the expression of a reporter gene that is operatively linked to a promoter that is included in the nucleic acid molecule. Thus, the method  150  employs a “switchable” reporter, meaning that no amount of the reporter molecules is present in the sample until the conditions (e.g., the presence of the target cell) are such that the reporter molecules are produced. Notably, because the method  150  employs a “switchable” reporter molecule, no washing and/or removal of the transduction particles and/or other constituents within the sample is necessary. The reporter molecule can be any one of a bacterial luciferase, eukaryotic luciferase, fluorescent protein, enzyme suitable for colorimetric detection, protein suitable for immunodetection, peptide suitable for immunodetection or a nucleic acid that functions as an aptamer or that exhibits enzymatic activity. 
     In some embodiments, the method  150  can be used as a viable cell reporter assay. When the method  150  is used as a viable cell reporter assay, in some embodiments, antibiotics (e.g., cefoxitin) can be added to and/or mixed with the sample to kill and/or eliminate all drug-susceptible target cells (e.g., in a bacteria) thereby allowing the method  150  to be used to identify particular target cell drug resistant phenotype (e.g., methicillin resistant  Staphylococcus aureus  (MRSA), Salmonellavancomycin-resistant Enterococci (VRE)) within the sample. 
     For example, in some embodiments, a MSSA/MRSA reporter assay can be developed in accordance with the method  150 . In such embodiments, a non-replicative transduction particle (e.g., the transduction particle  110 , the transduction particle  160  or the like) is developed from a  S. aureus -specific bacteriophage and the bacterial luciferase genes luxAB under the control of a constitutive promoter are incorporated. When this transduction particle is mixed with the sample (operation  152 ) thus introducing the reporter system into  S. aureus , the constitutive promoter can express luxAB suitable for reporting on the presence of a viable  S. aureus , as discussed below with reference to operations  154  and  158 . If in addition, the antibiotic cefoxitin is also added prior to or simultaneously with mixing the transduction particles with  S. aureus  cells, if the cells do not contain and express the mecA gene, no luxAB will be expressed in the assay, thus indicating that the cells are MSSA. If, however, the cells do contain and express the mecA gene, luxAB will be expressed in the assay, thus indicating that the cells are MRSA. 
     In other embodiments, the nucleic acid molecule can be formulated to cause the target cell to produce the series of reporter molecules only when the target cell includes a particular target gene (e.g., a drug resistant gene, a drug-susceptibility gene, a toxin, or a species specific gene). For example, in some embodiments, the method  150  can be performed in conjunction with a transduction particle and/or reporter system in which a promoter-less reporter gene is placed downstream of a nucleic acid sequence that is homologous to a target gene sequence and this reporter construct is incorporated into a non-replicative transduction particle. When the transduction particle introduces the reporter construct into a target cell, the reporter gene will not be expressed unless the target cell contains the target gene and a homologous recombination event integrates the reporter gene within the target gene loci in the target cell such that the reporter gene becomes operatively linked to the target gene promoter within target cell allowing for the expression of the reporter genes driven by the target gene promoter. 
     In one such embodiment, a MRSA reporter system can be developed by incorporating into a  S. aureus -specific non-replicative transduction particle (e.g., the transduction particle  110 , the transduction particle  160  or the like) a reporter construct consisting of a nucleic acid sequence that is homologous to the mecA gene upstream of promoter-less bacterial luciferase genes, luxAB. When the transduction particle introduces the reporter construct into a target  S. aureus  cell, the reporter gene will not be expressed unless the target cell contains the target mecA gene and a homologous recombination event integrates the luxAB genes within the mecA gene loci in the target cell such that the reporter gene becomes operatively linked to the mecA gene promoter within target cell allowing for the expression of luxAB driven by the mecA gene promoter. 
     The sample with the transduction particles mixed therein can be maintained at any suitable temperature and for any suitable time to promote production of the reporter molecules and/or growth of the target cells within the sample. For example, in some embodiments the sample and the transduction particles are maintained at a temperature of greater than or equal to room temperature, 25 degrees Celsius, or 37 degrees Celsius, and for a predefined time period of less than 2 hours, 2 hours, 3 hours, 4 hours, 6 hours, up to 18 hours or even more, inclusive of any ranges therebetween. In this manner, the maintaining of the sample at the predefined temperature for the predefined time period is sufficient to generate a quantity of the series of reporter molecules sufficient to produce a measurable signal. In some embodiments, the maintaining need only be sufficient to promote the production of the reporter molecules in the target cells initially present in the sample. Said another way, in some embodiments, the conditions under which the sample is maintained (e.g., the temperature and/or duration) prior to the detection operation need not be sufficient to promote repeatable target cell replication. 
     In some embodiments, the method optionally includes disposing a second substance into the sample,  156 . The second substance can be formulated to react with the series of reporter molecules to catalyze, enhance the production of and/or produce a measureable signal, such as, for example, a luminescence signal, a fluorescence signal, a color-based signal, a chemical signal or electrochemical signal. For example, in some embodiments, the nucleic acid molecule can include luxA/luxB sequences such that the reporter molecule produced can be luciferase. In such embodiments, the second substance (or reagent) can be an aldehyde reagent (e.g., tridecanal). The tridecanal urges the luciferase to produce luminescence that can be measured. In some embodiments, the reagent can include a 6-carbon aldehyde (hexanal), a 13-carbon aldehyde (tridecanal) and/or a 14-carbon aldehyde (tetradecanal), inclusive of all the varying carbon chain length aldehydes therebetween. In some embodiments, the reagent formulation can also include a maintaining medium and/or buffer, e.g., TSB broth, citrate buffer, etc., a surfactant, e.g., Tween 20, and be adjusted to a predetermined pH, e.g., pH 3. 
     The identification of the target cell is performed by receiving a signal associated with a quantity of the series of the reporter molecules,  158 . The signal can be measured using any suitable detector as described herein, (e.g., the detector  1200  of the instrument  1100  described above, the detector  11200  of the instrument  11000  described below, or the like). In some embodiments, the magnitude of the signal is independent from a quantity of transduction particles mixed with the sample. More particularly, because the transduction particles are not “tagged” with the reporter molecule (i.e., they do not include the reporter molecule), the strength of the signal is dependent not upon the initial quantity of the transduction reporters, but rather upon the production of the reporter molecules by the target cell. Thus, the signal is independent from the quantity of transduction particle (when the quantity is above some de minimus amount or lower threshold). 
     Any of the steps of the method  150  can be performed using any of the containers and/or instruments described herein. For example, the method  150  can be performed using the containers  1700 ,  2700 ,  3700 ,  4700 , etc. and the instrument  1100 ,  11000  or the like. For example, in some embodiments, the sample can be disposed within a portion of a container that is fluidically isolated from a region outside the container. For example, the sample can be disposed or maintained in a reaction chamber (e.g., the reaction chamber  3732  or  4732  of the container assemblies  3700  and  4700 , respectively) that is sealed and/or closed via a reagent module (e.g., the reagent module  3740  or  4740 ). In some embodiments, the transduction particles can also be maintained in fluidic isolation from the sample before the mixing, e.g., in an internal volume of the container assembly (e.g., such as the reagent module  3740  or  4740 ). In some embodiments, the mixing includes disposing the transduction particles into the sample while maintaining fluidic isolation between the container and an outside region. In this manner, the method can be performed in a closed system and/or a homogeneous assay. In some embodiments, the reagent can also be maintained in fluidic isolation from the sample before disposing, e.g., stored in an internal volume of the container. In some embodiments, the reagent can also be disposed into the sample while maintaining fluidic isolation between the container and the outside region. 
     In some embodiments, the system  1000  and/or the method  150  (or any other systems and methods described herein) can be used to identify and/or detect a drug resistant strain of bacteria. In some embodiments, a method according to an embodiment can use bacterial viability as the method of identification, using viral vectors and/or transduction particles associated with a particular target bacteria. More particularly, in some embodiments, the transduction particles can be a biologically derived viral vector engineered, selected and/or formulated to perform a detection function. For example, as shown in  FIG. 5 , in some embodiments, a transduction particle  160  can be derived from a bacteriophage in accordance with any of the methods and descriptions herein. Similarly stated, the transduction particle  160  can include the structural proteins and/or envelope from a bacteriophage. In particular, the transduction particle  160  can be engineered to include a capsid  162  of a phage engineered to retain the capability to bind to the target bacteria (e.g., via the sheath  164 , tail fibers  166  and/or base plate  168 . In this manner, the transduction particle  160  can selectively identify, bind to and deliver a nucleic acid molecule  170  into a desired target bacteria. 
     As shown in  FIG. 5 , the transduction particle  160  contains a nucleic acid molecule  170  formulated to cause the target cell to produce a plurality of reporter molecules. In some embodiments, the transduction particle  160  and/or the nucleic acid molecule  170  are substantially devoid of the native DNA of the phage from which the transduction particle  160  is derived. Similarly stated, the DNA of the phage from which the transduction particle  160  is replaced by the engineered plasmid or nucleic acid molecule  170 . Said another way, the transduction particle  160  is substantially devoid of a wild-type DNA capable of exhibiting wild-type viral functions, such as replication functions, associated with a phage from which the transduction particle  160  is derived. Thus, in such embodiments, the transduction particle  160  is “replication-deficient” or incapable of reproducing or replicating by any means (e.g., by lysogenic and/or lytic replication). 
     As shown in  FIG. 5 , the engineered nucleic acid molecule  170  in the transduction particle  160  contains a reporter sequence  174  that provides instructions for the target bacteria to express a reporter molecule. For example, the reporter sequence  174  can include promoter less sequences luxA/luxB for expressing luciferase, which cannot be expressed by the transduction particle  160  autonomously. Rather after the luxA/luxB sequences are inserted into the target bacteria by the transduction particle  160  and are operatively coupled with the target bacteria DNA, the natural transcription machinery of the target bacteria is used to express the reporter molecule, i.e., luciferase. In other embodiments, the reporter sequence  174  can also include a promoter included with the luxA/luxB sequences. In such embodiments, after the promoter coupled luxA/luxB sequences are inserted into the target bacteria by the transduction particle  160 , the promoter coupled luxA/luxB sequences can express luciferase without coupling with the target bacteria DNA. 
     As described herein, in some embodiments, the transduction particle  160  can be engineered for reporting on the presence of viable bacteria. In such embodiments, the transduction particle  160  is engineered to identify and/or recognize a target bacteria, attach thereto and communicate the engineered nucleic acid  170  into the target bacteria. Upon being conveyed into the target bacteria, the engineered nucleic acid  170  can produce reporter molecules due to the incorporation of a promoter operatively linked to the reporter genes (e.g., the reporter sequence luxA/luxB as described before herein) within the engineered nucleic acid. The engineered nucleic acid  170  then causes the target bacteria to produce the reporter molecules using the natural transcription and translation systems of the target bacteria. In such viable cell reporter embodiments, further specificity can be achieved by eliminating all other phenotypes. For example, in some embodiments, MRSA can be identified in a cell viability assay by killing or otherwise suppressing signal generation from all non-drug resistant phenotypes within the sample by using antibiotics. 
     As shown schematically in  FIGS. 6A, 6B, and 6C , the transduction particle  160  can be used to detect target bacteria  180  in any sample S. In the first operation (indicated by the schematic illustration  192 ), the transduction particle  160  is brought into contact and/or mixed with the sample S containing the target bacteria  180 . The transduction particle  160  can be mixed with and/or introduced into the sample S using any suitable methods or mechanisms as described herein. The transduction particle  160  is selected, formulated and/or engineered to specifically identify and bind to the cell wall of the target bacteria  180 , as shown by arrow A. At operation  194 , the transduction particle  160  communicates the engineered nucleic acid  170  contained therein, into the target bacteria  180  cytoplasm, as shown by arrow B. In some embodiments, when viable cell reporting is performed, the engineered nucleic acid  170  can include the reporter sequence  174  (e.g., luxA/luxB) coupled to a promoter and configured to cause the production of reporter molecules in the target cell  180 , as shown in operation  196 . 
     The presence of reporter molecules  130  indicates that the target bacteria  180  are present in the sample S. Accordingly, the reporter molecules  130  are “switchable” (i.e., only present under certain conditions). Moreover, because in some embodiments the transduction particle  160  is non-replicative (i.e., incapable of lytic or lysogenic replication), the target bacteria  180  remain alive or otherwise un-inhibited during the assay. Therefore, the systems and methods described herein can be used to detect live bacteria. Furthermore, while not shown in  FIGS. 6A, 6B , or  6 C, an antibiotic (e.g., cefoxitin) can be added to the sample S, for example, before adding the transduction particle  160 . The antibiotic can eliminate or otherwise inhibit all non-antibiotic resistant bacteria (e.g., MSSA) such that only the antibiotic resistant strains (e.g., MRSA) remain viable in the sample S. In this way, only the antibiotic resistant bacteria, for example, target bacteria  180  are able to produce a detectable signal. 
     In some embodiments, the signal produced by the reporter molecules  130  is independent of the quantity of the transduction particles  160  mixed with the sample (when the quantity is above some de minimus value or predetermined quantity). This is illustrated by  FIGS. 7A and 7B .  FIG. 7A  shows a schematic of the sample S containing the target bacteria  180 , and that has been mixed with a series of transduction particles  160 . A portion of the transduction particles  160  are bound to the target bacteria cells  180  in the sample S, such that the engineered nucleic acid  170  is conveyed into the target bacteria cells  180 , as described above. The engineered nucleic acid  170  can then mediate the production of reporter molecules (e.g., either via the viable cell reporter methods or the gene reporter methods). After a first time period T 1 , a first quantity of reporter molecules  130  is produced by the target bacteria  180 . As shown in  FIG. 7B , after a second time period T 2  greater than the first time period, the number of reporter molecules  130  increases to a second quantity, greater than the first quantity. Because the reporter molecules  130  are not tagged by and/or contained within the transduction particles  160 , the amount of reporter molecules is substantially independent of the amount of transduction particles  160  initially mixed with the sample S. Moreover, as shown in  FIG. 7B , the transduction particles  160  are non-replicative, and there is no increase in the quantity of transduction particles  160  between the first time period T 1  and the second time period T 2 . Because the transduction particles  160  are incapable of lytic replication, there is no decrease in the quantity of target bacteria. 
       FIG. 8  is a flow chart of a method  200  of identifying viable bacteria in biological samples, according to an embodiment. The method  200  can be performed using any of the containers described herein (e.g., container  1700 ,  2700 ,  3700 ,  4700  or the like), and any of the instruments (e.g., instrument  1100 ,  11000 ) and/or any components shown and described herein. The method  200  can also be performed using any of the transduction particles and/or viral vectors described herein, such as, for example, the transduction particle  160 . More particularly, the operations of the method  200  described below can be performed in a container, without exposing the samples, and/or reagents to outside conditions. For purposes of the description, the method  200  is described as being performed with the container  1700  and instrument  1100 , shown and described above with reference to  FIGS. 2-3 . 
     The method  200  includes communicating a collected sample that can contain target bacteria, for example, a patient nasal swab, to a container,  202 . In some embodiments, this operation can be optional. For example, in some embodiments, the container can be received by a user with the sample predisposed therein. The container can be any suitable container, such as, for example, the container  1700  or any other container described herein. The container can have a solution disposed in an interior region of the container. The solution can include, for example, a bacterial nutrient media, buffers, surfactants or any other component to facilitate growth of the target bacteria, production of reporter molecules within the target bacteria, detection of bacteria or the like. In some embodiments, the solution can be added after the sample is conveyed into the container. In some embodiments, the solution can be predisposed in the container, isolated from the sample, e.g., in a separate compartment in the container or the cap of the container such that it can be communicated to the sample on demand and/or in a closed-system environment. 
     The container is then sealed,  204 , for example, with a cap, reagent module or the like. In some embodiments, the seal can be formed by a reagent module (see e.g., the reagent modules  3740  and  4740  described below), that can include compartments, frangible portions, reagents, actuators, and/or nozzles. In some embodiments, an antibiotic or a series of antibiotics is optionally added to the sample disposed in the container,  206 . The antibiotics can be selected and/or formulated to kill other non-targeted bacterial strains, for example, non-drug resistant strains, so that only the drug resistant strain survives. In this manner, the reporter molecules produced are necessarily produced by the remaining, targeted bacterial strains. In some embodiments, the antibiotic/series of antibiotics can be predisposed in the container (for example, in the solution). In other embodiments, the antibiotic/series of antibiotics can be disposed in a separate compartment (e.g., in the body or cap of the container assembly), and can be communicated into the sample solution on demand or at a predetermined time. 
     A first reagent or substance containing the transduction particles, is communicated into and/or mixed with the sample,  208 . The transduction particles can be any of the transduction particles described herein, such as, for example the transduction particle  160 . In particular, the transduction particles include a nucleic acid molecule that contains a reporter sequence that provides instructions for the target bacteria to express a reporter molecule. In some embodiments, the transduction particles need not be added to the solution, but rather are predisposed in the solution. In such embodiments, the transduction particles are mixed with the sample to enable identification of the target bacterium by the transduction particles. In some embodiments, for example, the transduction particles are disposed in a separate compartment of the cap of the container, and are released and/or mixed with the sample on demand or at a predetermined time. 
     In some embodiments, the container solution can optionally be agitated,  210  to efficiently mix the transduction particles and the solution to facilitate interaction. Methods of mixing can include vortexing, manual shaking, stirring or the like, automated agitation (e.g., via a shaker table), or any other suitable agitation method. The container is then placed in the instrument or a portion of an instrument,  212 , and maintained for a predefined time and/or at a predetermined temperature,  214 . Such conditions can include, for example maintaining the sample for less than 2 hours, approximately 2 hours, 4 hours, 6 hours, 8 hours, up to 18 hours, or even more, at temperature, e.g., less than or equal to approximately 37 degrees Celsius. The conditions under which the sample is maintained are defined to allow the transduction particle to bind to the target bacteria and communicate engineered nucleic acid to the target bacteria, and to promote the expression of the reporter molecules (e.g., luciferase). In the viable cell reporter embodiment, the engineered nucleic acid can be introduced to all of the target bacteria irrespective of, for example, the presence of a gene imparting drug resistance in the bacteria. Further specificity can be achieved, for example, by eliminating all other phenotypes imparted by particular genotypes, e.g., by adding anti-biotic to the sample as described above with reference to operation  206 , and thereby eliminating or otherwise preventing the generation of a signal from cells lacking a drug resistance gene and/or expressed drug resistant genotype. 
     In some embodiments, a reagent is then communicated into the sample to enhance, catalyze and/or promote the production of a signal from the reporter molecules,  216 . For example, the reagent can be a substrate formulated to catalyze the production of a light signal by the reporter molecules. Such substrates can include an active ingredient, for example, tridecanal that can interact with the reporter molecule to produce a detectable signal, for example, luminescence. In some embodiments, the substrate can include a 6-carbon aldehyde (hexanal), a 13-carbon aldehyde (tridecanal) and/or a 14-carbon aldehyde (tetradecanal), inclusive of all the varying carbon chain length aldehydes therebetween. In some embodiments, the reagent can be formulated to include Tween 20 or other surfactants, tridecanal or other aldehydes, and adjusted to a particular pH. In some embodiments, the substrate can be stored in the container, for example, in an isolated compartment in the container cap, and can be delivered to the sample on demand or at predetermined time. 
     The signal is detected,  218 , using any suitable the detector. The detector can be, for example, the detector  1200  disposed in the instrument  1100  or the detector (PMT)  11200  shown and described below. If a measureable signal is detected, then the target bacteria are present in the sample,  220 . If no signal is detected, then the sample is free of target bacteria,  222 . 
     Although, the method  200  shown and described above can be used for detection of viable bacteria and identification (e.g., by optionally including antibiotics to eliminate non-targeted strains), in other embodiments, methods can include transduction particles and/or engineered viral vectors that can selectively identify and/or recognize a bacteria by genotype. Said another way, the transduction particles can conditionally produce reporter molecules only after recognizing and/or identifying a gene sequence within the target bacteria, as described below. 
     The transduction particle can be engineered to encapsulate and deliver an engineered nucleic acid molecule, such as the nucleic acid molecule  170 , into the target bacteria. In some embodiments, the nucleic acid molecule is engineered and/or formulated to include a nucleic acid sequence that is homologous to a target gene, a reporter gene, and any other suitable regulatory genes. The recognition gene can be, for example, homologous to a portion of the target bacteria gene and configured to probe for and recognize the portion of the bacterial gene, and operably couple itself to the bacterial gene and result in the integration of the reporter gene within the target gene locus, e.g., using homologous recombination. In some embodiments, the reporter gene can be a promoter-less gene and thus is only expressed if it becomes operatively linked to a target gene promoter after insertion of the reporter gene into a target gene locus. 
     In some embodiments, an engineered nucleic acid molecule can be formulated and/or configured to conditionally recombine in the presence of a target gene present in and/or specific to particular drug-resistant bacteria genotype. For example,  FIG. 9  is a schematic illustration of formulation of an engineered nucleic acid molecule  570  and/or plasmid specific for MRSA, according to an embodiment. The engineered nucleic acid sequence  500  includes plasmid regulatory elements  576  (e.g. an origin of replication, etc.), a mecA gene fragment  572 , a luxA gene  574   a , a luxB gene  574   b , and a selectable marker (e.g. tetracycline resistance gene, etc.) (not shown). The plasmid regulatory elements  576  can be any plasmid regulatory element as known in the arts. The mecA gene fragment  572  is homologous to a segment of the mecA gene. Once inside the bacteria, the mecA gene fragment  572  can probe for and/or identify the mecA sequence on the MRSA gene, and mediate the integration of the reporter genes into the mecA gene locus via homologous recombination in a manner that operatively links the mecA gene promoter to the luxAB genes. In some embodiments, the engineered nucleic acid  500  can include any other recognition sequence, e.g., tcdB, vanA, etc., specific for any gene sequence on any other bacteria, for example,  E. coli, Salmonella, C. difficile , VRE, etc. The luxA  574   a  and luxB  574   b  genes, together serve as the reporter gene that can be controlled by the natural bacteria transcription and translation cycle to express the reporter molecule luciferase. In some embodiments, any other reporter gene can be used, for example, a gene for expressing an enzyme (e.g., glucose oxidase, horseradish peroxidase) or a fluorescent protein (e.g., green fluorescent protein, etc.). 
       FIG. 10  is a flow chart of a method  300  for genotypic identification of bacteria using a transduction particle and/or engineered viral vector, e.g., transduction particle  160  that contains an engineered nucleic acid molecule (e.g., the nucleic acid molecule  570 ). The method  300  can be performed using any of the containers described herein, for example, container  1700 ,  2700 ,  3700 ,  4700  and the like, and any instruments and components thereof described as herein, such as, for example instruments  1100  and  11000 . 
     The method  300  includes adding a transduction particle to a sample, e.g. a patient nasal swab that can contain target bacteria genotype,  302 . The sample can be disposed in a container, such as, for example, container  1700 , and can further include solutions such as, for example, bacterial nutrient media, buffers, and/or surfactants. In some embodiments, the transduction particle can be included in the solution and disposed in the container prior to adding the sample. The transduction particles and the solution are maintained under conditions such that the transduction particles identify and bind to the target bacteria present in the sample,  304 . The transduction particle then inserts the engineered plasmid or engineered nucleic acid molecule into the target bacteria,  306 . 
