1) Sample preparation. Standard sample preparation as outlined under large throughput design. The outcome of Step 1 is a 1 ml homogenized sample in a 2 ml tube, ready for subsequent testing.
2) Encapsulation of single cells into droplets and substrate conversion reaction. The homogenized sample is manually mixed with VPCIR reagents, hydrogel beads functionalized with specific DNA substrates, and bacteria-specific bacteriophages. Through a manual rapid pipetting mix, bacteria cells are encapsulated into droplets together with the VPCIR reagents, beads and bacteriophages. The time duration of this step is 5 minutes. The ensuing chemical reaction taking place over a duration of 1.5 hours is the same as described under high-throughput design. The outcome of Step 3 is fluorescent samples now ready for readout.
3) Read-out. The result is read as for high-throughput design by a flow cytometer. Benchtop/handheld instruments with no automation may be used.