Loop-mediated isothermal amplification (LAMP) based assay for detecting microbes

A system for detecting a target microorganisms in a sample suspected of containing the target microorganism, comprising:

• reaction agents including:
• loop mediated isothermal amplification (LAMP) reagents comprising a plurality of primers including a fluorophore labeled primer;
• and
• a polyethylene glycol (PEG) hydrogel at a concentration of 10% (w/v) of the reaction agents, the polyethylene glycol hydrogel being formed through Michael addition between a four-arm PEG acrylate having a molecular weight (MW) of 10K and thiol-PEG-thiol having a MW 3.4K, at mole ratio of 1:2, wherein crosslinking of the PEG hydrogel is tuned to form a predetermined mesh size of the PEG hydrogel and a predetermined molecular weight between crosslinkers in the PEG hydrogel that restricts diffusion of DNA/RNA templates of the target microorganism within the PEG hydrogel while allowing free diffusion within the PEG hydrogel of molecules having a MW<100 kDa;
• a chamber for combining the reaction agents and the sample to form a mixture;
• an incubator configured to heat the mixture;
• a slide configured to receive the mixture to allow visual detection of the presence or absence of one or more amplicons that are produced as a result of a LAMP reaction amplifying the DNA/RNA templates of the target microorganism if the target microorganism is present in the mixture, wherein the presence of the amplicons is indicative of the presence of the target microorganism in the sample and the absence of the amplicons is indicative of the absence of the target microorganism in the sample;
• and
• a camera configured to visually detect the presence or absence of amplicons in the mixture received on the slide.