Systems, apparatus, and methods for inline sample preparation

A sample preparation device, comprising:

• a sample holder configured to receive a sample;
• a first chamber including:
• a first compartment to receive the sample holder, the sample holder being configured to be removable from the first compartment and hermetically seal the sample preparation device when placed in the first compartment;
• a second compartment operably coupled to the first compartment;
• and
• a first valve disposed within the first compartment, the first valve being configured to permit fluid flow from the first compartment to the second compartment and to block fluid flow from the second compartment to the first compartment, the second compartment being configured to draw at least a portion of the sample from the first compartment to the second compartment upon moving away from the first compartment, the first chamber including at least one extraction reagent preloaded within the first chamber to extract nucleic acid from target microorganism in the sample;
• and
• a second chamber including:
• a third compartment operably coupled to the second compartment;
• and
• a second valve disposed between the second compartment and the third compartment, the second valve being configured to permit fluid flow from the second compartment to the third compartment and to block fluid flow from the third compartment to the second compartment, the second compartment being configured to transport at least a portion of the sample from the second compartment to the third compartment upon moving closer to the first compartment, the second chamber including at least one oligomer preloaded within the second chamber to amplify the nucleic acid extracted by the at least one extraction reagent.