     The recognition gene portion of the engineered nucleic acid molecule, for example, a mecA gene fragment, as described herein, then probes the bacteria DNA for a homologous sequence,  308 . If the homologous sequence is present, the engineered nucleic acid molecule inserts into and operatively couples the reporter gene sequences with an endogenous promoter of the target gene  310 . In this manner, the target bacteria express reporter molecules, for example luciferase, through its natural transcription/translation process,  312 . 
     The sample is then maintained for a predefined time and/or at a predetermined temperature,  314 . Such conditions can include, for example maintaining the sample for less than 2 hours, approximately 2 hours, 4 hours, 6 hours, 8 hours, up to 18 hours, or even more, at temperature, e.g., less than or equal to approximately 37 degrees Celsius. The conditions under which the sample is maintained are defined to allow the transduction particle to bind to the target bacteria and communicate engineered nucleic acid to the target bacteria, and to promote the expression of the reporter molecules (e.g., luciferase). 
     In some embodiments, a reagent is then communicated into the sample to enhance, catalyze and/or promote the production of a signal from the reporter molecules,  316 . For example, the reagent can be a substrate formulated to trigger the production of a light signal by the reporter molecules. Such substrates can be any suitable substrates of the types shown and described herein. The signal is detected,  318 , with any suitable instrument. If the sample contained any other bacteria genotype, the gene sequence homologous to the recognition gene would not be present in the bacteria DNA. Accordingly, there would be no homologous recombination of transduction particle DNA with bacteria DNA and the reporter molecule would not be produced. Therefore, adding substrate to the sample solution  316  would not produce any detectable signal indicating that the sample does not contain the target bacteria genotype. 
       FIGS. 11A, 11B, 11C, and 11D  show a schematic illustration of portions of the method  300  for genotypic identification and detection of a target bacteria. As shown in  FIG. 11A , a transduction particle  660  added to and/or mixed with a sample S to detect a particular genotype of a target bacteria  680  that may be present in the sample S. In the first operation (indicated by the schematic illustration  692 ), the transduction particle  660  is brought into contact with the sample S containing the target bacteria  680 . The transduction particle  660  can specifically identify and bind to the target bacteria  680  cell wall as shown by arrow C. The transduction particle  660  then communicates an engineered nucleic acid or plasmid  670  contained therein, into the target bacteria  680  cytoplasm, as shown by arrow D (see operation  694 ). 
     The engineered nucleic acid  670  can be any of the engineered nucleic acid molecules described herein, such as, for example, the nucleic acid molecule  570 . In particular, the engineered nucleic acid molecule  670  includes a recognition sequence  672 , engineered and/or formulated to recognize a target gene  684  in the DNA  682  of the target bacteria  680 . The engineered nucleic acid also includes a reporter gene sequence  674  (e.g., the reporter sequence luxA/luxB). If the target bacteria  680  contains the target gene  684 , the engineered nucleic acid  670  will recognize the target gene  684  and inserts the reporter gene sequence  674  into the target gene loci in a manner that operatively links the reporter gene sequences  674  with a target gene  682  promoter (see operation  696 ). For example, the engineered nucleic acid  670  can include a recognition sequence  672  specific for the mecA sequence on MRSA DNA. In the final operation (see schematic  698 ), the transcription and translation machinery of the target bacteria  680  read the genes encoding the reporter sequence  674  and produce the reporter molecules  630 . If the target gene  684  is not present, recombination does not take place and the reporter molecules  630  are not expressed. Therefore, presence of the reporter molecules  630  indicates that the target gene is present in the viable bacteria  680  in the sample S. Since the transduction particle  660  is non-replicative and is incapable of lytic or lysogenic replication, the target bacteria  680  remain alive during the assay. Therefore, the systems and methods described herein can be used to detect genes within live bacteria. 
     In some embodiments, a system  1000  and/or any of the methods disclosed herein can include and/or be performed with a container configured to facilitate communication of a solution (e.g., nutrient media, buffers, surfactants), transduction particles, biologic vectors such as engineered viral vector, abiologic vectors consisting of polymers, liposomes or virus-like particles, and/or reagent (e.g., substrate, antibiotics, etc.) into the sample. For example,  FIGS. 12-14  show a container assembly  1700  according to an embodiment, in a first configuration, a second configuration and a third configuration, respectively. One or more container assemblies  1700  can be disposed within any suitable instrument of the type disclosed herein (see e.g., instrument  11000  described below) configured to manipulate, actuate and/or interact with the container assembly  1700  to perform the methods associated with the identification of the target cell described herein. The container assembly  1700  allows for efficient and accurate diagnostic testing of samples by limiting the amount of sample handling during assay. Moreover, modular arrangement of the container components (e.g., the reaction chamber  1732  and the reagent module  1740 ) allows any number of different reagent modules  1740 , each containing different reagents and/or formulations to be interchangeably used to detect a different type of target cell. This arrangement also allows the transduction particles and the reagents to be stored separately and communicated to the sample on demand, as described below. Separate storage can be useful, for example, if the reagents included within the reagent module  1740  have different storage requirements (e.g., expiration dates, lypophilization requirements, storage temperature limits, etc.) than the reagents, solution and/or sample included within the reaction chamber  1732 . 
     As shown, the container assembly includes a reaction chamber  1732  and a reagent module  1740 . The reaction chamber  1732  can be coupled to the reagent module  1740  to form an integrated assembly. The reaction chamber  1732  can be formed from any suitable material, such as, for example, light weight, rigid and inert materials (e.g., plastics). At least a portion of the reaction chamber  1732  can be at least partially transparent to allow viewing and/or detection of the internal volume of the reaction chamber  1732  (for example, to view luminescence in the reaction chamber  1732 ). In some embodiments, the reaction chamber  1732  can be shaped as a cylinder with a rounded bottom, or flat base. In other embodiments, the reaction chamber  1732  can have any other suitable shape, e.g., square, rectangular, oval, polygonal, etc. In some embodiments, the reaction chamber  1732  can have a diameter of  12  mm and a height of 75 mm. In some embodiments, the diameter of the reaction chamber  1732  can be sized to optimally match the cross-section of a detector (e.g., detector  1200 , or  11212  included in the instrument  11000 , or any other detector). In some embodiments, the container assembly  1700  can be provided with one or more solutions and/or reagents of the types shown and described herein (e.g., bacterial nutrient solution, buffers, surfactants, transduction particles, and/or antibiotics), predisposed within the reaction chamber  1732 . 
     The reagent module  1740  of the container  1700  includes a housing  1741 , a first actuator  1750  and a second actuator  1760 . The housing  1741  is configured to be removably coupled to the reaction chamber  1732  by any suitable mechanism. For example, in some embodiments, the housing  1741  can be coupled to the reaction chamber  1732  by a threaded coupling, an interference fit, snap-fit, or the like. In some embodiments, the housing  1741  and the reaction chamber  1732  define a substantially fluid tight seal. 
     The housing  1741  defines a first reagent volume  1742  and a second reagent volume  1744 . The first reagent volume  1742  and the second reagent volume  1744  can be separated by a sidewall  1746 . In some embodiments, the first reagent volume  1742  contains biologic or abiologic vectors, transduction particles and/or a viral vector (e.g., transduction particle  110 ,  160  or any of the other transduction particles described herein), that includes an engineered nucleic acid molecule (e.g., engineered nucleic acid  170 ) formulated to cause the target cell (e.g., bacteria) to produce a series of reporter molecules (e.g., luciferase). In some embodiments the transduction particle is formulated to be non-replicative (i.e., incapable of replication), as described herein. In some embodiments, the second reagent volume  1744  can contain a reagent formulated to interact with the reporter molecule to catalyze, enhance the production of and/or produce a measurable signal, such as, for example an optical signal. In some embodiments, the reagent is a luciferase substrate of the types shown and described herein, such as, for example, a composition including tridecanal. Although the transduction particles and the reagent are shown as being disposed directly within the first reagent volume  1742  and the second reagent volume  1744 , respectively, in other embodiments, the transduction particles and/or reagents can be disposed inside reagent containers (not shown) shaped and sized to be disposed substantially inside the first reagent volume  1742  and/or the second reagent volume  1744 . 
     In some embodiments, the housing  1741  and/or any reagent containers therein (not shown) can include frangible portions configured to rupture when actuated or compressed (e.g., by the first actuator  1750  and/or the second actuator  1760 ). In this manner, the reagents and constituents can be stored in isolation and released upon actuation. In some embodiments, the housing  1741 , first actuator  1750 , second actuator  1760  and/or such reagent containers can include features to facilitate repeatable delivery, e.g., curved edges, flat bottom, bellowed walls, or any other suitable feature. In some embodiments, for example, the housing  1741  can include a puncturer or a series of puncturers (not shown) disposed within the first reagent volume  1742 , configured to puncture a portion of a reagent container when the plunger portion  1754  of the first actuator  1750  is moved within the first reagent volume  1742 . In some embodiments, a puncturer can also be disposed within the second reagent volume  1744 . 
     The first reagent volume  1742  and the second reagent volume  1744  can have any suitable shape, orientation and/or size. In some embodiments, as shown in  FIGS. 12-14 , the first reagent volume  1742  and the second reagent volume  1744  can be concentric. In other embodiments, the first reagent volume  1742  and the second reagent volume  1744  can be located parallel to each other. Although shown as having a substantially constant cross-sectional area, in some embodiments, a cross-sectional dimension, e.g., diameter or area, of the housing  1741  and/or the first reagent volume  1742  and the second reagent volume  1744  can be varied to increase/decrease a volume of the reagent contained therein. In this manner, the housing  1741  can be configured to provide the desired quantity and/or a flow rate of reagent to be delivered into the reaction chamber  1732 . 
     The housing  1741  includes a delivery portion  1770  that, when the housing  1741  is coupled to the reaction chamber  1732 , defines a first fluidic pathway  1772   a  between the first reagent volume  1742  and the reaction chamber  1732 , and a second fluidic pathway  1772   b  between the second reagent volume  1744  and the reaction chamber  1732 . As shown, the first fluidic pathway  1772   a  and the second fluidic pathway  1772   b  are separate from each other. The first fluidic pathway  1772   a  and the second fluidic pathway  1772   b  include a first outlet  1774   a  and a second outlet  1774   b , respectively, that each open into the reaction chamber  1732 . The first fluidic pathway  1772   a  and the second fluidic pathway  1772   b  provide a pathway for the transduction particles and reagents disposed in the first reagent volume  1742  and/or the second reagent volume  1744 , respectively, to be communicated into the reaction chamber  1732 . 
     The delivery portion  1770  can be configured to provide any suitable pathway and/or mechanism for delivering the transduction particles and reagents disposed in the first reagent volume  1742  and/or the second reagent volume  1744  into the reaction chamber  1732 . For example, in some embodiments, the delivery portion  1770  can include a single fluidic pathway for communicating fluids from the first reagent volume  1742  and the second reagent volume  1744  into the reaction chamber  1732 . In some embodiments, the delivery portion  1770  can be configured to deliver reagents from the first reagent volume  1742  and/or the second reagent volume  1744  into the reaction chamber  1732  in a manner that promotes mixing and/or that minimizes aeration, overspray and/or undesirable turbulence. In some embodiments, the first fluidic pathway  1772   a  and/or the second fluidic pathway  1772   b  can have a varying cross-sectional (or flow) areas (e.g., the pathways can resemble nozzles) to produce a controlled flow rate of the substances flowing therethrough. In some embodiments, the flow rate of the transduction particles and/or reagents, can be 1 ml/sec, 2 ml/sec,3 ml/sec, 4 ml/sec, 5 ml/sec, or any suitable flow rate to sufficiently mix the substance and/or to minimize aeration. 
     The reagent module  1740  includes the first actuator  1750  at least partially disposed in the housing  1741 . The first actuator  1750  includes an engagement portion  1752  and a plunger portion  1754 , which is disposed within the first reagent volume  1742 . The engagement portion  1752  of the first actuator  1750  is configured to be manipulated (for example, by any instrument shown and described herein, such as the instrument  11000 ) to move the plunger portion  1754  within the first reagent volume  1742 . In some embodiments, the plunger portion  1754  of the first actuator  1750  and a portion of the housing  1741  define and/or include a seal to fluidically isolate the first reagent volume  1742  from a volume outside of the housing  1741 . In some embodiments, the seal can be, for example, a gasket, an o-ring, a rubber seal, or any suitable seal. As shown, the engagement portion  1752  and the plunger portion  1754  of the first actuator  1750  can have different cross-sectional dimensions (e.g., diameter). In other embodiments, however, the engagement portion  1752  and the plunger portion  1754  of the first actuator  1750  can have the same cross-sectional dimension (e.g., diameter). In some embodiments, the engagement portion  1752  can be offset from (e.g., non-coaxial with) the plunger portion  1754 . 
     The reagent module  1740  includes the second actuator  1760  at least partially disposed in the housing  1741 . The second actuator  1760  includes an engagement portion  1762  and a plunger portion  1764 , which is movably disposed within the second reagent volume  1744 . The engagement portion  1762  of the second actuator  1760  is configured to be manipulated (for example, by any instrument shown and described herein, such as the instrument  11000 ) to move the plunger portion  1764  of the second actuator  1760  within the second reagent volume  1744 . In some embodiments, the plunger portion  1764  of the second actuator  1760  and a portion of the housing  1741  define and/or include a seal to fluidically isolate the second reagent volume  1742  from a volume outside of the housing  1741 . In some embodiments, the seal can be, for example, a gasket, an o-ring, a rubber seal, or any suitable seal, and can be substantially similar to the seal of the first actuator  1750 . As shown, the engagement portion  1762  and the plunger portion  1764  of the second actuator  1760  can have different cross-sectional dimensions (e.g., diameter). In other embodiments, however, the engagement portion  1762  and the plunger portion  1764  of the second actuator  1760  can have the same cross-sectional dimension (e.g., diameter). In some embodiments, the engagement portion  1762  can be offset from (e.g., non-coaxial with) the plunger portion  1764 . 
     As shown, the engagement portion  1762  of the second actuator  1760  at least partially surrounds the engagement portion  1752  of the first actuator  1750 . Similarly stated, at least a portion of the first actuator  1750  and a portion of the second actuator  1760  are disposed concentrically in the housing  1741 . In this manner, the reagent module  1740  can be coupled to the reaction chamber  1732  and/or disposed in an instrument in any angular orientation about the longitudinal axis of the container assembly  1700 . This arrangement allows a single actuator assembly to manipulate both the first actuator  1750  and the second actuator  1760 . 
     More particularly, the second actuator  1760  defines a channel  1766  within which the engagement portion  1752  of the first actuator  1750  can move when the first actuator  1750  is manipulated to move the plunger portion  1754 . In some embodiments the engagement portion  1762  of the second actuator  1760  can define an opening within which the engagement portion  1752  of the first actuator  1750  can be substantially disposed. Although a longitudinal axis of the plunger portion  1754  of the first actuator  1750  is shown as being concentric to a longitudinal axis of the plunger portion  1764  of the second actuator  1760 , in other embodiments, the longitudinal axis of the plunger portion  1754  can be offset from and/or nonconcentric with the longitudinal axis of the plunger portion  1764 . In some embodiments, for example, the first actuator  1750  and the second actuator  1760  can be disposed adjacent but not concentric to each other. In some embodiments, the first actuator  1750  and the second actuator  1760  can be disposed parallel to each other. In some embodiments the engagement portions  1752  and/or the engagement portion  1762  can be recessed in the housing  1741 , e.g., to prevent accidental actuation. 
     The first actuator  1750  and the second actuator  1760  can be moved in any suitable manner to perform the functions described herein. For example, in some embodiments, the plunger portion  1754  of the first actuator  1750  can be moved independently of the movement of the plunger portion  1764  of the second actuator  1760 . In some embodiments, the first actuator  1750  and second actuator  1760  can have the same stroke length. In other embodiments, the first actuator  1750  and second actuator  1760  can have different stroke lengths. In this manner, different volumes (and/or different flow rates) of transduction particles or reagents can be conveyed into the reaction chamber  1732 . 
     In use, the container assembly  1700  is configured to be manipulated to perform the methods and/or assays described herein while maintaining fluidic isolation of the reaction chamber  1732 . Similarly stated, the reaction chamber  1732  and the reagent module  1740  of the container assembly  1700  can collectively define a closed system within which target cell identification can be performed (i.e., without decoupling the reagent module  1740  from the reaction chamber  1732 ). In particular, the container assembly  1700  can be delivered to the user in a first configuration ( FIG. 12 ), in which the first actuator  1750  and the second actuator  1760  are each their respective first positions. Although the reagent module  1740  is shown as being coupled to the reaction chamber  1732  in  FIG. 12 , the reagent module  1740  can initially be decoupled from the reaction chamber  1732  to allow a sample containing the target cell (e.g., bacteria) to be disposed in the internal volume defined by the reaction chamber  1732 . The reagent module  1740  can be coupled to the reaction chamber  1732  to define a fluid-tight seal. 
     To move the container assembly  1700  and/or the reagent module  1740  to the second configuration ( FIG. 13 ), the engagement portion  1752  of the first actuator is manipulated to move within the channel  1766 . In this manner, the plunger portion  1754  of the first actuator  1750  moves within the first reagent volume  1742  to convey and/or expel the reagent (e.g., transduction particles) from the first reagent volume  1742  through the first fluidic pathway  1742   a  and first outlet  1744   a , and into the reaction chamber  1732  as shown by arrow EE. In some embodiments, the reagent includes transduction particles that interact with the target cell contained in the sample such that the target cells produce a series of reporter molecules according to any of the methods described herein. Manipulation and/or maintaining of the container assembly  1700  (and the sample contained therein) can be performed by the instruments  1100  and/or  11000  as described herein and/or any other instruments or components described herein. 
     To move the container assembly  1700  and/or the reagent module  1740  to the third configuration ( FIG. 14 ), the engagement portion of  1762  of the second actuator  1760  is manipulated to move at least partially about the first actuator  1750 . The movement of the engagement portion  1762  moves the plunger portion  1764  of the second actuator  1760  from the first position to a second position within the second reagent volume  1744 . The displacement of the plunger portion  1764  conveys and/or expels the reagent (e.g., a substrate such as tridecanal) from within the second reagent volume  1744  through the second fluidic pathway  1772   b  and second outlet  1774   b  into the reaction chamber  1732 , as shown by arrow FF. In some embodiments, the reagent is a substrate that can interact with the reporter molecules produced to urge, catalyze and/or enhance the reporter molecules to produce a signal, e.g., via a luminescence reaction. 
     In some embodiments, a container assembly can include a mechanism for collecting a sample and/or disposing a sample into the container assembly. For example, in some embodiments, a sample can be collected using a swab, which is then disposed into the reaction chamber of the container.  FIGS. 15-17  show a container assembly  2700  in a first configuration, a second configuration, and a third configuration, respectively. The container assembly  2700  includes a reaction chamber  2732  and a temporary cap  2739 . The reaction chamber  2732  of the container assembly  2700  can be coupleable to any reagent module, such as, for example, the reagent module  1740  as described above, or any other reagent module described herein. 
     The sample S containing the target cell can be collected in a swab  2734 , which can be a nasal swab, saliva swab, environmental swab, or the like. In some embodiments, after collecting the sample S, the nasal swab  2734  is broken at a predefined position and/or length of the swab  2734  as shown by the line GG (FIG. 15 ). The reaction chamber  2732  can contain a solution  2702 , e.g., nutrient media, buffers, surfactants, and/or any other reagents formulated to maintain the target cells, promote the production of reporter molecules or the like. The swab  2734  is inserted into the reaction chamber  2732 , as shown by arrow HH, until it is immersed in the solution  2702 . 
     The temporary cap  2736  can then be coupled to the reaction chamber  2732  to place the container assembly  2700  in the second configuration ( FIG. 16 ). In some embodiments, the temporary cap  2736  can define a substantially fluid-tight seal when coupled to the reaction chamber  2732 . In this manner, the container assembly  2700  can be agitated, e.g., vortexed or shaken, to allow a significant portion of the sample S containing the target cells to communicate into the solution  2702  from the swab  2734 . In some embodiments, the swab  2734  and the sample collection protocol can be defined such that as much as 50%, 60%, and up to 70%, and any quantity therebetween or even higher, of the collected target cells are transferred into the solution  2702 . 
     In some embodiments, the swab  2734  can be removed for testing. Removal of the swab, in certain situations, can limit interference with sample measurements. Accordingly, in some embodiments, the temporary cap  2736  can include a gripping mechanism, e.g., notches, grooves, sleeve, or any other feature for gripping the swab  2734 . In such embodiments, when the temporary cap  2736  is removed from the reaction chamber  2732  as shown in the third configuration by arrow II ( FIG. 17 ), the swab  2734  is also removed with it. In some embodiments, the reaction chamber  2732  can include one or more labels  2738  disposed on an exterior surface of the reaction chamber  2732 . The labels  2738  can include information associated with the container assembly  2700 , e.g., target cell, serial number, lot number, expiration date, and/or warning information. In some embodiments, the container  2700  can also include a tracking mechanism  2739 , e.g., bar codes on labels and/or RFID tags. 
       FIGS. 18-25  show a container assembly  3700  according to an embodiment that includes a reaction chamber  3732  and a reagent module  3740  that is coupleable to the reaction chamber. The container assembly  3700  can be used with and manipulated by any of the instruments described herein, e.g., instrument  11000 , and/or any of the components described herein. The container assembly  3700  can also be used to perform any of the methods described herein, e.g., such as the methods  150 ,  200  and  300  described above. 
     The reaction chamber  3732  is configured to contain a sample and/or other reagents, and can be formed from a light weight, rigid and inert material. At least a portion of the reaction chamber  3732  (e.g., the distal end portion) can be at least partially transparent to allow viewing, optical access and/or detection of the internal volume of the reaction chamber  3732 . Although shown as being shaped as a cylinder with a rounded bottom, in other embodiments, the reaction chamber  3732  can have any other suitable shape, e.g., square, rectangular, oval, polygonal, etc. In some embodiments, the reaction chamber  3732  can have a diameter of 12 mm and a height of 75 mm. In some embodiments, the container assembly  3700  can be provided with one or more solutions/reagents (e.g., bacterial nutrient solution, buffers, surfactants, transduction particle, and/or antibiotics), predisposed within the reaction chamber  3732 . 
     The reagent module  3740  includes a housing  3741 , a first actuator  3750 , a second actuator  3760 , a delivery portion  3770 , a first reagent container  3780   a  and a second reagent container  3780   b . As shown in  FIG. 18 , the housing  3741  is configured to be removably coupled to the reaction chamber  3732  by any suitable mechanism. For example, in some embodiments, the housing  3741  can be coupled to the reaction chamber  3732  by a threaded coupling, an interference fit or the like. In some embodiments, the housing  3741  and the reaction chamber  3732  define a substantially fluid tight seal. 
       FIG. 20  shows a top view of the housing  3741 . The housing  3740  defines a first reagent volume  3742  and a second reagent volume  3744  that can be separated by a sidewall  3746 . The housing  3741  can be formed from a lightweight and rigid material, such as, for example, injection molded plastic. In some embodiments, the housing  3741  can have a diameter of approximately 24 mm. In some embodiment, the diameter of the housing  3741  can be varied to increase or decrease the capacity of the first reagent volume  3742  and the second reagent volume  3744 . In some embodiments, the diameter of the first reagent volume  3742  and/or the second reagent volume  3744  can be varied (i.e., not equal to each other). 
