Devices and methods for monitoring genomic DNA of organisms

A method of detecting the absence or presence of an organism in a sample comprising the steps of:

• (a) providing a microfluidic device comprising a microfluidic reagent assembly area which forms two or more sample plugs, said microfluidic reagent assembly area being in fluid communication with at least one microfluidic inline channel that runs through an amplification area and a detection area, said microfluidic reagent assembly area comprising:
• i. a sample droplet forming area which receives one or more samples containing the same or different genomic material and forms one or more samples into said one or more sample droplets, said sample droplet forming area comprises a sample droplet microfluidic path in fluid communication with said microfluidic inline channel which forwards the one or more sample droplets to said microfluidic inline channel;
• ii. a primer plug producing area comprising a primer assembly apparatus which assembles one or more primer plugs comprising amplification reagents including at least one primer, wherein said primer assembly apparatus is controlled to assemble said one or more primer plugs containing the same primers or different primers, said primer plug producing area further comprises a primer plug microfluidic path in fluid communication with said microfluidic inline channel which forwards the one or more primer plugs to the microfluidic inline channel;
• and
• iii. a sample plug mixing area which forms sample plugs by mixing said sample droplet and primer plug, said sample plug mixing area being in fluid communication with the microfluidic inline channel;
• wherein said microfluidic reagent assembly area is controlled to form sample plugs that comprise the same or different genomic material and the same or different primers;
• and
• wherein the microfluidic device further comprising at least one microfluidic inline channel that runs through (i) an amplification area within a first temperature-controlled area and (ii) a detection area within a second temperature-controlled area, wherein the at least one microfluidic inline channel comprises a valve downstream of the detection area through which a sample selectively flows and wherein the device controls fluid movement within the microfluidic inline channel, heating and cooling of the first and second temperature-controlled areas and data acquisition from the microfluidic device;
• (b) acquiring a sample that may contain an organism;
• (c) isolating at least one copy of the genomic material of the organism, if present in the sample, in the reagent assembly area of the micro fluidic device;
• (d) introducing at least one sample droplet into one microfluidic inline reaction channel;
• (e) driving the at least one sample droplet along the microfluidic inline channel through the reagent assembly area;
• (f) forming at least one sample plug by mixing the at least one sample droplet with at least one primer plug in the microfluidic inline channel in the reagent assembly area of the device, wherein each primer plug comprises amplification reagents and at least one primer, and wherein the primer plugs contain the same or different primers;
• (g) driving the at least one sample plug along the microfluidic inline channel through the amplification area;
• (h) amplifying the genomic material, if present, in the at least one sample plug in the microfluidic inline channel in the amplification area of the device;
• (i) driving the at least one sample plug along the microfluidic inline channel through the detection area;
• (j) detecting the absence or presence of amplified products in the microfluidic inline channel in the detection area of the device to produce a detection result, wherein the presence of the amplified products is indicative of the presence of the organism;
• (k) selecting the sample plug for further analysis or waste removal on the basis of the detection result;
• (l) driving the at least one sample plug along the microfluidic inline channel to a valve;
• and
• (m) directing flow of the sample plug through the valve in the microfluidic inline channel on the basis of the selection in step (k).

A method of detecting the presence or absence of genomic material in two or more samples, comprising the steps of:

• (a) providing a microfluidic device comprising a microfluidic reagent assembly area which forms two or more sample plugs, said microfluidic reagent assembly area being in fluid communication with at least one microfluidic inline channel that runs through an amplification area and a detection area, said microfluidic reagent assembly area comprising:
• i. a sample droplet forming area which receives one or more samples containing the same or different genomic material and forms one or more samples into said one or more sample droplets, said sample droplet forming area comprises a sample droplet microfluidic path in fluid communication with said microfluidic inline channel which forwards the one or more sample droplets to said microfluidic inline channel;
• ii. a primer plug producing area comprising a primer assembly apparatus which assembles one or more primer plugs comprising amplification reagents including at least one primer, wherein said primer assembly apparatus is controlled to assemble said one or more primer plugs containing the same primers or different primers, said primer plug producing area further comprises a primer plug microfluidic path in fluid communication with said microfluidic inline channel which forwards the one or more primer plugs to the microfluidic inline channel;
• and
• iii. a sample plug mixing area which forms sample plugs by mixing said sample droplet and primer plug, said sample plug mixing area being in fluid communication with the microfluidic inline channel;
• wherein said microfluidic reagent assembly area is controlled to form sample plugs that comprise the same or different genomic material and the same or different primers;
• (b) selecting two or more samples for detecting the presence or absence of the genomic material in each of said samples;
• (c) introducing one or more sample droplets of each of the selected samples into the microfluidic inline channel of the microfluidic device, wherein each sample droplet contains genomic material if present;
• (d) selecting two or more primer plugs to input into said microfluidic inline channel, wherein each primer plug comprises amplification reagents and at least one primer, wherein the primer plugs contain the same primers or different primers based on the selection of the primer plugs and wherein the primers are selected on the basis of the genomic material to be detected;
• (e) forming two or more sample plugs in said microfluidic inline channel by mixing the sample droplets with the primer plugs in the microfluidic inline channel, wherein the sample plugs comprise the same or different genomic material and the same or different primers;
• (f) amplifying the genomic material in the sample plugs in said microfluidic inline channel to produce amplified products if genomic material is present in the sample plugs;
• and
• (g) detecting the presence or absence of the resulting amplified products in each of the sample plugs,
• wherein the presence of amplified products in a sample plug is indicative of the presence of the genomic material in the sample.