     As shown in the top view of the housing  3741  in  FIG. 20  and inclined bottom view of the housing  3741  shown in  FIG. 21 , the housing  3741  includes a delivery portion  3770  that, when the housing  3741  is coupled to the reaction chamber  3732 , defines a first fluidic pathway  3772   a  between the first reagent volume  3742  and the reaction chamber  3732 , and a second fluidic pathway  3772   b  between the second reagent volume  3744 , and the reaction chamber  3732 . The first fluidic pathway  3772   a  and the second fluidic pathway  3772   b  include a first outlet  3774   a  and a second outlet  3774   b , respectively, that open into the reaction chamber  3732 , when the reaction chamber  3732  is coupled to the housing  3741 . The first fluidic pathway  3772   a  (and the outlet  3774   a ) and the second fluidic pathway  3772   b  (and the outlet  3774   b ) provide a pathway for reagents disposed in the first reagent volume  3742  and the second reagent volume  3744  to be communicated into the reaction chamber  3732 . Although the first fluidic pathway  3772   a  and the second fluidic pathway  3772   b  are shown as being separate from each other, in other embodiments, the first fluidic pathway  3772   a  and the second fluidic pathway  3772   b  can include a common boundary and/or be in fluid communication with each other. 
     The delivery portion  3770  is configured to provide any suitable pathway and/or mechanism for delivering the transduction particles and reagents disposed in the first reagent volume  3742  and/or the second reagent volume  3744  into the reaction chamber  3732 . For example, in some embodiments, the first fluidic pathway  3772   a  and the second fluidic pathway  3772   b  can be configured to deliver reagents from the first reaction volume  3742  and the second reaction volume  3744 , respectively, to the reaction chamber  3732  in a manner that promotes mixing and/or minimizes aeration, overspray and/or undesirable turbulence. The first fluidic pathway  3772   a  and the second fluidic pathway  3772   b  can accommodate any suitable flow rate, e.g., 1 ml/sec, 2 ml/sec, 3 ml/sec, 4 ml/sec, 5 ml/sec. In some embodiments, at least a portion of the delivery portion  3770 , can be disposed within the reaction chamber  3732  when the housing  3741  is coupled to the reaction chamber  3732 . 
     As shown in  FIG. 19  and the side cross-section of the container shown in  FIG. 23  the reagent module  3740  includes the first actuator  3750  disposed in the housing  3741 . The first actuator  3740  includes an engagement portion  3752  and a plunger portion  3754 , which is movably disposed within the first reagent volume  3742 . When actuated, the engagement portion  3752  of the first actuator  3750  moves the plunger portion  3754  within the first reagent volume  3742 . As shown, the plunger portion  3754  of the first actuator  3750  includes a seal  3769   a  to fluidically isolate the first reagent volume  3742  from a volume outside of the housing  3741 . In some embodiments, the seal  3769   a  can be, for example, a gasket, an o-ring, a rubber seal, or any suitable seal. 
     The reagent module  3740  includes the second actuator  3760 . The second actuator  3760  includes an engagement portion  3762  and a plunger portion  3764  that is movably disposed within the second reagent volume  3744 . When actuated, the engagement portion  3762  of the second actuator  3760  moves the plunger portion  3764  of the second actuator  3760  within the second reagent volume  3744 . The plunger portion  3764  of the second actuator  3760  includes a seal  3769   b  to fluidically isolate and/or prevent leakage of any reagent contained in the second reagent volume  3744 . 
     The first actuator  3750  and the second actuator  3760  can be disposed in a nested configuration in the housing  3741 . Said another way, the first actuator  3750  and the second actuator  3760  can be disposed concentrically, such that the first actuator  3750  is nested within the second actuator  3760 . In this manner, the reagent module  3740  can be coupled to the reaction chamber  3732  and/or disposed in an instrument in any angular orientation about the longitudinal axis of the container assembly  3700 . More particularly, the second actuator  3760  defines a channel  3766  within which the engagement portion  3752  of the first actuator  3750  can move when the first actuator  3750  is manipulated to move the plunger portion  3754 . Further, the engagement portion  3762  of the second actuator  3760  defines an opening  3767  within which the engagement portion  3752  of the first actuator  3750  is substantially disposed (when the reagent module  3740  is in the first configuration or the third configuration). A longitudinal axis of the plunger portion  3754  of the first actuator  3750  is offset from (i.e., non-coaxial with) a longitudinal axis of the plunger portion  3764  of the second actuator  3760 . The plunger portion  3754  of the first actuator  3750  can be moved independently of the movement of the plunger portion  3764  of the second actuator  3760 . Furthermore, the first actuator  3750  and the second actuator  3760  can be recessed inside the housing, for example, to prevent accidently actuation of the first actuator  3750  and the second actuator  3760 . 
     The first reagent volume  3742  can include the first reagent container  3780   a  and the second reagent volume  3744  can contain the second reagent container  3780   b . As shown in  FIG. 22  (which only shows the first reagent container  3780   a  for clarity), the first reagent container  3780   a  (and the second reagent container  3780   b ) includes a sidewall  3782   a  and a frangible member  3784   a , that together define an internal volume  3786   a . In some embodiments, the sidewall  3782   a  can also be frangible. The internal volume  3786   a  can be completely or partially filled with a reagent. For example, in some embodiments, the first reagent container  3780   a  can contain transduction particles (e.g., transduction particles  110 ,  160  or any other transduction particles described herein) that includes an engineered nucleic acid (e.g., engineered nucleic acid  170 ) formulated to cause the target cell (e.g., bacteria) to produce a plurality of reporter molecules. The second reagent container  3780   b  can contain a second reagent formulated react with the reporter molecules to enhance the production of a signal. For example, in some embodiments, the reagent is a substrate, such as tridecanal, that can interact with the reporter molecule (e.g., luciferase), to produce a measurable signal, e.g., via a luminescence reaction. 
     The reagent containers can be shaped and sized to be disposed substantially inside the first reagent volume  3742  and the second reagent volume  3744 . The housing  3741  include a first puncturer  3792   a  and a second puncturer  3792   b  disposed within the first reagent volume  3742  and the second reagent volume  3744 , respectively. The puncturers are configured to rupture the respective frangible portions of the first reagent containers  3780   a  and the second reagent container  3780   b  when the plunger portion  3754  and the plunger portion  3764  are displaced within the first reagent volume  3742  and the second reagent volume  3744 , respectively. In some embodiments, the reagent containers can include curved edges (see e.g., the curved edge  3789   a ) and a bottom portion (see e.g., the bottom portion  3788   a ) that can be substantially flat. The flat bottom portion and the curved edges can allow for spreading of the compressive force applied by the first actuator  3750  and the second actuator  3760  on the first reagent container  3780   a  and the second reagent container  3780   b , respectively, to ensure repeatable delivery. 
     The reagent containers can be constructed from materials that are substantially impermeable to and/or substantially chemically inert from the substance contained therein, e.g., transduction particle, substrate, antibiotics, buffers, surfactants, or any other reagent that can be required for the detection assay. In this manner, the reagents can be stored in the reagent containers for extended periods of time. For example, the side wall  3782   a  of the reagent container  3780   a  can be formed from a flexible and inert material, e.g., blister plastic, aluminum foil, aluminum laminate or any other suitable material. Moreover, in some embodiments, the frangible member  3784   a  can be constructed from a material having certain temperature characteristics such that the desired properties and integrity of the frangible member  3784   a  are maintained over a certain temperature. For example, in some embodiments, it can be desirable to store the reagent container  3780   a  containing reagent or substrate in a refrigerated condition. In some embodiments, the frangible member  3784   a  can be constructed from a polymer film, such as any form of polypropylene. In some embodiments, the frangible member  3784   a  can be constructed from bi-axially oriented polypropylene (BOP). In some embodiments, the frangible member  3784   a  can be constructed from aluminum. 
     The reaction chamber  3732  and the reagent module  3740  of the container assembly  3700  can collectively define a closed system within which target cell identification can be performed (i.e., without decoupling the reagent module  3740  from the reaction chamber  3732 ). The container assembly  3700  and/or the reagent module  3740  can be moved between multiple different configurations to transfer reagents and/or substances from the first reagent chamber  3742  and the second reagent chamber  3744 . In particular,  FIGS. 23-25  show the reagent module  3740  in a first configuration, a second configuration and a third configuration, respectively. The reaction chamber  3732  is not shown for clarity. 
     The container assembly  3700  can be delivered to the user in the first configuration ( FIG. 23 ), wherein the first actuator  3750  is in a first position and the second actuator  3760  is in a first position. The first reagent volume  3742  includes the reagent container  3780   a  containing the reagent (e.g., transduction particles), and the second reagent volume  3744  contains the second reagent container  3780   b  that includes a reagent (e.g., tridecanal, formulated to react with the reporter molecules). 
     To move the container assembly  3700  to the second configuration ( FIG. 24 ), the engagement portion  3752  of the first actuator  3750  is manipulated to displace the plunger portion  3754  of the first actuator  3750  within the first reagent volume  3742  from the first position to a second position. Similarly stated, the engagement portion  3752  moves distally within the channel  3766  and/or the opening  3767  of the second actuator  3760 . In this manner, the plunger portion  3754  of the first actuator  3750  applies a force on the bottom portion  3788   a  of the first reagent container  3780   a . This pushes the frangible portion  3784   a  of the first reagent container  3780   a  against the puncturer  3769   a , until the frangible portion  3784   a  ruptures, releasing the reagent contained therein e.g., transduction particle, into the first reagent volume  3742 . Further displacement of the plunger portion  3754  of the first actuator  3750  towards the second position decreases the internal volume  3786   a  of the reagent container  3780   a  and the first reagent volume  3742 . This communicates the reagent e.g., transduction particle from the first reagent volume  3742  through the first fluidic pathway  3772   a  and the first outlet  3774   a  of the delivery portion  3770 , and into the reaction chamber  3732 . As shown, the first actuator  3750  include a recess  3758  configured to receive a portion of the puncturer  3792   a  to prevent the puncturer from damaging the first actuator  3750  and/or from limiting the travel of the first actuator  3750  towards the second position. In some embodiments, the reagent, e.g., transduction particle can interact with the target cell contained in the sample and urge the target cell to produce the reporter molecule as described herein. 
     To move the container assembly  3700  to the third configuration ( FIG. 25 ), the engagement portion of  3762  of the second actuator  3760  is manipulated to displace the plunger portion  3764  of the second actuator  3760  from the first position to a second position within the second reagent volume  3744 . Similar to the second configuration, the displacement of the second actuator  3760  causes a puncturer  3792   b  to rupture the frangible portion  3784   b  of the second reagent container  3780   b  and communicate the substrate contained therein (e.g., tridecanal) through the second fluidic pathway  3772   b  and second outlet  3774   b  into the reaction chamber  3732 . The substrate can interact with the reporter molecules and urge, enhance and/or catalyze the reporter molecule to produce a signal, e.g., via a luminescence reaction. As shown, the second actuator  3760  include a recess  3768  configured to receive a portion of the puncturer  3792   b  to prevent the puncturer from damaging the second actuator  3760  and/or from limiting the travel of the second actuator  3760  towards the second position. In some embodiments, the reagent, e.g., transduction particles, can interact with the target cell contained in the sample and urge the target cell to produce the reporter molecule as described herein. 
     Although the exit portions of the first fluidic pathway  3772   a  and the second fluidic pathway  3772   b  are shown as being substantially linear, and having a substantially constant flow area, in other embodiments, a delivery portion can define any suitable flow pathways through which the reagents, substances, transduction particles and the like can be delivered. For example, in some embodiments, a delivery portion can be configured to deliver one or more reagents into a reaction chamber in a manner that promotes mixing, that minimizes aeration, overspray and/or undesirable turbulence. 
     For example, in some embodiments, a reagent module can be configured to deliver a substance containing transduction particles of the types shown and described herein into a reaction chamber in a manner that efficiently mixes the transduction particles with the sample. For example, in those embodiments in which a swab (such as the swab  2734 ) is retained within the reaction chamber, a reagent module can include a delivery nozzle or other mechanism for delivering transduction particles that enhances removal of portions of the sample from the swab. In this manner, the mechanism of delivery can enhance the performance of the assay by improving the mixture of the sample and the transduction particles. Such mechanisms can include, for example, high pressure jet nozzles, angled nozzles, multiple flow paths from a single reagent chamber into a reaction chamber, or the like. 
     In other embodiments, a reagent module can be configured to deliver a reagent formulated to enhance, catalyze or trigger the production of a light signal (e.g., a substrate of the types shown and described herein) into a reaction chamber in a manner that enhances the measurement of the light signal. For example, in some embodiments, a method of detecting the reporter molecules includes detecting the intensity (or strength) of a luminescence reaction triggered by the addition of a substrate into the sample in which reporter molecules have been expressed. More particularly, in some embodiments, the expressed reporter molecules and the substrate are collectively formulated to produce a flash reaction in response to the addition of the substrate to the sample. Flash reactions are luminescence reactions in which a distinct peak intensity occurs very quickly after the addition of the substrate (e.g., substantially instantaneously, within several seconds and/or less than one minute). Although flash reactions can produce very sensitive results (which are beneficial for detection of small quantities, etc.), the accurate measurement of such transient reactions can be challenging. In contrast, glow reactions are longer lasting luminescence reactions characterized by a stable signal that can be maintained for up to an hour or more. Although less sensitive than flash reactions, glow reactions can allow time for additional sample operations (e.g., mixing, transporting, or the like) to be completed before the signal is detected. 
     In some embodiments, a reagent module can be configured to deliver a substrate into a reaction chamber in a manner that enhances the measurement of the light signal. More particularly, in some embodiments, a reagent module can be configured to deliver a substrate in a manner that allows the substrate to sufficiently mix with the sample, while also minimizing aeration of the sample, the production of bubbles, excessive splashing, or the like, all of which can be detrimental to the optical detection to be completed within seconds after delivering the substrate. For example, in some embodiments, a reagent module can define a fluidic pathway that is angled with respect to a longitudinal axis of the reaction chamber, such that the reagent and/or substrate is delivered to a sidewall of the reaction chamber and then into the sample solution. In other embodiments, a reagent module can define a fluidic pathway that is substantially parallel with respect to a longitudinal axis of the reaction chamber, but that includes an exit opening positioned such that the reagent and/or substrate is delivered to a sidewall of the reaction chamber. In yet other embodiments, a reagent module can define a fluidic pathway that has a curved, arced and/or helical shape. In yet other embodiments, a reagent module can define a fluidic pathway that includes grooves, ribs, slots, or any other flow-adjusting features, to maximize mixing and/or minimize aeration. 
     As another example,  FIGS. 26-28  show a container assembly  4700  that include a reaction chamber  4732  and a reagent module  4740 . The container assembly  4700  can be used and/or manipulated by any instrument described herein, e.g., instrument  1100 ,  11000 , and/or any components described herein. The container assembly  4700  can also be used to perform any methods described herein, e.g., methods  200  and/or  300 . 
     The reagent module  4740  includes a housing  4741 , a first actuator  4750 , a second actuator  4760 , a first delivery member  4772   a  and a second delivery member  4772   b . As shown in the side cross-section view of  FIG. 28 , the housing  4741  defines a first reagent volume  4742  and a second reagent volume  4744 . The housing  4741  can also include a delivery portion  4770 . The first reagent volume  4742  can include a first reagent container  4780   a  that contains a first reagent (e.g., transduction particle). The second reagent volume  4744  can include a second reagent container  4780   b  that contains a second reagent (e.g., substrate). The housing  4741  of the container assembly  4700  can be substantially similar to the housing  3741  of the container assembly  3700  described before, and is therefore not described further in detail herein. The first reagent containers  4780   a  and the second reagent container  4780   b  are also substantially similar to the first reagent container  3780   a  and the second reagent container  3780   b , respectively, of container assembly  3700  and are therefore not described in detail herein. 
     The first actuator  4750  includes an engagement portion  4752  and a plunger portion  4754 . The second actuator  4760  includes an engagement portion  4762  and a plunger portion  4764 . The first actuator  4750  and the second actuator  4760  are substantially similar to the first actuator  3750  and second actuator  3760 , respectively, of container assembly  3700  as described before in structure and function, and are therefore not described in further herein. 
     As shown in the bottom view of the reagent module  4740  in  FIG. 27  and the side cross-section of the container assembly  4700  in  FIG. 28 , the delivery portion  4770  of the housing  4741  includes a first delivery member  4772   a  that provides a conduit for fluid communication of a reagent, e.g., transduction particle, from the first reagent volume  4742  to the reaction chamber  4732  through a first outlet  4774   a . The delivery portion  4770  of the housing  4741  includes a second delivery member  4772   b  that provides a conduit for fluid communication of a reagent, e.g., substrate, from the second reagent volume  4742  to the reaction chamber  4732  through a second outlet  4774   a.    
     As shown in  FIG. 28 , the first delivery member  4772   a  includes a first portion  4775   a  and a second portion  4776   a . The first portion  4775   a  is at least partially disposed inside the first reagent volume  4742 . The second portion  4776   a  is at least partially disposed inside the reaction chamber  4732 . The first portion  4775   a  defines a longitudinal axis that is substantially parallel to a longitudinal axis defined by the reagent module  4740  and/or the reaction chamber  4732 . The second portion  4776   a  is angularly offset from a centerline of the first portion  4775   a  such that the outlet  4774   a  points towards a sidewall of the reaction chamber  4732 . Similarly stated, the second portion  4776   a  is nonparallel to a longitudinal axis defined by the reagent module  4740  and/or the reaction chamber  4732 . In some embodiments, the angle can be between the longitudinal axis and the second portion  4776   a  can be about 15-45 degrees, inclusive of all angles therebetween. In such embodiments, the reagent and/or transduction particles conveyed from the first reagent volume  4742  into the reaction chamber  4732  does not impinge directly upon a surface of the sample, but instead is propelled onto or along the sidewall of the reaction chamber, such that it can flow at a controlled speed into the sample solution. 
     As shown in  FIG. 28 , the second delivery member  4772   b  includes a first portion  4775   b  and a second portion  4776   b . The first portion  4775   b  is at least partially disposed inside the second reagent volume  4744 . The second portion  4776   b  is at least partially disposed inside the reaction chamber  4732 . The first portion  4775   b  defines a longitudinal axis that is substantially parallel to a longitudinal axis defined by the reagent module  4740  and/or the reaction chamber  4732 . The second portion  4776   b  is angularly offset from a centerline of the first portion  4775   b , such that the outlet  4774   b  points towards a sidewall of the reaction chamber  4732 . Similarly stated, the second portion  4776   b  is nonparallel to a longitudinal axis defined by the reagent module  4740  and/or the reaction chamber  4732 . In some embodiments, the angle can be between the longitudinal axis and the second portion  4776   b  can be about 15-45 degrees, inclusive of all angles therebetween. In such embodiments, the reagent and/or substrate conveyed from the second reagent volume  4744  into the reaction chamber  4732  does not impinge directly upon a surface of the sample, but instead is propelled onto or along the sidewall of the reaction chamber, wherein it can flow at a controlled speed into the sample solution. 
     The first portion  4775   a ,  4775   b  of each of the delivery members  4772   a ,  4772   b  includes a puncturer  4792   a ,  4792   b  (respectively) at an end portion thereof. In this manner, the puncturer  4792   a  protrudes into the first reagent volume  4742 , and the puncturer  4792   b  protrudes into the second reagent volume  4744 . In particular, the end of the fluidic pathways delivery members can be tapered or chamfered to produce a sharp edge that serves as the puncturers. The puncturer  4792   a  and the puncturer  4792   b  can be used to puncture the frangible portion  4784   a  and the frangible portion  4784   b , respectively, of the reagent containers to release the reagents, transduction particles or other substances contained therein. Although the delivery member  4772   a  and the deliver member  4772   b  are shown as being constructed separately from the housing  4741 , in some embodiments, a delivery member can be integrally formed with the delivery portion  4770 , e.g., manufactured in a single manufacturing step. In some embodiments, the delivery member  4772   a  and/or the delivery member  4772   b  can be manufactured separately, and then disposed in cavity  4778   a  and cavity  4778   b , respectively of the delivery portion  4770 . 
     In some embodiments, the reagent module of the container can include or define fluidic pathways configured to communicate the reagents directly into the sample solution, and having an exit point at any suitable distance within the container. For example,  FIG. 29  shows a side cross-section view of a container assembly  5700  according to an embodiment. The container assembly  5700  includes a reaction chamber  5732  and a reagent module  5740 . The reagent module includes a housing  5741  that defines a first reagent volume  5742  and a second reagent volume  5744 . The housing  5741  contains a first actuator  5750  and a second actuator  5760 . The housing  5741  also includes a delivery portion  5770 . The container assembly  5700  can be used and/or manipulated by any instrument described herein, e.g., instrument  1100 ,  11000  and/or any components described herein. The container assembly  5700  can also be used to perform any methods described herein, e.g., methods  200  and/or  300 . 
     The first reagent volume  5742  includes a first reagent container  5780   a  that can contain a first reagent (e.g., transduction particle of the types shown and described herein). The second reagent volume  5744  includes a second reagent container  5780   b  that can contain a second reagent (e.g., substrate of the types shown and described herein). The housing  5741  of the container assembly  5700  can be substantially similar to the housing  3741  of the container assembly  3700 , and is therefore not described further in detail. The reagent containers  5780   a ,  5780   b  are substantially similar to the reagent containers  3780 ,  3780   b  of container assembly  3700  and are therefore not described in detail herein. The first actuator  5750  includes an engagement portion and a plunger portion. The second actuator  5760  includes an engagement portion and a plunger portion. The first actuator  5750  and the second actuator  5760  are substantially similar to the first actuator  3750  and second actuator  3760  of container assembly  3700 , and are therefore not described in further herein. 
     The delivery portion  5770  of the housing  5741  defines a first fluidic pathway  5772   a  that provides a conduit for fluid communication of a first reagent, e.g., transduction particles, from the first reagent volume  5742  to the reaction chamber  5732  through a first outlet  5774   a . The delivery portion  5770  of the housing  5741  also includes a second fluidic pathway  5772   b  that provides a conduit for fluid communication of a second reagent, e.g., substrate, from the second reagent volume  5744  to the reaction chamber  5732  through a second outlet  5774   b.    
     As shown, the fluidic pathways  5772   a ,  5772   b  define a longitudinal axis that is parallel to the longitudinal axis defined by the reaction chamber  5732 . This arrangement can allow the reagents to flow from the first reagent volume  5742  and the second reagent volume  5744  through the outlet  5774   a  and the outlet  577   b , respectively, and straight into a sample solution disposed in the reaction chamber  5732 . In some embodiments, a diameter of the fluidic pathway  5772   a  and/or the fluidic pathway  5772   b  at the respective outlet  5774   a  and  5774   b  can be smaller than a diameter at the interface of the fluidic pathway  5772   a  and/or the fluidic pathway  5772   b  and the first reagent volume  5742  and the second reagent volume  5744 , respectively. In this manner, the fluidic pathways  5772   a ,  5772   b  perform substantially as nozzles to accelerate the flow of the transduction particles, reagents or the like. In some embodiments, the cross-sections can be configured such that the reagents are expelled from the outlet  5774   a  and/or the outlet  5774   b  at predefined flow rate, e.g., 1 ml/sec, 2 ml/sec, 3 ml/sec, 4 ml/sec, 5 ml/sec, or any other suitable flow rate, for example, to ensure rapid and complete mixing and/or minimize aeration. In some embodiments, the fluidic pathway  5772   a  and/or the fluidic pathway  5772   b  can be configured such that the outlet  5774   a  and/or the outlet  5774   b  are disposed beneath a surface of the sample within the reaction chamber  5732 . 
     In some embodiments, the housing  5741  can include a series of puncturers  5792   a ,  5792   b  located at a base of the first reagent volume  5742  and the second reagent volume  5744 , respectively. The series of punctures can be configured to rupture the frangible portion  5784   a ,  5784   b  of the reagent container  5780   a ,  5780   b  at multiple locations, for example, to ensure efficient expulsion of the reagents contained therein. 
     In some embodiments, a reagent module of a container can include a single actuator and a single reagent volume.  FIG. 30-32  shows a side cross-section view of a container assembly  6700  according to an embodiment, in a first configuration, a second configuration and a third configuration, respectively. The container assembly  6700  includes a reaction chamber  6732  reversibly coupleable to a reagent module  6740 . The reagent module  6740  includes a housing  6741 , that defines a reagent volume  6742  that contains a first reagent container  6780   a  and a second reagent container  6780   b . The housing also includes an actuator  6750  disposed in the reagent volume  6742 , and a delivery portion  6770 . The container assembly  6700  can be used and/or manipulated by any instrument described herein, e.g., instrument  1100 ,  11000  and/or any components described herein. The container assembly  6700  can also be used to perform any methods described herein, e.g., methods  200  and/or  300 . 
     In some embodiments, the actuator  6750  can include an engagement portion  6752  and a plunger portion  6754 . The engagement portion  6752  of the actuator  6750  can be configured to move the plunger portion  6754  within the reagent volume  6742 . In some embodiments, the plunger portion  6754  of the actuator  6750  includes a fluid-tight seal  6769  to fluidically isolate the reagent volume  6742  from a volume outside of the housing  6741 . In some embodiments, the seal  6769  can be, for example, a gasket, an o-ring, a rubber seal, or any suitable seal. 
     In some embodiments, the reagent containers  6780   a ,  6780   b  can be disposed in the reagent volume  6742 , such that the first reagent container  6780   a  is proximal to the delivery portion  6770  of the housing  6741 . In particular, the first reagent container  6780   a  is disposed between the delivery portion  6770  and the second reagent container  6780   b . The first reagent container can contain a first reagent, e.g., the transduction particle. The second reagent container  6780   b  can be disposed on top of the first reagent container  6780   a , such that the frangible portion  6784   b  of the second reagent container  6780   b  abuts the bottom portion  6788   a  of the first reagent container  6780   a , and the bottom portion  6788   b  of the second reagent container  6780   b  abuts the plunger portion  6754  of the actuator  6750 . The second reagent container  6780   b  can contain a second reagent, e.g., a substrate such as tridecanal. The reagent volume  6742  can also include a series of puncturers  6792  disposed in the reagent volume  6742 , that are configured to puncture the frangible portion  6784   a  of the reagent container  6780   a , and the frangible portion  6784   b  of the reagent container  6780   b.    
     The delivery portion  6770  defines a fluidic pathway  6772  that can define a longitudinal axis that is parallel to a longitudinal axis defined by the reaction chamber  6732 . In some embodiments, a diameter of the fluidic pathway  6772  at the outlet  6774  can be smaller than a diameter of the fluidic pathway  6772  at the interface of the reagent volume  6742 , such that the fluidic pathway  6772  substantially resembles and/or performs as a nozzle. In some embodiments, the fluidic pathways can be configured such that the reagents are expelled from the outlet  6774  at predefined flow rate, e.g., 1 ml/sec, 2 ml/sec, 3 ml/sec, 4 ml/sec, 5 ml/sec, or any other suitable flow rate, for example, to ensure rapid and complete mixing and/or minimize aeration. 
     In operation, any suitable instrument can manipulate the engagement portion  6752  of the actuator  6750 , such that the plunger portion  6754  is displaced from a first position as shown in the first configuration ( FIG. 30 ) to a second position as shown in the second configuration ( FIG. 31 ) within the reagent volume  6742 . The plunger portion  6754  applies a force on the bottom portion  6788   b  of the second reagent container  6780   b , displacing the second reagent container  6780   b  from a first position to a second position. The second reagent container  6780   b  communicates the pressure applied by the plunger portion  6754  to the bottom portion  6788   a  of the first reagent container  6780   a , through the frangible portion  6784   b . The force causes the frangible portion  6784   a  of the first reagent container  6780   a  to press against the series of puncturers  6792 , such that the frangible portion  6784   a  ruptures and the reagent contained therein is communicated through the outlet  6774  of the fluidic pathways  6772  into the reaction chamber  6732 . 
     In the third configuration ( FIG. 31 ), the engagement portion  6752  of the actuator is manipulated further such that the plunger portion  6754  is displaced from the second position to a third position within the reagent volume  6742 . Displacement of the plunger portion  6754  to the third position also displaces the second reagent container  6780   b  from the second position to a third position. In this configuration, the first reagent container  6780   a  is emptied of the contents contained therein and is in a collapsed state such that the puncturer  6792  penetrates through the bottom portion  6788   a  of the first reagent container  6780   a  and ruptures the frangible portion  6784   b  of the second reagent container  6780   b . The second reagent container  6780   b  therefore is placed in fluid communication with the fluidic pathway  6772  and communicates the reagents container therein, e.g., substrate, through the outlet  6774  and into the reaction chamber  6732 . 
     In some embodiments, a container can include a single actuator with staged actuation for delivery of a first reagent (e.g., biologic or abiologic vectors, transduction particles and/or engineered viral vector) and a second reagent (e.g., a substrate) at different stages of actuation.  FIG. 33  shows an exploded view of a container assembly  7700  that includes a reaction chamber  7732  and a reagent module  7740 .  FIGS. 34-36  show the container assembly  7700  in a first configuration, a second configuration and a third configuration, respectively. The reaction chamber  7732  can be removably coupleable to the reagent module  7740 . The container assembly  7700  can be used with and/or manipulated by any of the instruments described herein, e.g., instrument  1100 ,  11000  and/or any of the components described herein. The container assembly  7700  can also be used to perform any of the methods described herein, e.g., methods  200  and  300 . 
     The reaction chamber  7732  can be formed from a light weight, rigid and inert material, e.g., plastics. At least a portion of the reaction chamber  7732  can be partially transparent, e.g., to allow detection and/or viewing of the internal volume of the reaction chamber  7732 , for example, to detect a luminescence reaction occurring therein. In some embodiments, the reaction chamber  7732  can be shaped as a cylinder with a rounded bottom, or flat base. In some embodiments, the reaction chamber  7732  can have any other suitable shape, e.g., square, rectangular, oval, polygonal, etc. In some embodiments, the reaction chamber  7732  can have a diameter of 12 mm and a height of 75 mm. In some embodiments, the container assembly  7700  can include one or more solutions/reagents (e.g., bacterial nutrient solution, buffers, surfactants, transduction particle, and/or antibiotics), predisposed within the reaction chamber  7732 . The reaction chamber  7732  can include threads  7745  for removably coupling with the reagent module  7740 . In some embodiments, the reaction chamber  7732  can be removably coupled to the reagent module  7740  via a snap-fit, friction fit, or any other suitable mechanism. 
     As shown in  FIG. 33 , the reagent module  7740  can include a housing  7741 . The housing  7741  can be formed from a lightweight and rigid material, e.g., injection molded plastic. The housing  7741  includes a first compression support  7748   a  and a second compression support  7748   b . The compression supports  7748   a ,  7748   b  are configured to fixedly or removably mount a first reagent container  7780   a  and a second reagent container  7780   b , respectively, and provide a rigid support during compression to the first reagent container  7780   a  and the second reagent container  7780   b , as described further below. The compression supports  7748   a ,  7748   b  can include features for mounting the reagent containers  7780   a ,  7780   b  thereto. Such mounting features can include, for example, notches, grooves, detents, indent, slot, and/or an adhesive surface. A surface of the each of the compression supports  7748   a ,  7748   b  on which the respective reagent container  7780   a ,  7780   b  are mounted, are angled with respect to a longitudinal axis defined by the housing  7741  and/or the reaction chamber  7732 . The angled surface can be beneficial, for example, to allow smooth (e.g., even and/or controlled) flow of the reagent and/or substrate and with low dead volume, from the reagent containers  7780   a ,  7780   b  into the reaction chamber  7732 . 
     The reagent module  7740  includes an actuator  7750 , that is configured to slide within an internal volume defined by the housing  7741 . The actuator  7750  is configured such that a sidewall of the actuator  7750  and a sidewall of the housing  7741  form a fluid-tight seal. Thus, in use, the actuator  7750  can be displaced within the housing  7741  while maintaining a substantially fluid-tight seal. As shown in  FIG. 34 , the housing  7741  and the actuator  7750  can be configured to define a first reagent volume  7742  and a second reagent volume  7744  that are separated at least partially by a sidewall  7746  ( FIG. 34-36 ), and at least partially by a sidewall of the compression supports  7748   a ,  7748   b . The actuator includes an engagement portion  7752  configured to be manipulated by an instrument, e.g., instrument  1100  or any other instrument shown and described herein. 
     The actuator  7750  includes a first compression member  7754  that can be shaped to resemble, for example, an angled clip. The first compression member  7754  can be a separate component that can be formed from a rigid material, e.g., aluminum, steel, stainless steel, or plastics. The first compression member  7754  has an engagement portion  7755  and a compression portion  7756 , that is inclined at an angle away from the longitudinal axis defined by the housing  7741 . In particular, the angle is substantially similar to the angle defined by the angled surface of the first compression support  7748   a . The first compression member  7754  also includes a sliding portion  7757  that abuts the sidewall  7746  of the actuator  7750  and is configured to slide in a space  7747  between the sidewall  7746  and the first compression support  7748   a  as described further below. The engagement portion  7755  of the first compression member  7754  can include an engagement spring  7758  coupled to the engagement portion  7755 . The engagement spring  7758  can be a compression spring, for example, a helical spring, coil spring, Belleville spring, or tapered spring and can include washers (not shown) for mounting on the engagement portion  7755 . An end of the engagement spring  7758  distal to the first compression member  7754  can be coupled to the actuator  7750 , for example, mounted on a pin, mandrel, or the likes, further configured such that engaging the actuator  7750 , engages the engagement spring  7758  and the first compression member  7754 . 
     The actuator  7750  can also include a second compression member  7760  that can be an integral part of the actuator  7750 , for example, formed in the same injection molded process. The second compression member  7760  can be shaped to resemble an inclined plane that is angled away from the longitudinal axis defined by the housing  7741 . The angle can be substantially similar to the angle defined by the inclined surface of the second compression support  7748   b . In some embodiments, the first compression member  7754  and/or the second compression member  7760  can include one or a series of puncturers, e.g., thorns, barbs, pins, or any other suitable puncturing member to puncture a frangible portion of the reagent containers  7780   a ,  7780   b , as described herein. 
     The housing  7741  can also include a first fluidic outlet  7774   a  and a second fluid outlet  7774   b  for communicating reagents from the first reagent volume  7742 , e.g., the biologic or abiologic vectors, transduction particle and/or engineered viral vector, and the second reagent volume  7744  e.g., substrate, into the reaction chamber  7732 . The fluidic outlets  7774   a ,  7774   b  can be an opening and/or space between the compression supports  7748   a ,  7748   b  and a sidewall of the housing  7741 . In some embodiments, the housing  7741  can include fluidic pathways, e.g., nozzles, angled nozzles, tubes, and/or any other suitable fluid conduit, e.g., to facilitate rapid mixing and/or minimize aeration, as described herein. 
     The first reagent container  7780   a  and the second reagent container  7780   b  can be disposed on the first compression support  7748   a  and the second compression support  7748   b , respectively as described before. The reagent containers  7780   a ,  7780   b  can each include a sidewall  7782   a ,  7782   b  and a frangible member  7784   a ,  7784   b  that collectively define an internal volume. The internal volume of the reagent containers can be completely or partially filled with a reagent, e.g., the first reagent container  7780   a  can contain transduction particles (e.g., transduction particle  160  or any other transduction particles described herein), that can include an engineered nucleic acid (e.g., engineered nucleic acid  170 ) formulated to cause the target cell (e.g., bacteria) to produce a plurality or reporter molecules (e.g., luciferase). The second reagent container  7780   b  can contain a substrate, e.g., tridecanal, that can interact with the reporter molecule, e.g., luciferase, to trigger, catalyze, produce and/or enhance the production of a measurable signal, e.g., via a luminescence reaction. 
     The reagent containers  7780   a/b  can be constructed from materials that are substantially impermeable to and/or substantially chemically inert from the substance contained therein, e.g., transduction particle, substrate, antibiotics, buffers, surfactants, or any other reagent that can be required for the detection assay. In this manner, the reagents can be stored in the reagent containers  7780   a/b  for extended periods of time. For example, the reagent containers  7780   a/b  side wall  7782   a/b  can be formed from a flexible and inert material, e.g., blister plastic, aluminum foil, or any other suitable material. Moreover, in some embodiments, the frangible member  7784   a/b  can be constructed from a material having certain temperature characteristics such that the desired properties and integrity of the frangible member  7784   a/b  are maintained over a certain temperature. For example, in some embodiments, it can be desirable to store the reagent container  7780   a/b  containing reagent or substrate in a refrigerated condition or it can be desirable to manufacture the reagent container  7780   a/b  by thermally laminating the frangible member  7784   a/b . In such embodiments, the frangible member  7784   a/b  can be selected such that the refrigeration condition and/or thermal lamination condition do not substantially degrade the desired properties and integrity of the frangible member  7784   a/b  for the intended application. In some embodiments, the frangible member  7784   a/b  can be constructed from a polymer film, such as any form of polypropylene. In some embodiments, the frangible member  7784   a/b  can be constructed from bi-axially oriented polypropylene (BOP). In some embodiments, the frangible member  7784   a/b  can be constructed from aluminum. The frangible portions  7784   a/b  of the reagent containers can be configured to rupture when compressed, e.g., by the compression members  7754 / 7760  of the actuator  7750  as described further below, and release the reagent contained therein. 
     As shown in  FIG. 34  the container assembly  7700  can initially be maintained in a first configuration, in which the reagent module  7740  is coupled to the reaction chamber  7732 , and the actuator  7750  is in a first position. The first compression member  7754  is in a first position, in which the engagement portion  7756  is in contact with the frangible portion  7784   a  of the first reagent container  7780   a  but not applying any compressive force, and the engagement spring  7758  is fully uncompressed. The second compression member  7760  is also in a first position wherein the second compression member is not contacting the frangible portion  7784   b  of the second reagent container  7780   b.    
     In the second configuration ( FIG. 35 ), the engagement portion  7752  of the first actuator  7750  is manipulated to displace the actuator  7750  within the housing  7741  from the first position, to a second position. The displacement of the actuator  7750  urges the engagement spring  7758  to compress and exert a force on the first compression member  7754 . The force displaces the first compression member  7754 , from the first position to a second position as shown in  FIG. 35 , wherein the sliding portion  7757  of the first compression member  7754  slides with the sidewall  7746  into the opening  7747  between the first and second compression supports  7748   a ,  7748   b . The engagement portion  7756  of the first compression member  7754  exerts a compressive force on the frangible portion  7784   a  of the first reagent container  7780   a , such that the frangible portion  7784   a  ruptures, releasing its contents (e.g., transduction particles) into the first reagent volume  7742 . The reagent then flows through the first outlet  7774   a  and into a solution in the reaction chamber  7732 , e.g., a patient sample containing target cell. The second compression member  7760  is also displaced from the first position to a second position, wherein it is near the frangible portion  7784   b  of the second reagent container  7780   b  and/or contacting the frangible portion  7784   b  without rupturing it. 
     In the third configuration ( FIG. 36 ), the engagement portion  7752  of the actuator  7750  is manipulated to displace within the housing  7741  from the second position to a third position. The displacement of the actuator  7750  further urges the engagement spring  7758  to compress and exert a force on the first compression member  7754 . In this position further displacement of the first compression member  7754  is prevented by the first compression support  7748   a , and the engagement spring  7758  is substantially compressed. The second compression member  7760  is also displaced from the second position to a third position, wherein the second compression member  7760  exerts a compressive force on the frangible portion  7784   b  of the second reagent container  7780   b . This causes the frangible portion  7784   b  to rupture and release its contents, e.g., substrate into the second reagent volume  7744 . The reagent then flows through the second outlet  7774   b  and into a solution in the reaction chamber  7732 , e.g., a sample containing target cell and reporter molecules produced by the target cells. 
     As described above, in some embodiments, a delivery portion can be configured to deliver one or more reagents into a reaction chamber in a manner that promotes mixing, that minimizes aeration, overspray and/or undesirable turbulence. For example, in some embodiments, a reagent module of a container can include a delivery portion that is inclined and/or angularly offset with respect to a longitudinal axis of the reagent module and/or the reaction chamber. Such an arrangement can direct a flow of reagent (e.g., transduction particles, substrate or the like) in a manner that improves mixing, detection or the like. In particular,  FIGS. 37-38  show a side cross-sectional schematic view of a container assembly  8700  according to an embodiment, in a first configuration and a second configuration, respectively. The container assembly  8700  can be used with and/or manipulated by any of the instruments described herein, e.g., instrument  1100 ,  11000  and/or any of the components described herein. The container assembly  8700  can also be used to perform any of the methods described herein, e.g., methods  150 ,  200  and  300 . 
     The container assembly  8700  includes a reaction chamber  8732  that is reversibly coupleable to a reagent module  8740 . The reaction chamber  8732  can have a sample S disposed therein, e.g., a sample solution including a patient sample, target cell, transduction particles, and/or reporter molecules. In use, the container assembly  8700  can be operatively coupled to a detector  1200  such that reaction chamber  8732  is in communication (e.g., optical communication) with the detector  1200 . Although the embodiments described herein have been shown as being optically coupled to the detector  1200 , any other detector described herein can be used. 
     The reagent module  8740  includes a housing  8741 , a delivery member  8770  and an actuator  8750 . The housing  8741  defines a reagent volume  8742 , which can contain a reagent disposed therein. The reagent can be any suitable reagent, such as any of the substrates described herein. 
     The actuator  8750  includes a plunger portion  8754  configured to be in fluid communication with the reagent disposed in the reagent volume  8742 . The actuator  8750  can be configured to convey the reagent from the reagent volume  8742  to the reaction chamber  8732  through the delivery member  8770  (e.g., via a fluidic pathway  8772 ). The delivery member  8770  includes a first portion  8774  that is disposed substantially inside the reagent volume  8742  and proximal to the plunger. The delivery member  8770  also includes a second portion  8776  disposed substantially inside the reaction chamber  8732 , when the reaction chamber  8732  is coupled to the reagent module  8740 . 
     The delivery member  8770  is angularly offset with respect to a longitudinal axis of the reagent module  8740  and/or the reaction chamber  8732 . More particularly, as shown in  FIG. 37 , the centerline of the fluidic pathway that defines the axis of the delivery member  8770  is oriented at an angle θ away from the longitudinal axis. In some embodiments, the angle θ can be about 30 degrees. In some embodiment, the angle θ can be between about 15-45 degrees. 
     In operation, the actuator  8750  can be manipulated by applying a force on the actuator  8750  as shown by the arrow AA in  FIG. 38 , e.g., using a manipulation mechanism of the instrument  1100 . This urges the plunger portion  8754  to be displaced within the reagent volume  8742  from a first position, as shown in the first configuration ( FIG. 37 ), to a second position as shown in the second configuration ( FIG. 38 ). The plunger portion  8754  conveys and/or expels the reagent (e.g., substrate) contained in the reagent volume  8742  through the fluidic pathway  8772 . Similarly stated, the plunger portion  8754  is moved within the reagent volume along the longitudinal axis to produce a flow of a reagent from the reagent volume via the fluidic pathway  8772 . 
     As shown in the  FIG. 38 , the inclined orientation of the delivery portion  8770  causes the expelled reagent to follow an inclined path as shown by arrow BB ( FIG. 38 ), such that the reagent stream impinges on a sidewall of the reaction chamber  8732 . The reagent stream then flows down the sidewall of the reaction chamber  8732  as shown by arrow CC ( FIG. 38 ) and mixes with the sample S at a lower fluid velocity, thereby minimizing and/or eliminating aeration and/or the production of bubbles within the sample. Minimizing aeration can, enable mixing of the reagent with the sample S and increase the quality of the signal that is detected by the detector  1200 . For example, in some embodiments, the container assembly  8700  can be used in conjunction with a reporter system and reagent (e.g., substrate) that are collectively formulated to produce a flash reaction in response to the addition of the substrate to the sample within which reporter molecules have been expressed. In such embodiments, the arrangement of the delivery member  8770  can allow the substrate to sufficiently mix with the sample, while also minimizing aeration of the sample, the production of bubbles, excessive splashing, or the like, all of which can be detrimental to the optical detection to be completed a short time period (e.g., within seconds) after delivering the substrate. 
     Although the reagent module  8740  is shown and described above as including a single delivery member that directs the flow of a reagent along a portion of a side wall of the reaction chamber  8732 , in other embodiments, a reagent module  8740  can include multiple different delivery members and/or a delivery member with multiple exit points to facilitate rapid delivery of the reagent therein, while also minimizing aeration, the production of bubbles or the like. In some embodiments, a reagent module of a container can include a delivery member that is configured to produce an annular flow of a reagent disposed in the reagent module, such that the reagent flows substantially circumferentially about the sidewall of the reaction chamber. For example,  FIGS. 39-40  show a side cross-sectional view of a container assembly  9700  according to an embodiment, in a first configuration and a second configuration. The container assembly  9700  includes a reaction chamber  9732  reversibly coupleable to a reagent module  9740 . The container assembly  9700  is coupled to a detector  1200  such that reaction chamber  9732  is in optical communication with the detector  1200 . The container assembly  9700  can be used and/or manipulated by any instrument described herein, e.g., instrument  1100 ,  11000  and/or any components described herein. The container assembly  9700  can also be used to perform any methods described herein, e.g., methods  150 ,  200  and/or  300 . In some embodiments, the container assembly  9700  can be used to detect a signal produced by a flash luminescence reaction. While the embodiments described herein have been shown optically coupled to the detector  1200 , any other detector described herein can be used. 
     The reaction chamber  9732  can have a sample S disposed therein, e.g., a sample solution including a patient sample, target cell, transduction particles, and/or reporter molecules. The reaction chamber  9732  can be similar to any of the reaction chambers described herein, and is therefore not described in detail. 
     The reagent module  9740  includes a housing  9741  defining a reagent volume  9742 , which can have a reagent disposed therein, e.g., a substrate. The housing  9741  also includes an actuator  9750  disposed in the reagent volume  9742 . The reagent module  9740  includes a frangible portion  9784  and a delivery member  9770 . 
     The actuator  9750  includes a plunger portion  9754  in fluid communication with the reagent disposed in the reagent volume  9742 . The plunger portion  9754  is configured to move within the housing  9741  to convey the reagent from the reagent volume  9742  to the reaction chamber  9732  through the frangible portion  9784 . 
     The delivery member  9770  is configured to define a puncturing portion  9772  and a rounded and/or curved sidewall  9774 . In some embodiments, the sidewalls  9774  can be tapered, contoured, and/or include gradations. Although the delivery portion  9770  is shown as being located substantially inside the reaction chamber  9732 , in other embodiments, a substantial portion of the delivery member  9770  can be disposed within and/or coupled to the reagent module  9740 . The delivery member  9770  can be an integral part of either the reaction chamber  9732  or the reagent module  9740 . 
     As shown, when the reagent module  9740  is in the first configuration ( FIG. 39 ), the puncturing portion  9772  is in contact with the frangible portion  9784  but is not applying any puncturing force on the frangible member  9784 . Accordingly, the reagent within the reagent volume  9742  is maintained in fluidic isolation from the reaction chamber  9732 . When the reagent module  9740  is moved to the second configuration ( FIG. 40 ), a force is applied on the actuator  9750  in a direction as indicated by arrow DD. This causes the plunger portion  9754  to displace from the first position to a second position. The displacement of the plunger portion  9754  exerts a force on the frangible member  9784  (via the reagent). This causes the frangible member to press against the puncturing portion  9772  of the delivery portion and puncture ( FIG. 40 ), thereby puncturing the frangible portion  9784 . The contour and/or shape of the delivery member  9770  produces an annular flow of the reagent around the entire sidewall  9774  of the reaction chamber  9732 , as shown by arrow EE. The reagent stream can then flow down along a sidewall of the reaction chamber  9732 , thereby minimizing and/or eliminating aeration, the production of bubbles or the like. 
     In some embodiments, a reagent module of a container can include a delivery portion or delivery member that is curved.  FIG. 41  shows a side cross-section of a container assembly  10700  according to an embodiment. The container assembly  10700  includes a reaction chamber  10732  reversibly coupleable to a reagent module  10740 . The reagent module  10740  includes a housing  10741  defining a reagent volume  10742 , which can have a reagent disposed therein, e.g., a substrate. The housing also includes an actuator  10750  disposed in the reagent volume  10742 . The container assembly  10700  includes a delivery member  10770 . The container assembly  10700  can be used and/or manipulated by any instrument described herein, e.g., instrument  1100 ,  11000  and/or any components described herein. The container assembly  10700  can also be used to perform any methods described herein, e.g., methods  150 ,  200  and/or  300 . In some embodiments, the container assembly  10700  can be used to detect a signal produced by a flash luminescence reaction. 
     The actuator  10750  includes a plunger portion in fluid communication with the reagent, e.g., a substrate, disposed in the reagent volume  10742 . The plunger portion  10754  is configured to displace within the reagent volume  10742  to convey the reagent from the reagent volume  10742  to the reaction chamber  10732  through the delivery portion  10770   
     The delivery member  10770  is shaped such that it defines a curved fluidic pathway  10772 . The curved fluidic pathway  10772  is configured such that the reagent is dispensed from the fluidic pathway in a swirling motion. The swirling motion can, for example, create turbulence in the reagent flow that can, for example, enhance mixing of the reagent with a sample contained in the reaction chamber  10732 . In some embodiments, the curved fluidic pathways  10772  can cause the reagent to impinge on a sidewall of the reaction chamber. The reagent can then flow along the sidewall of the container to reach the sample at a lower velocity, for example, to minimize aeration. 
     The container assembly  4700  or any of the container assemblies described herein, can be operably coupled to a detector of any suitable type to detect a signal produced and/or enhanced by the interaction of a reporter molecule (e.g., luciferase) with a substrate (e.g., tridecanal). As described above, in some embodiments, methods of detection can include detection of a signal produced by a flash luminescence reaction. Such methods can include, for example, directing a flow of a reagent (e.g., substrate) in a manner to enhance the accuracy with which the signal is read. Similarly stated, such methods can include, for example, directing a flow of a reagent (e.g., substrate) in a manner to minimize undesirable turbulence, aeration, the production of bubbles or the like. For example,  FIG. 42  shows a method  400  for detecting target cells using a container assembly and a detector. The method  400  can be used with any of the container assemblies described herein. The detector can be the detector  1200 , the detector assembly  11200 , or any other detector described herein. A reaction chamber of the container assembly can include a sample disposed therein. The sample can be, for example, a sample solution containing a patient sample target cell (e.g., a nasal swab potentially containing MRSA), biologic or abiologic vector such as a transduction particle (e.g., any of the transduction particles described herein), and a series of reporter molecules produced in accordance with any of the reporter systems disclosed herein. 
     The method includes operably coupling the reaction chamber of the container to a detector,  402 . A reagent is then communicated into the reaction chamber using a delivery member,  404 . In some embodiments, the reagent can be any suitable substrate. In some embodiments, the reagent can include a 6-carbon aldehyde (hexanal), a 13-carbon aldehyde (tridecanal) and/or a 14-carbon aldehyde (tetradecanal), inclusive of all the varying carbon chain length aldehydes therebetween. In some embodiments, the reagent can be formulated to include Tween 20 or any other surfactant, tridecanal or other aldehydes, and adjusted to a particular pH. The reagent can be disposed in a reagent module of the container, e.g., a reagent module  4740  of the container assembly  4700 , or any other reagent module as described herein. 
     The delivery member can be, for example, the delivery portion  3770 , the delivery member  4770 , or any other structure and/or mechanism that defines a flow path through which the reagent can be conveyed. The reagent is conveyed in a manner to flow along a surface of the reaction chamber and into the sample,  406 . In this manner, as described herein, the delivery of the reagent into the sample can be performed in a manner that enhances the accuracy with which the signal is read. In some embodiments, the conveying can include conveying the reagent in a direction non-perpendicular to a surface of the sample. In some embodiments, the reagent is conveyed at a flow rate of at least one milliliter per second. In some embodiments, the conveying includes moving a plunger in a direction within a reagent volume, a first end portion of the delivery member disposed within the reagent volume and a second end portion of the delivery member disposed within the reaction chamber. In some embodiments, the movement of the delivery member conveys the member in an exit direction non-parallel to the direction, e.g., the delivery portion  4770 . 
     On reaching the sample, the reagent reacts with the series of reporter molecules and produces a signal,  408 . The production of the reporter molecules can be in accordance with any of the systems, compositions and methods described herein. The signal is received via the detector,  410 . The signal can be used, for example, to determine a viable cell and/or to report a gene present within a target cell in the sample. In some embodiments, the receiving of the signal is performed for less than 60 seconds after the conveying of the reagent. 
     Any of the container assemblies described herein can be manipulated, handled and/or actuated by any suitable instrument to perform an identification and/or detection process on a sample contained within the container assembly in accordance with any of the methods disclosed herein. For example, in some embodiments, any of the container assemblies described herein can be manipulated and/or actuated by an instrument to perform viable cell reporting and/or gene reporting of a target cell within a sample using biologic or abiologic vectors such as transduction particles methods and/or reporter systems of the types shown and described herein. In this manner, a system (e.g., the container or a series of container, the transduction particles, reagents and other compositions, and an instrument) can be used for many different assays, such as, for example, the rapid and/or automated detection of MRSA,  C. difficile , Vancomycin resistant Enterococci, etc. In some embodiments, an instrument can also be configured to facilitate, produce, support and/or promote a reaction in a sample contained in a container and or series of containers of the types shown and described herein. Such reactions can include, for example, interaction and/or mixing of a transduction particles (e.g., any of the transduction particles described herein) with a sample, interaction and/or mixing of a reporter molecule (e.g., luciferase) with a substrate (e.g., tridecanal). Such reactions can, in accordance with the methods described herein, produce a signal, e.g., via a luminescence reaction, that can be detected by components included in the instruments described herein. 
     In some embodiment, a system can include an instrument including various subassemblies and configured to manipulate a container, actuate an actuation mechanism of a container, maintain a container and/or detect a signal produced in the container. For examples  FIGS. 43-45  show a portion of an instrument  1100  in a first configuration, a second configuration and a third configuration, respectively. The instrument  1100  is configured to receive a container, e.g., container  11700 , that can include a sample disposed therein, and can further be configured to manipulate the container  11700  and detect a signal produced therein, e.g., via a luminescence reaction. The container  11732  defines a reagent volume  11742  and a reaction volume  11732 . The instrument  1100  includes a housing  1110  that defines an internal volume that contains and/or supports a detector  1212 , a retention member  1610 , an activation member  1636  and an actuator  1652 . While shown as receiving container  11700 , the instrument  1100  can be configured to receive any container assembly described herein, and can be used to perform any methods described herein, e.g., method  150 ,  200 ,  300  or  400 . 
     As shown, the retention member  1610  is configured to contact a first portion  11733  of a sample container  11700  disposed in the instrument  1100  to limit movement of the container  11700 . Similarly stated, the retention member  1610  is configured to contact the sample container  11700  to limit movement lateral movement and/or rotation of the sample container  11700  relative to portions of the instrument  1100  (e.g., the detector  1212 ). In some embodiments, the retention member  1610  can be configured to limit periodic movement (e.g., vibration) of the sample container  11700 . 
     The activation member  1636  is coupled to the actuator  1652  and is also movably coupled to the retention member  1610 . The activation member  1636  is configured to engage a second portion  11752  of the container  11700  to convey a reagent, e.g., substrate (e.g., tridecanal) from the reagent volume  11742  into the reaction volume  11732 . The actuator  1652  is configured to move the activation member  1636  between a first position ( FIG. 43 ), a second position ( FIG. 44 ) and a third position ( FIG. 45 ). Similarly stated, the actuator  1652  is configured to move the activation member  1636  relative to the instrument  1100  and/or the retention member  1610 . 
     When the activation member  1636  is in the first position, the retention member  1610  is spaced apart from the first portion  11733  of the container  11700  and the activation member  1636  is spaced apart from the second portion  11752  of the container  11700 . In this manner, the container  11700  can be moved relative to the detector  1212  (e.g., to position the container or the like. When the activation member  1636  is in the second position ( FIG. 44 ) the retention member  1610  is configured to contact the first portion  11733  of the container  11700 . In this manner, movement of the sample container  11700  relative to portions of the instrument  1100 , such as the detector is limited. Furthermore, the activation member  1636  remains spaced apart from the second portion  11752  of the container  11700  in the second configuration. As shown in  FIG. 45 , when the assembly is moved to the second configuration, an engagement surface  1620  of the retention member  1610  is in contact with a corresponding surface  1644  included in the activation member  1636 . The surface  1644  is shaped and/or configured to urge the engagement surface  1612  of the retention member  1610  to contact the first portion  11733  of the container  11700 . 
     More particularly, as shown in  FIG. 44 , when the assembly is moved to the second configuration, the actuator  1652  moves the activation member  1636  in a first direction (shown by the arrow AA) defined by the longitudinal axis A L  of the container  11700 . The engagement of the engagement surface  1620  of the retention member  1610  and the corresponding surface  1644  of the activation member  1636  causes the retention member  1610  to move in a second direction, as shown by the arrow BB in  FIG. 44 . Similarly stated, the activation member  1636  engages the retention member  1610  to move the retention member  1610  in a direction perpendicular to the longitudinal axis A L  and towards the container  11700 . 
     As shown in  FIG. 44 , in the second configuration (when the activation member  1636  is in the second position), the container  11700  is disposed in the housing  1110  and/or in contact with a portion of the housing  1110  such that the container  11700  is separated from the detector  1212  by the distance d. The distance d defines the signal path length (e.g., optical path length) to be maintained during detection. Moreover, the retention member  1610  maintains the container  11700  in contact with a portion of the housing  1110  such that lateral movement, sideways wobble or vertical motion of the container  11700  is limited and/or eliminated (see, e.g., the arrow CC). Maintaining a consistent and repeatable signal path length can result in a repeatable and high quality measurement of the signal produced in the reaction volume of the container  11700 . In some embodiments, the instrument  1100  can be used in conjunction with any of the methods described herein to detect a signal produced by a flash luminescence reaction. 
     When the activation member  1636  is in the third position (corresponding to a third configuration), the activation member  1636  is engaged with the second portion  11752  of the container  11700  to convey the reagent from the reagent volume  11742  to the reaction volume  11732 , as shown by the arrow DD in  FIG. 45 . In some embodiments, the activation member  1636  can include a plunger portion configured to engage the container  11700  and move within the reagent volume  11742  of the container  11700 , when the activation member  1636  moves from the first position to the second position. More particularly, when moved to the third configuration ( FIG. 45 ), the actuator  1652  moves the activation member  1636  further along the direction shown by arrow AA, such that a plunger portion of the activation member  1636  contacts an engagement portion  11752  of the container  11700  and then moves into the reagent volume  11743 . As the activation member  1636  moves from its second position to its third position (i.e., within the reagent volume  11742 ), it conveys the reagent contained therein, e.g., substrate such as tridecanal, into the reaction volume  11732 . The reagent flows into the sample S and interacts with the sample S to produce a signal that can be detected by the detector  1212 . For example, the reagent can be tridecanal that interacts with the reporter molecule luciferase present in the sample solution. The interaction produces luminescence which is detected by the detector  1212  which can be, e.g., a photodetector. 
     When the assembly is moved from the second configuration to the third configuration, the retention member  1610  remains in contact with the first portion  11733  of the container  11700  in the third configuration. In this manner, the reagent, which can be, for example, a substrate, can be added to the sample when the container is in a fixed position relative to the detector  1212 . As discussed above, this arrangement facilitates repeatable measurement of the signal. 
     In some embodiments, the instrument  1100  can also include a second activation member (not shown) which can be configured to engage a third portion of the sample container  11700 , e.g., to convey a second reagent e.g., transduction particle, from the second reagent volume into the reaction volume. The second activation member can be movably coupled to the first activation member  1636 , and can be configured to contact the third portion of the container  11700  when the activation member  1636  is in the first position (i.e., the assembly is in the first configuration). Thus, in such embodiments, when the assembly is in the first configuration the second activation member can be moved (e.g., by a second actuator) to convey a second reagent. 
     In some embodiments, at least a portion of the second activation member can be movably disposed within the first activation member  1636 . In some embodiments, the retention member  1610  can also be configured to rotate when the activation member  1636  is displaced from the first position to the second position. 
     In some embodiments, a portion of an instrument  2100  can include a retention assembly that can include a series of grippers to manipulate and/or actuate a container of the types shown and described herein. For example, referring now to  FIGS. 46-48 , an instrument  2100  includes a detector  2212 , a retention assembly  2610 , an instrument  2100 , an activation member  2636  and an actuator  2652 . The instrument  2100  includes the container assembly  11700 , which is described herein with reference to  FIGS. 43-45 . The instrument  2100  can, however, be used to receive and/or manipulate any other container described herein, and can be used to perform any methods described herein, e.g., methods  150 ,  200 ,  300  or  400 . 
     As shown in  FIGS. 43-45 , the retention assembly  2610  includes a first gripper  2612   a  and a second gripper  2612   b  each configured to contact a first portion  11733  of the container  11700  to limit movement of the container  11700 . In this manner the retention assembly, among other functions, can facilitate repeatable detection as described before with reference to  FIGS. 43-45 . Each gripper is coupled to a biasing member  2622 , e.g., a spring, configured to exert a force on the corresponding grippers  2612   a ,  2612   b  to urge the grippers towards a closed configuration. 
     The activation member  2636  is movably coupled to the retention assembly  2610 , and is operably coupled to the actuator  2652 . The actuator  2652  is configured to move the activation member  2636  relative to the retention assembly  2610  and/or the container  11700  between a first position and a second position. The activation member includes a first surface  2642  configured to contact with a surface of the retention assembly  2610  to maintain the first gripper  2612   a  and the second gripper  2612   b  in an opened configuration when the activation member  2636  is in the first position. For example,  FIG. 46  shows the instrument  2100  in the first configuration such that the activation member  2636  is in the first position and the surface  2642  of the activation member  2636  is in contact with the retention assembly  2610 , thereby maintaining grippers  2612   a ,  2612   b  in the open configuration. 
     In the second position, a second surface  2644  of the activation member  2636  is configured to contact the surface of the retention assembly  2610  such that the biasing member  2622  urges the first gripper  2612   a  and the second gripper  2612   b  into a closed configuration. More particularly, when moving towards the second configuration ( FIG. 47 ), the actuator  2652  moves the activation member  2636  from its first position to its second position along a longitudinal axis B L  of the container  11700  in the direction shown by arrow FF. This motion of the activation member  2636  causes the retention assembly  2610  to be in contact with the second surface  2644  of the activation member  2636 . In this position, the biasing members  2622  urge the gripper  2612   a ,  2612   b  to move in a second direction as shown by the arrow EE such that the grippers  2612   a ,  2612   b  contact the first portion  11733  of the container  11700 . In some embodiments, the movement of the activation member  2636  from the first position to the second position can also cause the grippers to rotate towards the container  11700 . 
     The activation member  2636  is configured to engage a second portion  11752  of the container  11700  and convey a reagent, e.g., substrate such as tridecanal, from the reagent volume  11742  into the reaction chamber  11732 . More particularly, when moving towards the third configuration, as shown in  FIG. 48 , the actuator  2652  can continue to move the activation member  2636  in the direction shown by the arrow FF, until the plunger portion  2638  of the activation member  2636  contacts a second portion  11752  of the container  11700 , and moves from a first position to a second position within the reagent volume  11742  of the container  11700 . The plunger portion  2638  can therefore communicate the reagent disposed in the reagent volume e.g., substrate such as tridecanal, into the reaction volume  11732 . The substrate can react with reporter molecules, e.g., luciferase, included in the sample S disposed in the reaction volume  11732  to produce a signal, e.g., luminescence that can be detected by the detector  2212 . 
     As shown, the grippers  2612   a ,  2612   b  remain in contact with and otherwise engage, grasp, clamp or secure the container  11700  in the third configuration. This prevents lateral movement, sideway wobble or vertical motion of the container  11700  as shown by arrow GG, and maintains a consistent signal path length d from the detector  2212 , as described above. As shown, the retention and the actuation (e.g., the plunging) of the container assembly  11700  is accomplished using a single actuator, and with the retention assembly  2610  and the activation member  2636  cooperatively configured such that the reagent cannot be conveyed into the sample container  11700  unless the sample container  11700  is in the desired position for the detection operation. 
     In some embodiments, an instrument can include a detector assembly that can include a housing for receiving a sample container and a shutter configured to minimize background light, facilitate calibration of the signal detection or the like. For example, as shown in  FIGS. 49-50 , an instrument can include detector assembly  3200 . The detector assembly  3200  includes a housing  3202 , a detector  3212  and a shutter  3230 . The detector assembly  3200  is configured to receive a container  12700  to analyze a signal produced therein. Such signals can be produced by any of the methods described herein, such as, for example, resulting from the interaction of a substrate and a reporter molecule. In some embodiments, the signal can be produced by a flash luminescence reaction. The detector assembly  3200  can be configured to receive any other container, e.g., container  1700  or any other container described herein, and can be used to perform any method described herein, e.g., method  150 ,  200 ,  300  or  400 . 
     As shown, the housing  3202  defines a channel  3209  and a detection volume  3234 . The channel  3209  is configured to receive the container  12700 , or any other container. The detection volume  3234  is configured to place the channel  3209  in communication with the detector  3212 . The housing  3202  further includes a first seal surface  3206  and a second seal surface  3207 . In use, a first portion  12733  of the container  12700  and the first seal surface  12733  isolate the detection volume  3234  from a volume outside the housing  3202  when a second portion  12732  of the container  12700  is disposed within the detection volume  3234  (see e.g.,  FIG. 50 ). In this manner, the first portion  12733  of the container  12700  and the first seal surface  12733  can eliminate and/or limit the amount of background noise (e.g., ambient light) within the detection volume  3234  when the container  12700  is positioned within the channel  3209  for detection of the sample contained therein. 
     The shutter  3230  is disposed within the housing  3209 . The shutter  3230  is movable between a first shutter position ( FIG. 49 ) and a second shutter position ( FIG. 50 ). When the shutter is in the first shutter position (i.e., a first configuration of the assembly), the shutter  3230  is in the first position such that the second seal surface  3207  of the housing  3202  and a seal surface  3231  of the shutter are in contact and isolate the detection volume  3234  from the channel  3209 . In some embodiments, the first seal surface  3206  can be a gasket. In this manner, when in the first configuration, no background signal, e.g., light, can enter the detection volume  3232 . Thus, when in the first configuration, the detector  3212  can be calibrated and/or background signals can be detected for later use in processing the signal data. 
     As shown in  FIG. 50 , the shutter  3230  can be moved to a second shutter position such that the channel  3209  of the housing  3202  is in communication with the detection volume  3234 . When the shutter is in the second shutter position, the channel  3209  of the housing  3202  is in communication with the detection volume  3234 . More particularly, in some embodiments, the shutter  3230  includes an activation surface configured to be engaged by the second portion  12735  of the container  12700  such that shutter  3230  can be moved from the first position to the second position ( FIG. 50 ) when the container  12700  is moved within the channel  3209 . In this manner, when the second portion  12735  of the container  12700  is placed into communication with the detection volume  3234 , the shutter  3230  is moved. Said another way, in some embodiments, the shutter  3230  can be in the first shutter position when the second end portion  12735  of the container  12700  is within the channel  3209  outside of the detection volume  3234 , and the shutter  3230  can be in the second shutter position, when the second end portion  12735  of the container  12700  is disposed within the detection volume  3234 . 
     As shown in  FIG. 49 , the container  12700  can be moved from the first position downward (or distally) into the channel  3209  such that the second end portion  12735  of the container  12700  contacts the shutter  3230  to urge the shutter  3230  from the first shutter position to the second shutter position, as shown by the arrow GG. In some embodiments, the shutter  3230  can include a ramp configured to engage the second portion  12735  of the container  12700  when the second portion  12735  of the container  12700  moves within the channel  3209  towards detection volume  3234  to move the shutter  3230  towards the second shutter position. 
     In some embodiments, the shutter  3230  can be configured to translate within the housing  3202  in a direction offset a longitudinal axis of the channel  3209 . In some embodiments, the detector assembly  2200  can also include a biasing member configured to urge the shutter  3230  towards the first shutter position. 
     In some embodiments, the shutter  3230  can define a calibration port (not shown). When the shutter  3230  is in the first position, the calibration port can be aligned and/or configured place a calibration light source in communication with the detection volume  3234  e.g., to calibrate the detector  3212 . When the shutter  3230  is in the second position, the calibration port can be isolated from the detection volume  3234 , thereby preventing any signal leakage from the detection volume and/or ambient light from entering the detection volume. 
     In some embodiments, a detector assembly, e.g., the detector assembly  3200  or any other detector assembly described herein, can include a housing defining a channel configured to receive a sample container. The housing can also define a seal surface and detection volume configured to place the channel in communication with a detector. The detector assembly can further include a shutter, e.g., shutter  3230  or any other shutter described herein, having a portion movably disposed within the housing between a first shutter position and a second shutter position. The shutter can include a seal surface and an actuation portion which is configured to engage a distal end portion of the sample container to move the shutter from the first shutter position to the second shutter position when the distal end portion of the container is moved towards the detection volume. The seal surface of the shutter and the seal surface of the housing can be configured to isolate the detection volume from the channel of the housing when the shutter is in the first shutter position, while the channel of the housing can be in communication with the detection volume when the shutter is in the second shutter position. 
     In some embodiments, a detector assembly, e.g., the detector assembly  3200  or any other detector assembly described herein, can include a housing defining a channel configured to receive a sample container. The housing also defines a detection volume configured to place the channel in communication with a detector, and further includes a seal surface. The detector assembly can also include a shutter, e.g., shutter  3230  or any other shutter described herein, shutter defining a calibration port configured to receive a calibration light source. The shutter can be movably disposed within the housing between a first shutter position and a second shutter position such that a seal surface of the shutter and a seal surface of the housing is configured to isolate the detection volume from the channel of the housing when shutter is in the first shutter position. Furthermore, in the first shutter position, the calibration port can be in communication with the detection volume. The shutter can be configured such that the channel of the housing can be in communication with the detection volume when the shutter is in the second shutter position and the calibration port can be isolated from the detection volume. 
     Referring now to  FIGS. 51-95 , an instrument  11000  can include a housing  11100 , a heater assembly  11400 , a drive assembly  11500 , a manipulator assembly,  11600 , and a detector assembly  11200 . The housing  11100 , is configured to house, contain, and/or provide mounting for each of the components and/or assemblies of the instrument  11000 , as described herein. The heater assembly  11400  is configured to receive a container, e.g., container assembly  3700 , as described herein, and heat a sample contained therein. Similarly stated the heater assembly  11400  is configured to maintain a sample containing target cell, at a predetermined temperature and for a desired time period (e.g., at or above room temperature, 25 degrees Celsius, or 37 degrees Celsius, for approximately 2 hours or 4 hours, as described herein). The drive assembly  11500  is configured to drive, transfer and/or move the manipulator assembly  11600  (and the container assembly  3700  coupled thereto) in a 3-dimensional space within the housing  11100 . Said another way, the drive assembly  11500  can move the manipulator assembly  11600  in an X, Y and/or Z direction within the housing  11100 . The manipulator assembly  11600  is configured to manipulate, grip and/or actuate a container (e.g., the container assembly  3700 ) within the housing  11100 . For example, the manipulator assembly  11600  is configured to releasably couple to, engage, hold, lock, and/or secure the container assembly  3700  to transfer the container from a first location within the housing  11100  to a second location. Similarly stated, the manipulator assembly  11600  and the manipulator assembly  11600  are collectively configured to transfer the container assembly  3700  between a first subassembly and another subassembly, and/or actuate an actuation mechanism of the container assembly  3700 , to transfer reagents and/or solutions from one portion of the container assembly  3700  to another. The detector assembly  11200  is configured to detect a signal, e.g., luminescence, from within at least a portion of the container assembly  3700 . The detected signal can be produced by a chemical reaction occurring within a reaction chamber of the container, for example, interaction of a reporter molecule (e.g., luciferase), with a substrate (e.g., tridecanal). Each of these assemblies is described further below in detail, followed by a description of various methods that can be performed by the instrument  11000 . Although the instrument  11000  is shown and described as manipulating and/or actuating the container assembly  3700 , the instrument  11000  can receive, manipulate and/or actuate any of the container assemblies described herein. 
     As shown in  FIGS. 51-54 , the housing  11100  is defines an internal volume to house, contain and/or mount the subassemblies of the instrument  11000 . The housing  11100  can be formed from any suitable rigid, light weight and sturdy material. Example materials include polytetrafluoroethylene, high density polyethylene, polycarbonate, other plastics, acrylic, sheet metal such as aluminum, any other suitable material or a combination thereof. The housing can be relatively smooth and free of sharp edges. The housing includes sidewalls  11102 , a lid  11104  and a front panel  11106 . The lid  11104  is pivotally mounted on the sidewalls  11102 , and can swivel about its pivot mounts from a first position wherein the housing  11100  is closed, to a second position wherein the housing  11100  is open, e.g., to allow access of the subassemblies disposed within the housing  11100 . The front panel  11106  defines a first opening  11108  and a second opening  11110 . The first opening  11108  and the second opening  11110  are configured to removably receive a series of cartridges  11300  (e.g., 1, 2, 3, 4, or even more; see  FIG. 52 ) as described herein. Each cartridge  11300  can contain and/or hold a series of container assemblies, e.g., container assembly  3700 . The first opening  11108  can be configured to be a loading zone, i.e. configured to removably receive the series of cartridges  11300  having a series of container assemblies  3700  disposed therein. The series of containers can include samples for analysis in accordance with any of the methods shown and described herein. In particular, the containers can include samples for which screening for the presence of a target cell (e.g., MRSA). The second opening  11110  is configured to be an unloading zone, i.e., configured to removably receive a series of cartridges  11300  having containers disposed therein, the containers housing samples that have been analyzed by the instrument, e.g., analyzed for the presence of bacteria using any of the subassemblies of the instrument  11000 , and method described herein, e.g., method  400 . 
     The housing  11100  includes an interface  11112  located on a backside of the housing  11100 . The interface  11112  includes an electric plug  11122 , e.g., for communicating electrical power to the instrument  11000 . The interface  11112  also includes a communication interface  11124 , for example, to enable communication with an external device, e.g., local computer, remote computer, and/or a laboratory information system  1900 , via local area network (LAN), wide area network (WAN) and/or the Internet. The communication interface  11124  can be a hardwired interface, e.g., DSL and/or RJ45. The housing  11110  also includes vents  11114  on the backwall that are configured to allow air, e.g., air heated due to the heat generated by operation of the subassemblies of instrument  11000 , to exhaust. In some embodiments, the vents  11114  can includes fans to produce a flow of the exhaust air from the instrument  11000  with increased velocity, for example, to enable rapid cooling of the instrument. The housing  11100  also includes a series of bumpers (e.g., four, five or six) on a bottom surface configured to provide cushioned seating of the instrument  11000  on a surface. The bumpers can be made from a vibration absorbent and high friction material e.g., rubber, and can be configured to absorb any vibrations of the instrument  11000 , e.g., caused by a motion of the drive assembly  11500 , and/or prevent the instrument  11000  from sliding on the surface upon which it is placed. 
       FIGS. 55-57  show perspective views of the instrument  11000  from various angles with the housing  11100  removed, to more clearly show the internal components and subassemblies. The instrument  11000  includes a baseplate  11118  configured to provide mounts for coupling the components and subassemblies of the instrument  11000 . Referring also now to  FIG. 58 , the instrument includes a power supply  11120  mounted on the baseplate  11118 . The power supply  11120  can be any commercially available power supply as is commonly known in the arts. The power supply  11120  is configured to receive electric power from the electrical plug  11122 , e.g., 110V at 60 Hz or 220V at 50 Hz, and convert it into an electric power usable by the subassemblies of the instrument, e.g., step down the voltage, step up the voltage, control current, etc. 
     Referring also now to  FIG. 59 , the instrument  11000  includes a processor  11126  coupled to a frame  11127  e.g., via zip ties, and disposed on the base plate  11118  via the frame  11127 . The processor  11126  can be configured to control the operation of the various subassemblies included in the instrument  11000 . For example, the processor  11126  can be a computer, a programmable logic chip (PLC), a microprocessor, an ASIC chip, an ARM chip, and/or a combination thereof. In some embodiments, the processor  11126  can included algorithms or software that can include instructions for operating the instrument  11000  subassemblies, e.g., heater assembly  11400 , drive assembly  11500 , manipulator assembly  11600 , detector assembly  11200 , and/or any other component included in the instrument  11000 . In some embodiments, the processor  11126  can also be programmable, e.g., configured to accept instructions from a user, such as operating parameters of the instrument  11000 . In some embodiments, the processor  11126  can also include a memory, e.g., to store the status and/or any other information (e.g., containers analyzed, positive samples, negative samples) or instructions. 
     Referring also now to  FIG. 60 , the instrument  11000  also includes a communications module  11128  coupled to the mount  11129 , e.g. via zip ties and disposed on the base plate  11118 . The communications module  11128  is configured to communicate information to an external device, e.g., a laboratory information system (LIS), a remote computer, smartphone app and/or remote server from the processor  11126 . In some embodiments, the communications module  11128  can also be configured to receive instructions to facilitate the performance of the methods described herein. The communications module  11128  can employ and/or be compatible with standard communication protocols, e.g., USB, firewire, ZigBee, Bluetooth®, low powered Bluetooth®, and/or any other communication equipment. 
     As shown in  FIGS. 61-63  the instrument  11000  includes a series of cartridge receivers  11350  mounted on the baseplate  11118 . Each of the cartridge receivers  11350  is configured to removably receive a cartridge  11300 .  FIGS. 55-57  show the series of cartridges  11300  in a first configuration, such that the series of cartridges  11300  are coupled to the series of cartridge receivers  11350 , and are disposed substantially inside the housing  11100  of the instrument  11000 .  FIG. 61  shows the series of cartridges  11300  in a second configuration, wherein the series of cartridges  11300  are decoupled from the corresponding cartridge receiver  11350 , and are disposed substantially outside the housing  11100  of the instrument  11000 . Although the series of cartridges  11300  can include both “loading” and “unloading” cartridges  11300 , as shown, the cartridges  11300  are substantially similar to each other and can be used interchangeably. In other embodiments, an instrument can include different cartridges for loading (e.g., input) of the container assemblies and unloading (e.g., output) of the container assemblies. Each cartridge  11300  includes a proximal end  11302  and a distal end  11301 . The distal end  11301  is configured to engage with and reversibly couple to the cartridge receiver  11350 . The proximal end  11302  is configured to allow a user to manipulate the cartridge 11300 , for example, load or unload the cartridge  11300 , as described herein. 
       FIG. 62  shows a perspective view of a cartridge  11300 . The cartridge  11300  can be formed from a light weight and rigid material, e.g., plastics, and can have a surface that is smooth and relatively free of sharp edges. The cartridge  11300  defines a series of receptacles  11304  configured to removably receive at least a portion of a container, e.g., reaction chamber  3732  of the container assembly  3700 , or any other container described herein. As shown herein, the cartridge  11300  includes twelve receptacles  11304 . In other embodiments, however, the cartridge  11300  can include 1, 2, 4, 6, 8, 10, 14, 16 or an even higher number of receptacles  11304 . Each of the series of receptacles  11304  can be shaped and sized to receive a reaction chamber of a container, e.g., reaction chamber  3732  of the container assembly  3700  or any other container described herein, with close tolerance. In this manner, the cartridge  11300  and the receptacles  11304  can restrict lateral movement of the container. Further, receptacle  11304  of the series of receptacles can have a depth such a reagent module, e.g., reagent module  3740  of the container assembly  3700  or any other container described herein, is disposed substantially outside the receptacle  11304 . In this manner at least a portion of the container assembly can be exposed and/or accessible to be manipulated by the manipulator assembly  11600 . 
     Each of the series of receptacles  11304  also includes a slot  11306  along at least a portion of the sidewall of the receptacle  11306 . In some embodiment, the slot  11306  can be configured to allow a user to access a sidewall of a reaction chamber, e.g., reaction chamber  3732 , of a container disposed within the receptacle  11304 , e.g., to facilitate removal of the container from the receptacle  11304 . In other embodiments, the slot  11306  can be configured to allow for optical monitoring and/or identification (e.g., via a label) of the container assembly within the receptacle  11304 . 
     The proximal end  11302  of the cartridge  11300  includes an arm  11308  configured to be engaged by a user, e.g., to facilitate loading/unloading of the cartridge  11300  from the instrument  11000 . The arm  11308  can have an ergonomic shape, e.g., to minimize physical stress on a user manipulating the cartridge  11300 . 
     The cartridge  11300  includes a recess  11310  that runs from the proximal end  11302  to the distal end  11301  along the entire length of the cartridge. The recess can be shaped and sized to be slidably received by a guide rail  11352  of the cartridge receiver  11350 , as described herein. The distal end  11301  of the cartridge  11300  also includes a tab  11312 . The tab  11312  is configured to protrude from proximal end  11312  and interface with a sensor  11362  of the cartridge receiver  11350 , as described herein. 
       FIG. 63  shows a perspective view of a cartridge receiver  11350  included in the instrument  11000 . The cartridge receiver  11350  can be securely mounted on the base plate  11118 , e.g., via screws, bolts, rivets, or the likes. The cartridge receiver can be formed from a lightweight, rigid and wear resistant material, e.g., metals such as aluminum. The cartridge receiver  11350  includes a guide rail  11352  configured to slide into the recess  11310  of the cartridge  11300 , such that the cartridge  11300  can be slideably received by and/or coupled to the cartridge receiver  11350 . The cartridge receiver  11350  includes a latch  11354  that can be at least partially disposed in an opening in the guard rail  11352 . The latch  11354  includes a first portion  11355  configured to engage a notch  11314  ( FIG. 64 ) included in the recess  11310  of the cartridge  11300  to lock, hold and/or secure the cartridge  11300  to the cartridge receiver  11350 . The latch  11354  includes a second portion  11356  that is mounted on a shaft  11361  of an actuator  11360  included in the cartridge receiver  11350 . A spring  11358  is also mounted on the shaft  11361 . The spring  11358  is coupled to the latch  11354  and is operable to urge the latch  11354  to lock and/or engage the cartridge  11300  as described herein. The spring  11358  can be, e.g., a tension spring, such as e.g., a helical tension spring. The cartridge receiver  11350  includes the sensor  11362 . The sensor  11362  can be any suitable sensor, such as a motion sensor, a position sensor, an optical sensor, a piezoelectric sensor, or any other suitable sensor. As described above, the sensor  11362  is configured to interface with the tab  11312  of the cartridge  11300  to determine and/or validate a position of the cartridge  11300 , e.g., to ensure that the cartridge  11300  is completely in the second configuration, and is fully coupled to the cartridge receiver  11350 . 
       FIG. 64  shows a side cross-section of a cartridge  11300  in the second configuration, such that the cartridge  11300  is fully coupled with the cartridge receiver  11350 . In the second configuration, the guide rail  11352  of the cartridge receiver  11350  is disposed substantially into the recess  11310 , and the first portion  11355  of the latch  11354  is inserted into the notch  11314  included in the recess  11310  of the cartridge  11300 . The latch  11354  is pivotally mounted on a pin  11364 , such that the latch  11354  can pivot about the pin  11364  from a first position to a second position. In the first position, at least a portion of the first portion  11355  of the latch  11354  is inside the notch  11314 . In the second position the first portion  11355  is outside the notch  11355 . The spring  11358  is coupled to the second portion  11356  of the latch  11354 , and is operable to urge the latch  11354  into first position. 
     In use, the cartridge  11300  can be loaded into the instrument  11000  by sliding the cartridge along the guide rail  11352  until the proximal end  11301  of the cartridge  11300  contacts the first portion  11355  of the latch  11354 . The first portion  11355  of the latch  11354  has a tapered surface, such that an edge (e.g., a chamfered or tapered edge) of the proximal portion  11301  of the cartridge  11300  slides along the tapered surface of the first portion  11355  of the latch  11354 , urging the latch  11354  to pivot from the first position to the second position. As the cartridge  11300  moves further along the guide rail  11352  towards the second configuration, the first portion  11355  of the latch  11354  encounters the notch  11314 . The spring  11358  now urges the latch  11354  to pivot about the pin  11364  and move back into the first position such that the first portion  11355  of the latch  11354  is inside the notch  11314  and cartridge  11300  is locked in the second configuration. 
     In the second configuration, the tab  11312  engages the sensor  11362 , as described above. In some embodiments, the sensor  11362  produce a signal indicating that the cartridge  11300  is fully coupled to the cartridge receiver  11350 . The sensor  11362  can communicate the information validating the position of the cartridge  11300  to the processor  11126  and/or the user, e.g., using audio (e.g. beeps), visual (e.g., indicator lights) and/or tactile alerts. The actuator  11360  is configured to urge the latch  11354  from the first position to the second position to release the cartridge  11300  for removal from the instrument. For example, a user can actuate the actuator  11360  and/or the actuator  11360  can be configured to actuate after a given time period, such that the shaft  11361  extends towards the proximal end  11302  of the cartridge  11300 . This causes the latch  11354  to pivot about the pins  11364  from the first position to the second position, so that the cartridge  11300  is no longer secured by the latch  11354  and can be slideably removed from the cartridge receiver  11350 . 
     As shown in  FIG. 55-57 , the instrument  11000  includes a heater assembly  11400 , configured to receive a series of containers, e.g., container assembly  3700  and/or any other container described herein. The heater assembly  11400  is configured to heat and/or maintain a temperature of the container assemblies therein according to any of the methods described herein. Referring now also to  FIG. 65-67 , the heater assembly  11400  includes a housing  11410  configured to house a series of heating blocks  11420 . The housing  11410  is formed from a rigid, and heat insulating material such as thick stainless steel, other metals, polymers. The housing  11410  can include a lining of a heat resistant material, e.g., Mica, or any other heat insulation means. The housing  11410  defines a series of cavities  11412 , each being sized and shaped to receive a heating block  11420  with close tolerance. 
     The heating block  11420  can be formed from a heat conducting, rigid and wear resistant material, e.g., anodized aluminum. The heating block  11420  defines a series of receptacles  11422 , each of which is shaped and sized to receive at least a portion of a container, e.g., reaction chamber  3732  of the container assembly  3700 , or any other container described herein. For example, a container can be disposed on any of the series of receptacles  11422  of any of the series of heating blocks  11420  by the manipulator assembly  11600 , which is driven and/or positioned by the drive assembly  11500  as described herein. 
     Each heating block  11420  includes heating elements  11424  disposed on a bottom surface of the heating block  11420 . In some embodiments, the heating element  11424  can be a micro heater, e.g., a ceramic plate heater. In some embodiments, the heating elements  11424  can be electrical wires that pass a current through the heating block  11420  to heat the heating block  11420  using electrical energy (i.e., resistive heating). Each heating block  11420  also includes a temperature sensor  11426 , e.g., a thermocouple, disposed within a body of the heating block  11420 . The temperature sensor  11426  is in electrical communication with the heating element  11420  directly, or through a processing unit (not shown) of the instrument  11000 . In this manner, the heating elements  11424  can be deactivated and/or controlled to limit heating to the heating block  11420 , e.g., when the temperature of the sensors exceeds a predefined temperature level. In this manner, the temperature of the heating block  11424 , and the samples disposed therein can be controlled in accordance with the methods disclosed herein. 
     As shown in  FIG. 55-57 , the instrument  11000  includes a drive assembly  11500  configured to transport a container or assembly coupled thereto, e.g., by the manipulator assembly  11600 , as described herein. For example, the manipulator assembly  11600  can be coupled to a container, and the drive assembly  11500  can be configured to enable transport of the container from a first location within the housing  11100  to a second location, e.g., from a loading cartridge  11300  to the heater assembly  11400 , from the heater assembly  11400  to the detector  11200 , from the detector  11200  to an unloading cartridge  11300 , and/or any other location therewithin. 
     Referring also now to  FIG. 68-71 , the drive assembly  11500  includes a support  11502 , e.g., a frame or a chassis, on which the components of the drive assembly  11500  are mounted. The support  11502  is securely mounted on the baseplate  11118 , and can be configured to absorb any vibrations caused by the motion of the drive assembly  11500 . The support includes a first section  11503   a  that is oriented along an X axis with respect to the X axis of the instrument  11000 , as shown by the arrow XX, and a second section  11503   b  oriented along a Y-axis with respect to the instrument  11000 , as shown by the arrow YY. The second section  11503   b  is movably disposed on and/or coupled to the first section  11503   a  via the second guide block  11520 . The drive assembly  11500  includes a first actuator  11504   a  disposed on the first section  11503   a , a second actuator  11504   b  disposed on the second section  11503   b , and a third actuator  11504   c  mounted on the frame  11512 . The first actuator  11504   a  and the second actuator  11504   b  are configured to drive the frame  11512  and any subassembly, e.g., the manipulator assembly  11600 , disposed on the mount  11514 , in an X and Y direction, respectively, as described herein. The third actuator  11504   c  is configured to drive the mount  11514  and any subassembly mounted thereon, e.g., the manipulator assembly  11600 , in a Z direction with respect to the instrument  11000 , as shown by the arrow ZZ. The actuators can be substantially similar to each other and can include, e.g., stepper motors, configured to drive the frame  11512  and/or mount  11514  a fixed distance with every step, e.g., each portion of a rotation of the actuators  11504   a ,  11504   b  and/or  11504   c.    
     The first actuator  11504   a  and the second actuator  11504   b  include a first disc  11506  mounted on each of the actuators  11504   a ,  11504   b . A second disc  11508  ( FIG. 70 ) is disposed on each of the first section  11503   a  and the second section  11503   b  of the support  11502 . A belt  11510  is looped around the first disc  11506  and the second disc  11508  in a taut manner, such that a rotation of the disc  11506  caused by the actuator  11504   a/b  urges the belt  11510  to be driven along its length (or rotated) over the second disc  11508 . The belt  11510  can be, e.g., a rubber belt, a plastic belt or a polymer belt, and can include grooves on the surface contacting the discs  11506  and  11508 , e.g., to provide friction and/or no slip translation of the belt. The belt  11510  coupled to the first actuator  11504   a  is operably coupled to a first guide block  11516  which is mounted on a first guide rail  11518 . The belt  11510  is configured such that translation of the belt  11510  caused by the first actuator  11504   a  urges the first guide block  11516  and the second section  11503   b  of the support  11502  mounted thereon, to translate slidably along the guide rail  11518  in the X direction. Similarly, the second actuator  11504   b  also includes a belt  11510  disposed on the disc  11506  which is coupled to the second disc  11508  disposed on the frame  11512 . The frame  11512  is coupled to the second guide block  11520 . The second guide block  11520  is mounted on a second guide rail  11522 . Driving the belt  11510  by the second actuator  11504   b , drives the frame  11512  and the second guide block  11520  slidably along the second guide rail  11522 . In this manner, a combination of translation of the second section  11503  of the support  11502  caused by the actuation of the first actuator  11504   a  along the X axis, and the translation of the frame  11512  along the Y axis caused by the actuator  11504   b , can drive the frame to any location in an X-Y plane within the instrument  11000 . 
     The frame  11512  is coupled to a first chain  11524   a  slidably disposed in a first chain guide  11526   a , which is disposed on and coupled to the first section  11503   a . A second chain  11524   b  is also coupled to the frame  11512 , and is slidably disposed in a second chain guide  11526   b , which is disposed on and coupled to the second section  11503   b . The chains  11524   a/b  are configured to slide along the chain guides  11526   a/b  in close tolerance corresponding to an X-Y displacement of the frame  11512 , such that the chains prevent any lateral motion of the frame  11512 , e.g., to ensure accurate displacement of the frame  11512 . 
     As described herein, the third actuator  11504   c  is disposed on the frame  11512  and includes a first disc  11528   a  coupled to the actuator  11504   c . A belt  11530  is coupled to the first disc  11528 , such that the belt  11530  loops over the first disc  11528   a  and a second disc  11528   b . The second disc  11528   b  is coupled to a lead screw  11532  included in the frame  11512 . The belt  11530  can be substantially similar to the belt  11510 . The lead screw  11532  has a nut  11534  mounted on threads of the lead screw  11532 . The nut is coupled to the mount  11514 . The third actuator  11504   c  is configured to rotate the first disc  11528   a  which urges the belt  11530  to translate, thus rotating the second disc  11528   b . Rotation of the second disc  11528   b  rotates the lead screw  11532  that urges the nut  11534  to displace along the length of the lead screw  11532  from a first position ( FIG. 70 ), to a second position ( FIG. 71 ) in the Z direction. Displacement of the nut  11534  also causes the mount  11514  coupled to the nut  11534 , and any subassembly mounted thereon, e.g., the manipulator assembly  11600 , to move from the first position to the second position in the Z direction. The mount  11514  is also coupled to a third guide block  11536  slidably mounted on a third guide rail  11538 , such that displacement of the mount  11514  in the Z direction is guided by the third guide block  11536  and the third guide rail  11538 , e.g., to prevent any radial motion of the mount  11514  about a longitudinal axis defined by the lead screw  11512 . 
     The drive assembly  11500  includes sensors  11540  mounted each of the first section  11503   a , the second section  11503   b , and the frame  11512 . The sensors  11540  can be position sensors such as, e.g., optical sensors, motion sensors, piezoelectric sensors, or any suitable sensor. The sensors  11540  can be configured to detect a location of the second section  11503   b  and the frame  11512 , e.g., to prevent an overtravel that can damage the drive assembly and/or cause increased wear. As shown in  FIG. 57  and  FIG. 72 , the instrument  11000 , also includes circuitry  11500  for controlling the actuators  11504   a/b/c . The circuitry  11500  can be any commercially available circuitry used for control of actuators  11504   a/b/c , e.g., stepper motor controller circuitry. 
     As shown in  FIG. 55-57 , the instrument includes a manipulator assembly  11600  disposed on the mount  11514  included in the drive assembly  11500 . The manipulator assembly  11600  is configured to grasp, hold, clamp, contact, engage and/or otherwise secure a container, e.g., container assembly  3700  as described herein. For example, the manipulator assembly  11600  can be configured to releasably engage and/or grip container and/or engage one or more actuators included in the container, such as for example the container assembly  3700 . 
     Referring now to  FIGS. 73-84 , the manipulator assembly  11600  includes an articulation subassembly  11610 , a plunger subassembly  11630  and an actuator subassembly  11650 . The articulation assembly  11610  is configured to releasably contact, grasp or otherwise secure a container, e.g., container assembly  3700 . For example, the articulation assembly  11610  can be configured to secure or grasp a container disposed in a first location, such as the loading cartridge  11300 . The articulation subassembly  11601  can continuously secure the container during transport from the first location to a second location within the instrument  11000  by the drive assembly  11500 . Such changes in position can include moving the container assembly from the loading cartridge  11300  to the heater assembly  11400 , from the heater assembly  11400  to the detector assembly  11200  and/or from the detector assembly  11200  to the unloading cartridge  11300 . The plunger subassembly  11630  is configured to contact, engage or otherwise manipulate one or more actuators in a container, e.g., actuator  3750  and/or  3760  included in the container assembly  3700 , to urge the actuator and/or actuators to communicate a reagent (e.g., biologic or abiologic vectors such as transduction particles of the type shown and described herein) and/or a substrate (e.g., tridecanal) from a reagent volume to a reaction chamber of the container, as described herein. The actuator subassembly  11650  is configured to engage or manipulate the plunger subassembly  11630 , e.g., to manipulate an inner plunger  11632  and/or an outer plunger  11636  of the plunger assembly  11630 , as described herein. The actuator subassembly  11650  can also be configured to engage or manipulate the articulation subassembly  11610 , e.g., to manipulate or otherwise urge the articulation subassembly  11610  to secure or release a container, e.g., container assembly  3700 , as described herein. Similarly stated, the actuator subassembly  11650  can, with a single actuator, cause the manipulator assembly  11600  to both grip and/or secure a container, and actuate the container. 
     As shown in  FIGS. 74-75 , the articulation subassembly  11600  includes a set of grippers  11612 , coupled or mounted on a set of gripper bases  11614 . As shown two grippers  11612  are coupled to a single gripper base  11614 . In some embodiments, each gripper base  11614  can include more than two grippers  11612 , e.g., three or four. The grippers  11612  are configured to be elongated, pin-like members that can be formed from a strong and rigid material, e.g., metals such as stainless steel. In some embodiments, the grippers  11612  can include a surface that can have a high friction for contacting, grasping or otherwise securing a container, e.g., container assembly  3700 . For example, the surface of the grippers  11612  can include grooves, abrasions, rubber coating, soft plastic and/or rubberized carbon. Each gripper base  11614  defines a groove (or channel)  11615  configured to allow a plunger portion  11637  of the outer plunger  11636  included in the plunger subassembly  11630 , to move within a region between the grooves  11615 , without contacting a sidewall defining the grooves  11615 . 
     Each gripper base  11614  is coupled to a side plate  11616  by any suitable mechanism. The side plates  11616  are pivotally coupled to an actuator mount  11654  included in the actuator assembly  11650 , as described herein. The side plates are configured to pivot or articulate about their mounts relative to the plunger assembly  11630 , to urge the articulation assembly  11610  from a first configuration to a second configuration. In the first (or closed) configuration the set of grippers  11612  are in a closed position to selectively engage, grip, grasp or otherwise secure a container, e.g., container assembly  3700 . In the second (or opened) configuration the set of grippers  11612  are distal to each other, e.g., to disengage or release the container. A set of guide wheels  11620  is disposed on a side wall of the each of the set of side plates  11616 , e.g., mounted on pins, bolts, screws or the likes. Under certain conditions, the set of guide wheels  11620  is configured to be proximate to but not contacting, or in contact with a portion of a side wall of a set of guide members  11640  included in the plunger assembly  11630 , as described herein. The guide members  11640  are configured to urge the side plates  11616  and thus the articulation assembly  11610  from the first configuration to the second configuration, as described herein. 
     The side plates  11616  are coupled to a set of compression plates  11618 . The compression plates  11618  are in pressure contact with a set of springs  11622 , which are mounted to the actuator mount  11654  via pins. The set of compression plates  11618  are configured to angularly displace with the pivotal motion of the set of side plates  11616 , such that the set of compression plates  11618  engage the set of springs  11622 , e.g., compress the springs  11622 , when the articulation assembly  11610  is in the second configuration. Thus the compression plates  11618  are configured to urge the articulation assembly  11610  into the first configuration from the second configuration, e.g., to grasp or secure a container, e.g., container assembly  3700  or any other container described herein. The springs  11622  are configured to control the amount of force exerted by the grippers  11612  on the container, e.g., to prevent crushing of the container. At least one of the set of side plates  11616  can be configured to engage a position sensor  11662   a , e.g., an optical sensor, motion sensor, piezoelectric sensor, or any other suitable sensor. The sensor  11662   a  is coupled to a sensor mount  11664 , which is mounted a surface of the actuator mount  11654 . The sensor  11662   a  can be configured to inform a control system and/or user about the position of the articulation assembly  11610 , e.g., articulation assembly in first configuration (i.e., securing, engaging or grasping a container) or second configuration (i.e., disengaging or releasing a container). In some embodiments, the sensor  11662   a  can be a homing sensor, configured to identify a home position of the articulation assembly  11610 . 
     The plunger subassembly  11630  includes an inner plunger  11632  and an outer plunger  11636 . As shown, the inner plunger  11632  is also a lead screw of the actuator  11652 . Accordingly, the inner plunger  11632  can rotate about a longitudinal axis of the plunger assembly  11630 . The inner plunger  11632  can be configured to engage or manipulate a first actuator of a container, e.g., the actuator  3750  of the container assembly  3700  as described herein. The outer surface of the inner plunger  11632  is threaded and can be threadedly disposed within a collar  11634 . The collar  11634  is configured to move along the threads of the inner plunger  11632  during the rotation of the inner plunger  11632 . The collar  11634  is further coupled to an engagement portion  11637  of the outer plunger  11636 , such that a rotation of the inner plunger  11632  results in a longitudinal displacement of the outer plunger  11636 . This can, for example, allow control of the speed of the outer plunger  11636 , which can be used to control delivery of a substrate into a reaction chamber of a container, as described herein. The outer plunger  11636  includes an engagement portion  11638  which can be configured to engage or manipulate a second actuator in a container, e.g., actuator  3760  of the container assembly  3700 , as described herein. The outer plunger  11636  also includes a channel  11639  defined therethrough along a longitudinal axis of the outer plunger  11636 . At least a portion of the inner plunger  11632  can be disposed in the channel  11639 . 
     A set of guide members  11640  are disposed on a side wall of the outer plunger  11636 . Each of the set of guide members  11640  includes a first section  11642  having a first width, a second section  11644  having a second width greater than the first width, and a third section  11643  which is angled with respect to a longitudinal axis of the guide member  11640  and connects the first section  11642  to the second section  11644 . At least a portion of the plunger assembly  11630  e.g., the collar  11634 , the outer plunger  11636  and the guide members  11640 , are configured to move along a longitudinal axis defined by the inner plunger  11632 . Furthermore, the plunger assembly  11630  is configured to engage and or manipulate a container, e.g., container assembly  3700 , that is engaged, secured or otherwise grasped by the articulation assembly  11610 , as described herein. The plunger assembly  11630  is also configured to manipulate the articulation assembly  11610 , e.g., to urge the articulation assembly  11610  from the first configuration, in which the articulation assembly  11610  is engaging, grasping or otherwise securing a container, to the second configuration, in which the articulation assembly disengages or releases the container, as described below. A clip  11646  is also disposed on one of the guide members  11640  ( FIG. 75 ). The clip  11646  is configured to selectively engage a sensor  11662   b  to validate and/or determine a position of the plunger assembly  11630 . The sensor  11662   b  can be any suitable sensor, e.g., a position sensor, a motion sensor, an optical sensor, a piezoelectric sensor or any other suitable sensor, disposed on the actuator mount  11654 . The sensor  11662   b  can be used to determine a position of the plunger assembly  11630 , e.g., to prevent overtravel of the plunger assembly  11630 . 
     The actuator subassembly  11650  includes an actuator  11652 , e.g., a stepper motor, which is disposed on the actuator mount  11654 . The actuator mount  11652  defines corresponding recesses  11656   a  and  11656   b . The recess  11656   a  provides a mounting seat for at least a portion of the actuator  11652 . The groove  11656   b  defines an opening through which at least a portion of the plunger assembly  11630 , e.g., the inner plunger  11632 , the collar  11634  and the outer plunger  11636  can move. The actuator mount  11654  further includes a set of alignment pins  11658  disposed on a bottom surface of the actuator mount  11654 . The alignment pins  11658  are substantially parallel to the longitudinal axis defined by the plunger assembly  11630 . At least a portion of each alignment pin  11658  is disposed in a corresponding channel  11659  included in the collar  11634  and the engagement portion  11637  of the outer plunger  11636 . In this manner, the displacement of the plunger subassembly  11630  along the longitudinal axis defined by the plunger subassembly  11630 , e.g., caused by a rotation of the inner plunger  11632 , is guided by the alignment pins  11658 , e.g., to prevent any rotation or sideways motion of the plunger assembly  11630 . 
     As described herein, the manipulator assembly  11600  is configured to releasably contact, engage or otherwise secure a container.  FIG. 75  shows a side view of the manipulator assembly  11600  in a first configuration, in which the housing  3741  of the container assembly  3700  is not contacted, grasped or otherwise secured by the manipulator assembly  11600 .  FIG. 75  shows a side view of the manipulator assembly  11600  in a second configuration, in which the manipulator assembly  11600  is securing or gripping the container assembly  3700 . The manipulator assembly  11600  is configured such that the grippers  11612  secure the container assembly  3700  only from the top portion, i.e., the reagent module  3740 . This can allow a bottom read of the container assembly  3700  by the detector  11200  or any other detector described herein. 
     As shown in  FIG. 75 , when in the first configuration, the actuator  11652  has rotated the inner plunger  11632  to move the collar  11634  coupled to the inner plunger  11632  along the length of the inner plunger  11632  in a direction towards the actuator  11652 . In this manner, when in the first configuration the actuator  11652 , at least a portion of the collar  11634  and/or the outer plunger  11636  coupled to the collar  11634 , are within the opening defined by the recess  11656   b  of the actuator mount  11654 . Moreover, the position of the plunger assembly  11630  relative to the actuator assembly  11650  (i.e., in an upward position) is such that the guide members  11640  engage the articulation assembly  11610 . As shown in the first configuration illustrated in  FIG. 75 , the displacement of the guide member  11640  towards the actuator  11652  places the guide wheels  11620  in contact with the second section  11644 . In this configuration, the set of side plates  11616  pivot or articulate about their pivot mounts relative to the longitudinal axis of the plunger assembly  11630 , such that the gripper bases  11614  and the set of grippers  11612  are angled with respect to the longitudinal axis of the plunger assembly  11630 . An end of corresponding grippers  11612  is a first distance apart, such that the first distance is greater than a diameter of the housing  3741  of the container assembly  3700 . 
     In the first (or “open grip”) configuration, the manipulator assembly  11600  is configured to disengage or release the container assembly  3700  and/or is ready to receive the container assembly  3700 . For example, in some embodiments, the container assembly  3700  can be disposed in a cartridge  11300 . The manipulator assembly  11600  can be driven by the drive assembly  11500  to the location where the container assembly  3700  is disposed, and then urged into the first configuration. The manipulator assembly  11600  can then be displaced along a longitudinal axis defined by the manipulator assembly  11600  towards the container assembly  3700 , until the grippers  11612  are adjacent to the housing  3741 , and a bottom portion of the inner plunger  11632  is in close proximity to but not contacting an engagement portion  6752  of an inner plunger  6750  (not shown in  FIG. 75-76 ) disposed in the housing  3741  of the container assembly  3700 . 
     As shown in  FIG. 76 , the articulation assembly  11610  can be moved into the second configuration to engage, grip, grasp or otherwise secure the container assembly  3700 . For example, to move the articulation assembly to the second configuration, the inner plunger  11632  is rotated by the actuator  11652 . This urges the collar  11634  to move along the length of the inner plunger  11632  in a direction away from the actuator  11652  (e.g., downward as shown in  FIG. 76 ). Displacement of the collar  11634  also urges the outer plunger  11636  and the set of guide members  11640  coupled thereto, to move along a longitudinal axis defined by the plunger assembly  11630  away from the actuator  11650 . This causes the guide wheels  11620  to ride along a side wall of the second section  11644  of the guide member  11640  onto the narrower inclined section  11643 . In this configuration, the set of springs  11622  that are in pressure contact with the set of compression plates  11618 , urge the set of compression plates and hence the set of side plates  11616  to pivot relative to the longitudinal axis defined by the plunger assembly  11630 . This also causes the gripper bases  11614  and the set of grippers  11612  coupled thereto to displace towards the housing  3741  of the container assembly  3700 , such that in the second configuration, the set of grippers  11612  are contacting, engaging or otherwise securing the container assembly  3700 . The manipulator assembly  11600  can be maintained in the second configuration to transport the container assembly  3700  from a first location within the housing  11100  of the instrument  11000  to a second location as shown in  FIG. 77 , via the drive assembly  11500 . 
     As described herein, the manipulator assembly can also be used to engage and or manipulate the container assembly  3700 , e.g., the actuators  3750  and  3760  disposed in a housing  3741  of the container assembly  3700 .  FIGS. 78 and 79  show side views of the manipulator assembly  11600  in the first configuration (also referred to as “open grip”) and  FIG. 80  shows a side cross section of the manipulator assembly  11600  shown in  FIG. 78 . In this configuration, the plunger assembly  11630 , the articulation assembly  11610  and the actuator assembly  11650  are in the same relative positions as discussed above with regard to  FIG. 75 . The positioning of the manipulator assembly  11600  relative to the container assembly  3700 , however, is different. In particular, the inner plunger  11612  engages the engagement portion  3752  of the actuator  3750  as described below herein. 
     In this configuration (the “inner plunge” configuration), the container assembly  3700  can be disposed e.g., in a recess  11412  of a heating block  11420  included in the heater assembly  11400  as described herein, such that the container assembly  3700  cannot be displaced laterally with respect to a longitudinal axis of the manipulator assembly  11600 . When the articulation assembly  11610  is in the first configuration (“open grip” and the “inner plunge”), at least a portion the collar  11634  and the outer plunger  11636  is located within the opening defined by the recess  11656   b  such that a bottom portion of the inner plunger  11632  is protruding from the bottom of the channel  11639  of the outer plunger  11636 . Moreover, as described above, the set of guide wheels  11620  are contacting the surface  11644  of the set of guide members  11640  and the set of compression plates  11618  are compressing the set of springs  11622  to maintain the grippers in position. 
     To execute the “inner plunge” operation as shown in  FIG. 78-80 , the drive assembly  11500  is actuated to displace the manipulator subassembly  11600  in a downwards direction defined by a longitudinal axis of the plunger assembly  11630 , as shown by the arrow ZZ. The downwards motion of the manipulator assembly  11600  causes the inner plunger  11632  to move downwards, such that a bottom portion of the inner plunger  11632  contacts the engagement portion  3752  of the actuator  3750 , urging the plunger portion  3754  of the actuator  3750  within the internal volume  3742  defined by the housing  3741 . The plunger portion  3754  can move from a first position to a second position, such that the plunger portion  3754  communicates a reagent disposed in the internal volume  3742  into the container assembly  3700 , as described above. The reagent can be any reagent or substance described herein, such as a biologic or abiologic vector or transduction particle of the types described herein. After actuation of the first actuator  3750  by the manipulator assembly  11600 , the container assembly  3700  can remain disposed in the heater assembly  11400  for a predefined time period and at a predetermined temperature. As described above, in some embodiments, maintaining the container assembly will allow a target cell within the sample to express a sufficient quantity of reporter molecules such as, for example, luciferase or any other reporter molecule described herein. 
       FIG. 81  shows a side cross-section of the manipulator assembly  11600  in the second configuration (also referred to as “gripper closed”). In the second configuration, the manipulator assembly  11600  is in contact with, engaged, grasped or otherwise secured to the container assembly  3700 , as described herein with reference to  FIGS. 76 and 77 . In the gripper closed configuration, the inner plunger  11632  is disposed substantially within the outer plunger  11636 , such that the bottom portion of the inner plunger  11632  is proximal to but not contacting the engagement portion  3752  of the first actuator  3750  disposed in the housing  3741  of the container assembly  3700 , as described herein. Furthermore, the set of guide wheels  11620  are contacting the third section  11643  of the set of guide members  11640 . The gripper closed configuration can be used to transport the container assembly  3700 , e.g., from the heater assembly  11400  to the detector assembly  11200 . The articulation assembly  116500  is also configured to prevent overtravel. For example, if the in the closed grip configuration, the set of guide wheels contact the second surface  11644  of the set of guide members  11640 , this indicates the outer plunger  11636  has overtravelled. In this situation, a pin (not shown) mounted on one of the set of side plates  11616  triggers the position sensor  11662  a, that can send an overtravel signal, e.g., an alarm, to the processor  11126  or a user. 
     Referring now to  FIGS. 82-84 ,  FIGS. 82 and 83  show a side view of the manipulator assembly  11600  and  FIG. 84  shows a side cross-section of view shown in  FIG. 82 , in a third configuration (also referred to as “substrate plunge”). In the substrate plunge configuration, the outer plunger engages the engagement portion  3762  of the actuator  3760  as described below. In this configuration, the container assembly  3700  can be disposed, e.g., in the detector assembly  11200  as described herein, such that the container assembly  3700  cannot be displaced laterally with respect to a longitudinal axis of the manipulator assembly  11600 . For example, in this configuration, the reaction chamber  3732  of the container assembly  3700  can be disposed in a slot  11234  of a shutter  11230  included in the detector assembly  11200 , as described further below herein. Furthermore, when moved to the third configuration, the articulation assembly  11610  can be maintained in an engage, clamp, grip or otherwise secure configuration. In this manner, the container assembly  3700  can remain secured by the articulation assembly  11610  during the substrate plunge. This can, for example, ensure that all force of the outer plunge is transferred only to the second actuator  3760  of the container assembly  3700  and/or to maintain the container assembly  3700  flush with a gasket  11206  included in the detector assembly  11200  to prevent any ambient noise (e.g., light) from entering the detector assembly  11200 , as described herein. 
     To move from the second configuration to the third (“substrate plunge”) configuration, the inner plunger  11632  rotates in a direction opposite to the open grip configuration, e.g., as shown by the arrow RR in  FIG. 82 , such that the collar  11634  displaces along the longitudinal axis defined by the inner plunger  11632  in a direction away from the actuator  11652 . Displacement of the plunger also displaces the outer plunger  11636  and the set of guide members  11640  attached thereto, in the same direction. Displacement of the outer plunger  11636  effected by the rotation of the inner plunger  11632  is continued such that a bottom portion of the outer plunger  11636  engages the engagement portion  3762  of the second actuator  3760  urging the plunger portion  3764  of the actuator  3760  to displace within the internal volume  3744  defined by the housing  3741  of the container assembly  3700 . The plunger portion  3764  can move from a first position to a second position, such that the plunger portion  3764  communicates a reagent disposed in the internal volume  3742  through the delivery portion  3770  into the reaction chamber  3732  included in the container assembly  3700 . For example, the reagent can be a substrate, e.g., tridecanal or any other substrate described herein, that can be formulated to react with reporter molecules present in the reaction chamber  3732 , e.g., luciferase or any other reporter molecule, as described above. The reaction of the substrate with reporter molecules can produce a signal, e.g., luminescence or any other signal described herein, which can be detected by the detector assembly  11200 , as described further below herein. Longitudinal displacement of the outer plunger  11636  effected by a rotary motion of the inner plunger  11632  can allow, for example, better control over the displacement of the outer plunger  11636 , and therefore better control over communication of a substrate from the internal volume  3744  to the reaction chamber  3732  of the container assembly  3700 . 
     It is to be noted that a single actuator  11652  is employed by the manipulator assembly  11600  to perform a series a functions, including: i) manipulating outer plunger  11636  by actuating the inner plunger  11632  to cause the substrate plunge and; ii) manipulating the guide members  11640  coupled to the outer plunger  11636  to urge the articulation assembly  11610  from the open grip to the gripper closed configuration. A second actuator, e.g., actuator  11504   c  included in the drive subassembly  11500  as described herein, can be used to displace the manipulator assembly  11600  in the Z-direction. In some embodiment, the reagent plunge functionality can be included in the actuator  11652 , e.g., the actuator  11652  can also be capable of linearly displacing the inner plunger  11632 . 
     As shown in  FIG. 55-57 , the instrument includes a detector assembly  11200 . The detector assembly  11200  is configured to detect a signal, e.g., luminescence, produced by a chemical reaction, e.g., interaction of a reporter molecule (e.g., luciferase) with a substrate (e.g., tridecanal) in accordance with any of the methods described herein. The detector assembly  11200  is configured to receive a container assembly  3700 , and detect a signal produced therein. The detector assembly  11200  can include any suitable detector that can detect the signal produced by a reporter molecule, e.g., luciferase. For example, as shown, the detector is an optical detector. In some embodiments a detector can be a fluorescence detector (e.g. to detect a fluorescent reporter molecule such as GFP, etc.), a luminescence detector (e.g. to detect bioluminescence produced by a reporter molecule such as luciferase), color detector (e.g. to detect a colored precipitant produced by a reporter enzyme such as HRP), a spectrometer, and/or an image capture device. In some embodiments, the detector can further include a light source. Although described as being primarily based on optical detection, in some embodiments, the detector can be an electrochemical detector. For example, the detector can include an amperometric detector, potentiometric detector, conductometric, and/or impedometric detector, configured to detect a current, voltage, or conductance, resistance/impedance change produced by the reporter, e.g., luciferase. In some embodiments employing electrochemical detection, the detector can be configured to come in physical contact with the sample solution that can contain a sample. In some embodiments, the detector  11200  can use other detection methods, e.g. surface acoustic wave, surface plasmon resonance, Raman spectroscopy, magnetic sensors, and/or any other suitable detection method known in the art. 
     In some embodiments, the detector assembly  11200  can only provide a qualitative answer, for example, a YES/NO answer on the presence of target cell. In some embodiments, the detector  11200  can quantify the target cell, for example, determine the cfu/ml of target bacteria in the sample according to any of the methods described herein, e.g., method  400 . In some embodiments, the detector assembly  11200  can include an end read system, .e.g., to allow flexible placement of a label on the container, e.g., container assembly  3700 . In some embodiments, the end read system includes direct contact and/or proximal disposal of a transparent end of a container, e.g., container assembly  3700  with the detector  11200 , e.g., to minimize optical instruments and/or background signal interference. In some embodiments, the detector assembly  11200  is devoid of an incident light source. Said another way, no external light is needed for signal detection from the reporter molecules, e.g., luciferase, produced by a target cell, e.g., bacteria, disposed in the container, e.g., container assembly  3700 . 
     Referring now also to  FIGS. 85-94 , the detector assembly  11200  includes a detector  11212  and a shutter  11230  disposed in a housing  11202 . The detector assembly  11200  is configured to removably receive a container, e.g., container assembly  3700 , and detect a signal produced therein, e.g., a luminescence signal resulting from a chemical interaction of a reporter molecule (e.g., luciferase) with a substrate (e.g., tridecanal). 
     The housing  11202  can be formed from a strong, rigid and substantially opaque material, e.g., metals. In some embodiments, the housing can be painted a dark color, e.g., black, to minimize internal reflections and/or refractions because of a luminescence reaction produced in a container disposed in the detector assembly, e.g., container assembly  3700 . The housing  11202  is also configured to prevent external light from entering the detector assembly  11200 , e.g., to reduce background noise and/or signal quality. The housing  11202  includes a groove  11203 . A receptacle  11204  is disposed in the groove  11203  which defines an opening  11207  sized and shaped to removably receive a container, e.g., container assembly  3700 . The receptacle  11204  can be fixedly or removably coupled to the housing  11202 , e.g. via screws, bolts, rivets, glues, hot welded, or snap fitted in to the groove  11203  of the housing  11212 . As shown in  FIG. 86 , the receptacle  11204  includes a gasket  11206  fixedly disposed in the receptacle  11204 . The gasket  11206  can be formed from a rigid and crush and/or wear resistant material, e.g., high density neoprene. The gasket  11206  is configured such that when the container assembly  3700  is disposed in the receptacle  11204 , the gasket  11206  and a portion of the reagent module  3740  form a light-tight seal to prevent any external light from entering inside the housing  11202 . In some embodiments, the height of the receptacle  11204  can be varied, e.g., to accommodate containers of various lengths. This can ensure that any variations in length of the container, e.g., because of variations in the manufacturing process and/or user preference, does not change the distance of a bottom end of the container, e.g., container base, from the detector  11212  e.g., to enhance signal quality and/or repeatability. The housing  11202  further defines a channel  11209  configured to receive at least a portion of the container, e.g., a reaction chamber  3732  of the container assembly  3700 . The housing  11202  also includes an internal volume  11210  configured to house the shutter  11230 , such that the shutter  11230  is free to be manipulated and/or displaced from a first position to a second position within the internal volume  11210 . The housing  11202  further includes circuitry  11208  disposed on a sidewall of the housing  11202 . The circuitry is configured to control the operation of a light source  11246 , as described below herein. 
       FIG. 87  shows the internal components of the detector assembly  11200  with the housing  11202  removed and  FIG. 88  shows an exploded view of the components of the detector assembly  11200 . As shown herein, the detector assembly  11200  includes a baseplate  11211  configured to mount the detector assembly  11200  on the baseplate  11118  of the instrument  11000 . The base plate  11211  is also configured to provide a base for mounting the components of the detector assembly  11200  and the housing  11202 . 
     The detector assembly  11200  includes a detector  11212  disposed in a detector enclosure  11214 . The detector  11212  can be an optical detector, e.g., a photomultiplier tube (PMT), a luminometer, a spectrophotometer, fluorescence detector, and or any other suitable optical detector. The detector  11212  is configured to detect an optical signal, e.g., luminescence, produced due to a chemical reaction in a container, e.g., container assembly  3700  as described herein. In some embodiments, the detector  11212  can include an amperometric detector, potentiometric detector, conductometric, and/or impedometric detector, configured to detect a current, voltage, or conductance, resistance and/or impedance change produced by the reporter, e.g., luciferase. A bottom surface of the detector enclosure  11214  is coupled to a mount  11216  that is disposed on the base plate  11211 . The mount  11216  can be made from a rigid but soft material, e.g., rubber or foam pad, to provide a cushioned support to the detector enclosure  11214 . A top surface of the detector enclosure  11214  is coupled to a separator  11218 , e.g., screwed, bolted, and/or riveted to the separator  11218 . The separator  11218  can be made from strong, rigid and low friction material, e.g., a polished metal plate (e.g., aluminum, stainless steel, etc.). The separator  11218  is configured to provide a separation layer between the detector enclosure  11214  and the shutter  11230 , e.g., to prevent wear of the detector enclosure  11214  due to a displacement of the shutter  11230 , as described herein. The separator  11218  includes an aperture  11219  which is configured such that when the separator  11218  is coupled to the detector  11212 , the aperture  11219  is located directly above the detector  11212  and provides unhindered optical access to the detector  11212 . The aperture  11219  also includes a window  11220 , e.g., a circular glass or transparent plastic piece, disposed therein. The window  11220  is configured to protect the detector  11212 , e.g., from dust particles and/or physcial damage due to accidental contact by an end of a container, e.g., container assembly  3700 . A seat  11222  is also disposed in the aperture  11219 , configured to securely seat the window  11220  in the aperture  11219 . The seat  11222  can also be configured to contact a top surface of the detector enclosure  11214  and encircling the detector  11212 , for example, to light seal the detector  11212  from ambient light. In some embodiments, the seal  11214  can be formed from rubber, plastic and/or polymers and can be an o-ring. A seal  11224 , e.g., a rubber seal, is also disposed on the separator  11224 . The seal  11224  can be configured to light seal the internal volume  11210  of the housing  11202 , e.g., the internal volume  11210  housing the shutter  11230  from ambient light, e.g., to reduce background noise, increase signal quality and/or repeatability. 
     The detector assembly  11200  also includes a shutter  11230  slidably disposed on the separator  11218  and configured to move from a first shutter position wherein the shutter  11230  is closed and the detector  11212  is optically uncoupled with a container, e.g., container assembly  3700  disposed in the detector assembly  11200 , to a second shutter position wherein the shutter  11230  is open and the detector  11212  is optically coupled to the container. As shown in  FIG. 89-90 , the shutter  11230  includes a recess  11232 , which includes a slot  11234  and a surface  11236 . The slot  11234  is shaped and sized to receive an end portion of a container, e.g., container assembly  3700 . The surface  11236  is contoured, e.g., curved to conform to a contour of a bottom end of the container. The surface  11236  is inclined at angle leading from a top surface  11236  of the shutter  11230  to a top edge of the slot  11234 . In some embodiments, the surface  11236  can be inclined at an angle of 30 degrees, 40 degrees, 45 degrees, 50 degrees, or 60 degrees from a top horizontal surface of the shutter  11230 . The surface  11230  is configured to be engaged by a bottom end of the container, e.g., container assembly  3700 , to manipulate the shutter  11230  from the first position to the second position, as described herein. The shutter  11230  includes a sleeve  11238  having a spring  11240  disposed therein. A second end of the spring  11240  is disposed in a notch  11241  in the housing  11202  ( FIG. 85 ) mounted on a pin  11242 . The spring  11240  is configured to urge the shutter  11230  from the second shutter position to the first shutter position, and/or secure, hold and/or prevent lateral movement of a container, e.g., container assembly  3700  disposed in the slot  11234 , as described herein. 
     The shutter  11230  further includes a channel  11244  configured to define an optical pathway for an electromagnetic radiation, for example, luminescence emitted by a light source  11246 . The channel  11244  is configured such that the channel  11244  optically couples the light source  11246  to the detector  11212  only when the shutter is in the first position. In some embodiments, the light source  11246  can include a light emitting diode (LED) or a laser, and can further include a light guide, e.g., a fiber optic cable. The light source  11246  can be configured to emit a reference luminescent signal, e.g., a calibrating signal for calibrating the detector  11212 . 
     As described herein, the shutter  11230  is configured to displace from a first position within the internal volume  11210 , wherein the shutter  11230  is closed, to a second position wherein the shutter  11230  is open.  FIG. 91-94  show a side cross-section of the detector assembly  11200  in a first configuration, a second configuration, a third configuration and a fourth configuration. In the first configuration ( FIG. 72 ), no container is disposed in the detector assembly  11200 . The spring  11240  applies a force on the shutter  11230  along a horizontal axis H A  of the shutter in a direction shown by the arrow AA to manipulate and maintain the shutter  11230  into the first shutter position, such that the slot  11234  of the shutter  11230  is not aligned with the aperture  11219  and the detector  11212 , such that no ambient light is incident on the detector  11212 . The channel  11244  is aligned with the detector  11212 , such that the light source  11246  is optically coupled to the detector  11212 . Therefore, in the first configuration, the light source  11246  can be used to send a reference signal to the detector  11212 , e.g., to calibrate the detector  11212 . 
     In the second configuration ( FIG. 92 ), a container assembly  3700  as described before herein, is disposed in the detector assembly  11200  in a first position. The container assembly  3700  includes a reaction chamber  3732  and a reagent module  3740  as described before herein. The container assembly  3700  can be disposed in the detector assembly  11200 , e.g., by the manipulator assembly  11600 . The reaction chamber  3732  of the container assembly  3700  is substantially disposed in the channel  11209  while at least a portion of the reagent module  3740  is disposed in the receptacle  11204 . An end portion  3733  of the reaction chamber  3732  is in contact with the surface  11236 . A downwards force is applied on the container assembly  3700 , e.g., by the manipulator assembly  11600  as described herein, along a vertical axis VA of the detector assembly  11200  as shown by the arrow F which is communicated to the surface  11236  of the shutter  11230  by the end portion  3733  of the reaction chamber  3732  included in container assembly  3700 . Because the surface  11236  is inclined, e.g., at 45 degrees with respect to a horizontal axis of the shutter  11230 , the end portion  3733  of the container assembly  3700  exerts an angular force Fxy on the surface  11236  as shown. The force Fxy has a horizontal component Fx and a vertical component Fy as shown in  FIG. 92 . The horizontal component Fx urges the shutter  11230  assembly to displace horizontally along the horizontal axis H A  in the direction indicated by the arrow Fx such that the slot  11234  of the shutter  11230  displaces towards the detector  11212  as shown in the third configuration ( FIG. 93 ). The spring  11240  can be configured to exert a reactive force on reaction chamber  3732 , but not large enough to prevent the reaction chamber  3732  from manipulating the shutter  11230 . The channel  11209  of the housing  11202  can be in close tolerance or only slightly larger than the diameter of the reaction chamber  3732 , e.g., to prevent any lateral movement of the container assembly  3700  by the reactive force exerted by the spring  11240 . 
     The downward force F on the container assembly  3700  can be maintained until in the fourth configuration, the shutter  11230  is displaced to a second position such that the slot  11234  is aligned with the detector  11232  and the end portion  3733  of the reaction chamber  3732  is disposed in the slot  11234 , as shown in  FIG. 94 . The end portion  3733  of the reaction chamber  3732  can be proximal to but not contacting the window  11220 , e.g., to prevent scratching and/or wear of the window. In this configuration, the spring  11240  applies a force on the shutter  11230  urging the shutter  11230  towards the first shutter position. This force is communicated to a side wall of the end portion  3733  of the reaction chamber  3732  through a side wall of the slot  11234  included in the shutter  11230 , which prevents the shutter  11230  from sliding into the first shutter position. In some embodiments, the slot  11234  can define a detection volume configured to restrict any signal produced in the reaction chamber  3732 , e.g., luminescence produced by the interaction of a reporter molecule, e.g., luciferase, with a substrate, e.g., tridecanal, for example, to increase signal quality, sensitivity, repeatability and/or reduce background noise. Furthermore, a bottom surface  3735  of the reagent module  3740  included in the container assembly  3700  rests on and is flush with the gasket  11206  such that no ambient light can enter the housing  11202  of the detector assembly  11200 . In some embodiments, the manipulator assembly  11600  can maintain the downward force F on the container assembly  3700  in the fourth configuration, e.g., to maintain strong contact between the bottom surface  3735  of the reagent module  3740  included in the container assembly  3700 , and the gasket  11206   
       FIG. 95  shows the detector circuitry  11270  that can be used to control detector assembly  11200 , according to an embodiment. The circuitry  11270  is disposed in the housing  11202  of the instrument  11200 , mounted on the base plate  11118 . In some embodiments, the circuitry  11270  can include a photon detector and/or any other circuitry for processing opto-electronic signals, as are commonly known in the arts. 
     In some embodiments, a reagent, e.g., a substrate can be communicated into the reaction chamber  3732  in the fourth configuration such that a chemical reaction produces a signal in the reaction chamber  3732  which can be detected by the detector  11212 . For example, the second plunger  11636  included in the manipulator assembly  11600  can engage the actuator  3760  included in the reagent module  3740  of the container assembly  3700  to communicate a substrate, e.g., tridecanal or any other substrate described herein, into the reaction chamber  3732 . The substrate can interact with a reporter molecule present in a sample solution disposed in the container, e.g., the reporter molecule luciferase or any other reporter molecule described herein produced by the interaction of a biologic or abiologic vector such as a transduction particle (e.g., transduction particle  160  or any other transduction particle described herein) with a target cell, e.g., bacteria such as MRSA. The interaction of the substrate and reporter molecule can produce a signal, e.g., luminescence that is detected by the detector  11212 . In some embodiments, the reaction between the substrate and the reporter molecule can be an instantaneous, e.g., flash reaction, such that a signal is produced instantly after communication of the substrate into the sample solution including the reporter molecules. Detection of the signal indicates that the sample disposed in the reaction chamber  3732  contains the target cell. 
     As described herein, the detector  11212  or any other detector described herein can be calibrated before making a signal measurement.  FIG. 96  illustrates a flow diagram of a method for calibrating and making a measurement with a detector, e.g., detector  11212  included in an instrument, e.g., instrument  11000 . The method includes receiving a first signal associated with a magnitude of light emission in a detection volume,  702 , at a first time such that the detection volume is optically isolated from a channel by a movable shutter, e.g., shutter  11230 , which is disposed in a first shutter position. In some embodiments, a light emission e.g., a calibration signal, can be transmitted into the detection volume via a light channel defined by the shutter when the shutter is in the first position. A force is applied to sample container to move the shutter into the second position,  704 . The container can initially be in the at least partially disposed within the channel such that the application of a force on the container, allows a distal end portion of the container to move the shutter from the first shutter position to the second shutter position. This allows the distal end portion of the container to move into the detection volume,  706 , such that the channel is now in optical communication with the detection volume. In this position a second signal associated with a light emission in the detection volume can be received,  708 . In some embodiments, before receiving the second signal, a reagent, e.g., a substrate can be conveyed into the distal end portion of the container. The substrate, e.g., tridecanal can be configured to react with, for example, reporter molecules present in the sample to produce a light emission. In some embodiments, the detector  11212 , or any other detector described herein, can include internal calibration controls, e.g., software algorithms, such that an external calibration light source is not required. 
     As described herein, the instrument  11000  or any other instrument described herein can be used to manipulate a container (e.g., container assembly  3700  or any other container described herein), for example, to transport a container, communicate reagents into a reaction volume of the container and/or detect a signal, e.g., luminescence produced within the container.  FIG. 97  illustrates a flow chart of a method for manipulating a container within an instrument. A container that can have a sample disposed therein containing target cells, e.g., bacteria, can be loaded into a loading zone of the instrument  802 , e.g., the loading cartridge  11300 . The container is transported to a heater included in the instrument  804 , e.g., by the manipulator assembly  11600  via the drive assembly  11500  to the heater assembly  11400 . A biologic or abiologic vector such as a transduction particle is communicated into a reaction volume of the container  806 , e.g., by a manipulation of the inner plunger  11632  of the manipulator assembly  11600 . The container is maintained at a predetermined temperature for a predetermined time  808 , e.g., at 37 degrees Celsius for 4 hours by the heater assembly  11400 . The transduction particles interact with the target cells included in the sample, such that the target cells produce a series of reporter molecule  810 . In some embodiments, the heater assembly  11400  can be configured maintain the container (e.g., container assembly  3700  or any other container described herein) at a series of temperatures, for predetermined times. For example, the container and the sample disposed therein can be maintained at 37 degrees Celsius for a first time, e.g., 4 hours. The temperature of the container can then be lowered to a second temperature lower than the first temperature (e.g., 30 degrees Celsius), for example, by transferring to a heating block  11422  at the second temperature. The container can, for example, be maintained at the second temperature until detection. The container is then transported to a detector included in the instrument  812 , e.g., the detector assembly  11200 . For example, the manipulator assembly  11600  can be used to transport the container via the drive assembly  11500 . A substrate is then communicated into the container  814 , e.g., via a manipulation of the outer plunger  11636  of the manipulator assembly  11600 . The substrate interacts with reporter molecules to produce a signal  816  that is detected using the detector  818 . The analyzed container is then transported to an unloading zone of the instrument  820 , e.g., an unloading cartridge  11300 , and can be removed from the container  822 . 
     In some embodiments, an instrument, e.g., instrument  11000  or any other instrument described herein, can be in communication with a laboratory information system (LIS), e.g., the LIS  1900  as shown in  FIGS. 2-3 . 
     While various embodiments have been described above, it should be understood that they have been presented by way of example only, and not limitation. Where methods and/or schematics described above indicate certain events and/or flow patterns occurring in certain order, the ordering of certain events and/or flow patterns may be modified. Additionally, certain events may be performed concurrently in parallel processes when possible, as well as performed sequentially. While the embodiments have been particularly shown and described, it will be understood that various changes in form and details may be made. 
     In some embodiments, the fluidic pathways defined by any of the reagent modules (e.g.,  1740 ) can include valves or any other flow control mechanism. Such mechanisms include a flap valve, membrane valve, duckbill valve, umbrella valve, septum, or any other suitable valving mechanism to allow reagents to flow in one direction. In some embodiments, the valves can be pressure sensitive such that they allow fluid communication only above a predefined pressure threshold, e.g., to prevent accidental communication of reagents. 
     In some embodiments, any of the systems and methods described herein include a reporter system that reports on the presence of inducer molecules within target cells can be developed by incorporating into a non-replicative transduction particle, of the types shown and described herein, a reporter gene that is operably linked to an inducible promoter that controls the expression of a target gene within a target cell. When the reporter vector is introduced into the target cell that expresses the inducer of the target gene promoter, expression of the reporter gene is possible via induction of the target gene promoter in the reporter vector. 
     In one embodiment, a VanR reporter system can be developed for the purpose of detecting Vancomycin Resistant Enterococci (VRE). The Tn1546 transposon that can be present in  E. faecium  may contain the vanR inducer gene and the vanA target gene. A VRE reporter system can be developed by developing an  E. faecium -targetting non-replicative transduction particle that incorporates a reporter gene operatively linked to the promoter PH that controls the expression of the vanHAX operon that includes the vanA gene. When the transduction particle delivers the P H -controlled reporter gene into the  E. faecium  cell, the reporter gene will be expressed via induction of the PH promoter by the product of vanR. 
     In another embodiment, a reporter system for detecting TcdD, the inducer of the promoters of the toxins A and B genes (tcdA and tcdB, respectively) of  C. difficile  can be developed by developing a non-replicative transduction particle targeting  C. difficile  and that incorporates reporter gene that is operatively linked to the tcdA gene promoter. The PaLoc transposon in  C. difficile  may contain the tcdD gene and the tcdA target gene. In the native cell, when the tcdD gene is expressed and produces the TcdD protein, TcdD is able to induce PtcdA in the PaLoc transposon thus causing the expression of the tcdA gene and thus producing the toxin A protein. By introducing a reporter gene that operatively linked to the tcdA gene promoter (PtcdA) into a target cell, TcdD is then also able to induce PtcdA that controls the reporter gene, thus causing the expression of a reporter molecule. 
     A reporter system can be developed for reporting on the presence of a target intracellular enzyme by developing a non-replicative transduction particle-based viable cell reporter that employs a reporter that requires a substrate for signal generation and by caging the substrate such that it is not capable of triggering a signal via the reporter unless the substrate is un-caged via interacting with the target enzyme. A target cell is exposed to the transduction particle such that the reporter is expressed within the target cell and the caged substrate is applied. If the target cell contains a target enzyme, an interaction between the target enzyme and the caged substrate un-cages the substrate thus allowing the un-caged substrate to trigger a signal from the expressed reporter molecules. 
     In one embodiment, the reporter molecule to be expressed can be  Renilla luciferase  and the caged substrate can be  Renilla luciferin  that is caged such that a β-lactamase enzyme that is endogenous to the target cell is able to cleave the caging compound from the caged luciferin and release un-caged luciferin. By incorporating these components into a non-replicative transduction particle that targets a cell that may contain a β-lactamase enzyme, a target-cell-specific β-lactamase enzyme reporter system can be developed. 
     An intracellular molecule reporter system can be developed by incorporating into a non-replicative transduction particle a switchable reporter molecule that does not emit a signal unless it interacts with an intracellular target molecule. 
     In one embodiment, a non-replicative transduction particle can be designed to incorporate a gene expressing switchable aptamer designed to undergo a conformational change upon its binding to an intracellular target molecule. The conformational change allows the aptamer to then bind a fluorophore that exhibits enhanced fluorescence when bound by the aptamer. 
     An antisense RNA-based reporter system for detecting target transcripts within viable cells by causing the expression of a reporter molecule if a target transcript is present within a cell can be developed. In the general embodiment a non-replicative transduction particle incorporates a DNA sequence encoding an antisense message that is complementary to a region of a target transcript (target), and a sequence encoding a mutated version of the target transcript (target*) fused to a reporter gene (reporter) is used. The mutation of the target transcript is such that the antisense transcript binds to the mutated target transcript with a lower affinity than that of it&#39;s binding to the native target transcript. The antisense sequence is controlled by a promoter sequence (P), and the mutated target sequence linked to the reporter gene is controlled by an identical promoter sequence (P). When the reporter system is introduced into a cell that does not contain an endogenous target transcript, the expressed antisense transcript inhibits the translation of the reporter gene and the antisense transcript and reporter transcript are consumed in the process. However, when the vector is inserted into a cell that does contain an endogenous target transcript, the expressed antisense transcript preferably binds to the native target transcript and the antisense transcript and target transcript are consumed in the process, leaving the reporter gene to be translated thus producing a reporter protein that may be detected. In this manner, this vector causes the expression of a detectable signal when it is introduced into a target cell containing the target transcript. 
     In some embodiments, non-replicative transduction particles targeting  S. aureus  cells are designed to report on the presence of mecA transcripts thus resulting in a MRSA detection system. The transduction particles deliver DNA sequences that encode an antisense message that is complementary to a region of mecA transcript (mecA), and a sequence encoding a mutated version of mecA transcript (mecA*) fused to the bacterial luciferase genes luxA and luxB (luxAB). The mutation of the mecA* transcript is such that the antisense transcript binds to its transcript with a lower affinity than that of it&#39;s binding to the native mecA transcript. The mecA*-luxAB fusion and the antisense mecA gene fragment are each operatively linked to the constitutively expressed promoters. When the reporter construct is introduced into MRSA cells by the transduction particle, if the cell does not produce an endogenous mecA transcript, then the antisense sequence fragment of the mecA gene can only bind to the mecA sequence of the transcript of the modified fragment of the mecA gene fused to the luxAB genes. This binding event then prevents the translation of the luxAB genes thus preventing the production of luciferase within this cell. If, on the other hand, cell does contain an endogenous mecA transcript, then the transcript of the antisense sequence fragment of the mecA gene will preferentially bind to the endogenous mecA transcript over the transcript of the modified fragment of the mecA gene fused to the luxAB genes thus leaving this transcript available for translation of the luxAB genes thereby producing luciferase. In this manner, the mecA transcript reporter vector can report on the presence of endogenous mecA transcripts within a cell. 
     Although various embodiments have been described as having particular features and/or combinations of components, other embodiments are possible having a combination of any features and/or components from any of embodiments as discussed above.